scholarly journals The evolutionary pathway from a biologically inactive polypeptide sequence to a folded, active structural mimic of DNA

2016 ◽  
Vol 44 (9) ◽  
pp. 4289-4303 ◽  
Author(s):  
Nisha Kanwar ◽  
Gareth A. Roberts ◽  
Laurie P. Cooper ◽  
Augoustinos S. Stephanou ◽  
David T.F. Dryden
Keyword(s):  
Evolutionary Pathway ◽  
Polypeptide Sequence

The Effects of Protein Charge Patterning on Complex Coacervation

2021 ◽  
Author(s):  
Nicholas Zervoudis ◽  
Allie Obermeyer
Keyword(s):  
Phase Boundary ◽  
Phase Behavior ◽  
Predictive Models ◽  
Phase Portraits ◽  
Complex Coacervation ◽  
Protein Encapsulation ◽  
Protein Charge ◽  
Polypeptide Sequence ◽  
The Impact ◽  
Coacervate Phase

The complex coacervation of proteins with other macromolecules has applications in protein encapsulation and delivery and for determining the function of cellular coacervates. Theoretical or empirical predictions for protein coacervates would enable the design of these coacervates with tunable and predictable structure-function relationships; unfortunately, no such theories exist. To help establish predictive models, the impact of protein-specific parameters on complex coacervation were probed in this study. The complex coacervation of sequence-specific, polypeptide-tagged, GFP variants and a strong synthetic polyelectrolyte was used to evaluate the effects of protein charge patterning on phase behavior. Phase portraits for the protein coacervates demonstrated that charge patterning dictates the protein’s binodal phase boundary. Protein concentrations over 100 mg mL<sup>-1</sup> were achieved in the coacervate phase, with concentrations dependent on the polypeptide sequence. In addition to shifting the binodal phase boundary, polypeptide charge patterning provided entropic advantages over isotropically patterned proteins. Together, these results show that modest changes of only a few amino acids alter the coacervation thermodynamics and can be used to tune the phase behavior of polypeptides or proteins of interest.

Late Accretion and the Origin of Water on Terrestrial Planets in the Solar System

2021 ◽  
Author(s):  
Cédric Gillmann ◽  
Gregor Golabek ◽  
Sean Raymond ◽  
Paul Tackley ◽  
Maria Schonbachler ◽  
...  
Keyword(s):  
Solar System ◽  
Long Term Evolution ◽  
Terrestrial Planets ◽  
Evolutionary Pathway ◽  
Giant Impact ◽  
The Earth ◽  
Term Evolution ◽  
Surface Liquid ◽  
Venus Atmosphere

&lt;p&gt;Terrestrial planets in the Solar system generally lack surface liquid water. Earth is at odd with this observation and with the idea of the giant Moon-forming impact that should have vaporized any pre-existing water, leaving behind a dry Earth. Given the evidence available, this means that either water was brought back later or the giant impact could not vaporize all the water.&lt;/p&gt;&lt;p&gt;We have looked at Venus for answers. Indeed, it is an example of an active planet that may have followed a radically different evolutionary pathway despite the similar mechanisms at work and probably comparable initial conditions. However, due to the lack of present-day plate tectonics, volatile recycling, and any surface liquid oceans, the evolution of Venus has likely been more straightforward than that of the Earth, making it easier to understand and model over its long term evolution.&lt;/p&gt;&lt;p&gt;Here, we investigate the long-term evolution of Venus using self-consistent numerical models of global thermochemical mantle convection coupled with both an atmospheric evolution model and a late accretion N-body delivery model. We test implications of wet and dry late accretion compositions, using present-day Venus atmosphere measurements. Atmospheric losses are only able to remove a limited amount of water over the history of the planet. We show that late accretion of wet material exceeds this sink. CO&lt;sub&gt;2&lt;/sub&gt; and N&lt;sub&gt;2&lt;/sub&gt; contributions serve as additional constraints.&lt;/p&gt;&lt;p&gt;Water-rich asteroids colliding with Venus and releasing their water as vapor cannot explain the composition of Venus atmosphere as we measure it today. It means that the asteroidal material that came to Venus, and thus to Earth, after the giant impact must have been dry (enstatite chondrites), therefore preventing the replenishment of the Earth in water. Because water can obviously be found on our planet today, it means that the water we are now enjoying on Earth has been there since its formation, likely buried deep in the Earth so it could survive the giant impact. This in turn suggests that suggests that planets likely formed with their near-full budget in water, and slowly lost it with time.&lt;/p&gt;

scholarly journals Interaction Between Ploidy, Breeding System, and Lineage Diversification

2019 ◽  
Author(s):  
Rosana Zenil-Ferguson ◽  
J. Gordon Burleigh ◽  
William A. Freyman ◽  
Boris Igić ◽  
Itay Mayrose ◽  
...  
Keyword(s):  
Breeding System ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Whole Genome ◽  
Self Incompatibility ◽  
Evolutionary Pathway ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Biological Hierarchy ◽  
Lineage Diversification

AbstractIf particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be understood as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rate differences is complicated by the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs. polyploid states) and breeding system (self-incompatible vs. self-compatible states) have been repeatedly suggested as possible drivers of differential diversification. We investigate the connections of these traits, including their interaction, to speciation and extinction rates in Solanaceae. We show that the effect of ploidy on diversification can be largely explained by its correlation with breeding system and that additional unknown factors, alongside breeding system, influence diversification rates. These results are largely robust to allowing for diploidization. Finally, we find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization.

scholarly journals How development affects evolution

2021 ◽  
Author(s):  
Mauricio González-Forero ◽  
Andy Gardner
Keyword(s):  
Niche Construction ◽  
Fitness Landscape ◽  
Stabilizing Selection ◽  
Mathematical Framework ◽  
Phenotypic Evolution ◽  
Landscape Development ◽  
Developmental Constraints ◽  
Evolutionary Pathway ◽  
Punctuated Equilibria ◽  
Adaptive Radiations

How development affects evolution. A mathematical framework that explicitly integrates development into evolution has recently been derived. Here we use this framework to analyse how development affects evolution. We show that, whilst selection pushes genetic and phenotypic evolution uphill on the fitness landscape, development determines the admissible evolutionary pathway, such that evolutionary outcomes occur at path peaks, which need not be peaks of the fitness landscape. Development can generate path peaks, triggering adaptive radiations, even on constant, single-peak landscapes. Phenotypic plasticity, niche construction, extra-genetic inheritance, and developmental bias variously alter the evolutionary path and hence the outcome. Selective development, whereby phenotype construction may point in the adaptive direction, may induce evolution either towards or away landscape peaks depending on the developmental constraints. Additionally, developmental propagation of phenotypic effects over age allows for the evolution of negative senescence. These results help explain empirical observations including punctuated equilibria, the paradox of stasis, the rarity of stabilizing selection, and negative senescence, and show that development has a major role in evolution.

scholarly journals Dynamism and Cooperativity Essential for Efficient Catalysis in Aspergillus Niger Monoamine Oxidase

2019 ◽  
Author(s):  
Christian Curado-Carballada ◽  
Ferran Feixas ◽  
Sílvia Osuna
Keyword(s):  
Aspergillus Niger ◽  
Monoamine Oxidase ◽  
Active Site ◽  
Conformational Dynamics ◽  
Catalytic Efficiency ◽  
Building Blocks ◽  
Chiral Amine ◽  
Evolutionary Pathway ◽  
Accelerated Molecular Dynamics ◽  
Open States

<p><b> </b><i>Aspergillus niger </i>Monoamine Oxidase (MAO-N) is a homodimeric enzyme responsible for the oxidation of amines into the corresponding imine. Laboratory evolved variants of MAO-N in combination with a non-selective chemical reductant represents a powerful strategy for the deracemisation of chiral amine mixtures and, thus, is of interest for obtaining chiral amine building blocks. MAO-N presents a rich conformational dynamics with a flexible ß-hairpin region that can adopt closed, partially closed and open states. Despite the ß-hairpin conformational dynamics is altered along the laboratory evolutionary pathway of MAO-N, the connection between the ß-hairpin conformational dynamics and active site catalysis still remains unclear. In this work, we use accelerated molecular dynamics to elucidate the potential interplay between the ß-hairpin conformational dynamics and catalytic activity in MAO-N wild type and its evolved D5 variant. Our study reveals a delicate communication between both MAO-N subunits that impacts the active site architecture, and thus its catalytic efficiency. In both MAO-N WT and the laboratory evolved D5 variant, the ß-hairpin conformation in one of the monomers affects the productive binding of the substrate in the active site of the other subunit. However, both MAO-N WT and D5 variants show a quite different behaviour due to the distal mutations introduced experimentally with Directed Evolution. </p>

scholarly journals Brain ontogeny and life history in Pleistocene hominins

2015 ◽  
Vol 370 (1663) ◽  
pp. 20140062 ◽  
Author(s):  
Jean-Jacques Hublin ◽  
Simon Neubauer ◽  
Philipp Gunz
Keyword(s):  
Life History ◽  
Cognitive Complexity ◽  
Extended Period ◽  
Brain Structures ◽  
Human Model ◽  
Evolutionary Pathway ◽  
Life History Pattern ◽  
Delayed Maturation ◽  
High Level ◽  
The Brain

A high level of encephalization is critical to the human adaptive niche and emerged among hominins over the course of the past 2 Myr. Evolving larger brains required important adaptive adjustments, in particular regarding energy allocation and life history. These adaptations included a relatively small brain at birth and a protracted growth of highly dependent offspring within a complex social environment. In turn, the extended period of growth and delayed maturation of the brain structures of humans contribute to their cognitive complexity. The current palaeoanthropological evidence shows that, regarding life history and brain ontogeny, the Pleistocene hominin taxa display different patterns and that one cannot simply contrast an ‘ape-model’ to a ‘human-model’. Large-brained hominins such as Upper Pleistocene Neandertals have evolved along their own evolutionary pathway and can be distinguished from modern humans in terms of growth pattern and brain development. The life-history pattern and brain ontogeny of extant humans emerged only recently in the course of human evolution.

Acceptance

2021 ◽  
pp. 186-222
Author(s):  
Clive Gamble
Keyword(s):  
Stone Tools ◽  
Elliptical Orbit ◽  
Ice Age ◽  
Racial Groups ◽  
Stone Age ◽  
Evolutionary Pathway ◽  
Career Changes ◽  
The Earth ◽  
New Space ◽  
Guided Tour

By the end of the decade the time revolution was a done deal. Moulin-Quignon still reverberated, but in 1865 Lubbock produced the first guided tour of the Old Stone Age, in which he accused Lyell of plagiarism. In Pre-Historic Times he filled the new space of deep history with stone tools to show an evolutionary pathway from St Acheul to the Neolithic monuments of Avebury and Stonehenge. Tracing history back was matched by the anthropologist Edward Tylor, who traced it up. Both men were interested in the evolution of racial groups and accounting for the world’s hunters and gatherers. In a typically upbeat assessment, Lubbock saw the lesson of the past as providing hope for the future. Victorian ‘savages’ at the uttermost ends of the earth had not degenerated from a civilized state. They had the potential to evolve, as his ancestors in Europe had done. Unwritten history was making universal history possible. The decade saw deaths and career changes. Prestwich largely abandoned the time revolution, married Falconer’s niece, Grace McCall, and became an Oxford professor. Falconer and Boucher de Perthes died, while Lubbock entered Parliament in 1870. Prestwich’s fixed notion of a single ice age was challenged by James Croll, who painstakingly worked out the changes in the elliptical orbit of the Earth, and from these proposed multiple ice ages. As a bookend to the decade Evans published his fact-rich volume on ancient stone implements. The path of deep history was now set in stone.

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