scholarly journals Experimental Molecular Archeology: Reconstruction of Ancestral Mutants and Evolutionary History of Proteins as a New Approach in Protein Engineering

10.5772/56255 ◽  
2013 ◽  
Author(s):  
Tomohisa Ogawa ◽  
Tsuyoshi Shirai
Keyword(s):  
Protein Engineering ◽  
Evolutionary History ◽  
New Approach ◽  
History Of

scholarly journals Does relaxing the infinite sites assumption give better tumor phylogenies? An ILP-based comparative approach

2017 ◽  
Author(s):  
Paola Bonizzoni ◽  
Simone Ciccolella ◽  
Gianluca Della Vedova ◽  
Mauricio Soto
Keyword(s):  
Evolutionary History ◽  
Cancer Genomics ◽  
Fundamental Problem ◽  
Comparative Approach ◽  
Cancer Evolution ◽  
Perfect Phylogeny ◽  
New Approach ◽  
Recurrent Mutations ◽  
History Of ◽  
The One

AbstractMost of the evolutionary history reconstruction approaches are based on the infinite site assumption, which is underlying the Perfect Phylogeny model and whose main consequence is that acquired mutation can never lost. This results in the clonal model used to explain cancer evolution. Some recent results gives a strong evidence that recurrent and back mutations are present in the evolutionary history of tumors [5,21], thus showing that more general models then the Perfect Phylogeny are required. We propose a new approach that incorporates the possibility of losing a previously acquired mutation, extending the Persistent Phylogeny model [1].We exploit our model to provide an ILP formulation of the problem of reconstructing trees on mixed populations, where the input data consists of the fraction of cells in a set of samples that have a certain mutation. This is a fundamental problem in cancer genomics, where the goal is to study the evolutionary history of a tumor. An experimental analysis shows the usefulness of allowing mutation losses, by studying some real and simulated datasets where our ILP approach provides a better interpretation than the one obtained under perfect phylogeny assumption. Finally, we show how to incorporate multiple back mutations and recurrent mutations in our model.

scholarly journals Genetic distance between complex repeats

2018 ◽  
Author(s):  
Luca Ferretti ◽  
Aurora Ruiz-Herrera ◽  
Alice Ledda
Keyword(s):  
Evolutionary History ◽  
Point Mutations ◽  
Pairwise Alignment ◽  
Genetic Distances ◽  
Repeat Sequence ◽  
Evolutionary Analysis ◽  
New Approach ◽  
Repeat Units ◽  
Repeat Domain ◽  
History Of

AbstractComplex nucleotide or aminoacid repeats with long units play an important role in proteins. The evolutionary analysis of these variants is challenging due to genetic diversity within repeat units as well as variability in the arrangement of different units along the repeat sequence. Here we present a new approach for the computation of genetic distances between complex repeats. This method takes into account evolutionary processes including point mutations, insertions and deletions of repeat units, as well as duplication of single units. We provide an algorithm for the computation of these distances along with the corresponding global pairwise alignment of repeats. As an example, we apply our approach to the evolution of repeat units in the highly polymorphic zinc-finger repeat domain of the PRDM9 protein across wild populations of house mice. This approach opens the way for new insights into the evolutionary history of polymorphic repeats.

Elaborating the role of reflection and individual differences in the study of folk-economic beliefs

2018 ◽  
Vol 41 ◽  
Author(s):  
Kevin Arceneaux
Keyword(s):  
Decision Making ◽  
Individual Differences ◽  
Cognitive Processes ◽  
Evolutionary History ◽  
Behavioral Responses ◽  
History Of ◽  
Economic Beliefs

AbstractIntuitions guide decision-making, and looking to the evolutionary history of humans illuminates why some behavioral responses are more intuitive than others. Yet a place remains for cognitive processes to second-guess intuitive responses – that is, to be reflective – and individual differences abound in automatic, intuitive processing as well.

STRUCTURAL REARRANGEMENTS AT THE REGULATORY REGION OF THE DRAS1 GENE IN THE EVOLUTIONARY HISTORY OF PHYLOGENETICALLY DISTANT DROSOPHILA SPECIES

2018 ◽  
Author(s):  
A.I. CHEKUNOVA ◽  
◽  
S. YU. SOROKINA ◽  
E.A. SIVOPLYAS ◽  
G.N. BAKHTOYAROV ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Regulatory Region ◽  
Drosophila Species ◽  
Structural Rearrangements ◽  
History Of

A new approach to the logic of discovery

2007 ◽  
Vol 50 (1) ◽  
pp. 7-27
Author(s):  
Gerald Massey
Keyword(s):  
Modal Logic ◽  
Scientific Discovery ◽  
Traditional View ◽  
New Approach ◽  
Logic Of Discovery ◽  
Good Fortune ◽  
High Incidence ◽  
History Of ◽  
Deep Sense

Contending that the quest for a logic of scientific discovery was prematurely abandoned, the author lays down eight phenomena that such a logic or theory must explain: the banality of scientific discovery; the trainability of scientists; the high incidence of simultaneous discoveries; the ubiquity of relative novices; the fact of scientific genius; the barrenness of isolated workers; the incommensurability of concepts of successive theories; and the quasi-incorporation of old concepts, objects, and methods in successor theories, The author then presents a new theory or logic of discovery according to which discoveries are the termini of "tweak paths" generated when scientists "tinker" with the laws, concepts, methods, and instruments of a given theory. Tinkering and tweaking are illustrated by examples from many-valued and modal logic and from Darwinian biology. Through the history of planetary discovery, the accidental role played by luck or good fortune in some discoveries is explored, but the author emphasizes that in a deep sense serendipity is an in eliminable feature of all scientific discovery because scientists never know m advance whether their tweaks will lead to dead ends or to positive developments. The author's new theory of scientific discovery is shown to account for all eight explananda, ft also reveals science to be a more egalitarian enterprise than the traditional view of scientific discovery as ultimately inexplicable depicts it.

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