scholarly journals Reconstructing the Origins of a Neuropeptide Signaling System Using the Accelerated Evolution of Biodiverse Cone Snail Venoms

2021 ◽  
Author(s):  
Thomas Lund Koch ◽  
Iris Bea L Ramiro ◽  
Paula Flórez-Salcedo ◽  
Ebbe Engholm ◽  
Knud Jørgen Jensen ◽  
...  
Keyword(s):  
Purifying Selection ◽  
Orphan Receptor ◽  
Large Set ◽  
Gene Duplications ◽  
Cone Snail ◽  
Signaling System ◽  
Predator Prey ◽  
Accelerated Evolution ◽  
History Of ◽  
Striking Contrast

Somatostatin and its related peptides (SSRPs) form a family of hormones with diverse physiological roles. The ubiquitous presence of SSRPs in vertebrates and several invertebrate deuterostomes suggests an ancient origin of the SSRP signaling system. However, the existence of SSRP genes outside of deuterostomes has not been established and the evolutionary history of this signaling system remains poorly understood. Our recent discovery of SSRP-like toxins (consomatins) in venomous marine cone snails (Conus) suggested the presence of a homologous signaling system in mollusks and potentially other protostomes. Here we identify the molluscan SSRP-like signaling gene that gave rise to the consomatin family. Following recruitment into venom, consomatin genes experience strong positive selection and repeated gene duplications resulting in the formation of a hyper-diverse family of venom peptides. Intriguingly, the largest number of consomatins was found in worm-hunting species (> 400 sequences), indicating a homologous system in annelids, another large protostome phylum. Comprehensive sequence mining enabled the identification of orthologous SSRP-like sequences (and their corresponding orphan receptor) in annelids and several other protostome phyla. These results establish the existence of SSRP-like sequences in many major branches of bilaterians, including xenacoelomorphs, a phylum believed to have emerged before the divergence of protostomes and deuterostomes, ~ 600 My ago. Finally, having a large set of predator-prey SSRP sequences available, we show that while the cone snail's signaling SSRP-like genes are under purifying selection, in striking contrast, the consomatin genes experience rapid directional selection to target receptors in a changing mix of prey.

Genomic Background Predicts the Fate of Duplicated Genes: Evidence From the Yeast Genome

Genetics ◽  
2004 ◽  
Vol 166 (4) ◽  
pp. 1995-1999 ◽  
Author(s):  
Ze Zhang ◽  
Hirohisa Kishino
Keyword(s):  
Recombination Rate ◽  
Evolutionary Rate ◽  
Average Rate ◽  
Classical Model ◽  
Purifying Selection ◽  
Genomic Region ◽  
Yeast Genome ◽  
Duplicated Genes ◽  
Potential Force ◽  
Accelerated Evolution

Abstract Gene duplication with subsequent divergence plays a central role in the acquisition of genes with novel function and complexity during the course of evolution. With reduced functional constraints or through positive selection, these duplicated genes may experience accelerated evolution. Under the model of subfunctionalization, loss of subfunctions leads to complementary acceleration at sites with two copies, and the difference in average rate between the sequences may not be obvious. On the other hand, the classical model of neofunctionalization predicts that the evolutionary rate in one of the two duplicates is accelerated. However, the classical model does not tell which of the duplicates experiences the acceleration in evolutionary rate. Here, we present evidence from the Saccharomyces cerevisiae genome that a duplicate located in a genomic region with a low-recombination rate is likely to evolve faster than a duplicate in an area of high recombination. This observation is consistent with population genetics theory that predicts that purifying selection is less effective in genomic regions of low recombination (Hill-Robertson effect). Together with previous studies, our results suggest the genomic background (e.g., local recombination rate) as a potential force to drive the divergence between nontandemly duplicated genes. This implies the importance of structure and complexity of genomes in the diversification of organisms via gene duplications.

Signaling on the railway transport of Russia. History of origin and development

2021 ◽  
Vol 2 (4) ◽  
pp. 435-441
Author(s):  
A. I. Prisyazhnenko
Keyword(s):  
Technological Progress ◽  
Railway Transport ◽  
Signaling System ◽  
Early 19Th Century ◽  
Optical Signals ◽  
Single Row ◽  
Continuous Type ◽  
History Of ◽  
Free Block ◽  
Microprocessor Technology

The development of humanity is impossible without means of signaling. Signaling in any sphere of human activity has always been a means of ensuring the safety of his life. One of these areas was railway transport, the development of which and, accordingly, signalling facilities began in the early 19th century.With the progress of technological progress in Russia, signaling tools have also evolved, which have gone from the simplest sound and optical signals to modern ones using satellite technologies. Naturally, this path in the technical evolution of mankind is of interest to scientists and just curious people, since knowledge of the stages of the origin and development of signaling allows contemporaries to improve it and at the same time not forget the basics of this area.As a result of this process, the signaling system on railway transport, its means have undergone serious changes. Primitive ways of giving commands - optical (disk, flag) and sound (whistle) to the participants of the movement were pushed by more modern means of signaling, which already involve microprocessor technology and satellite technologies.An example of modern signaling means is the automatic locomotive signaling of a single row of continuous type (ALS-EN). The signal of this type of signaling is more informative: it contains information about the number of free block sections ahead of the train, as well as about the permissible speed of its movement.

scholarly journals Accelerated evolution and coevolution drove the evolutionary history of AGPase sub-units during angiosperm radiation

2012 ◽  
Vol 109 (4) ◽  
pp. 693-708 ◽  
Author(s):  
Jonathan Corbi ◽  
Julien Y. Dutheil ◽  
Catherine Damerval ◽  
Maud I. Tenaillon ◽  
Domenica Manicacci
Keyword(s):  
Evolutionary History ◽  
Accelerated Evolution ◽  
History Of

scholarly journals PROFESSOR ZDZISŁAW ŻYGULSKI JR.: AN OUTSTANDING PERSON, A GREAT PERSONALITY, A MUSEUM PROFESSIONAL, A RESEARCHER ON ANTIQUE WEAPONS, ORIENTAL ART AND EUROPEAN PAINTING (1921–2015)

Muzealnictwo ◽  
2017 ◽  
Vol 58 (1) ◽  
pp. 2-13
Author(s):  
Teresa Grzybkowska
Keyword(s):  
Museum Studies ◽  
The United States ◽  
Leonardo Da Vinci ◽  
Large Set ◽  
New York University ◽  
History Of Art ◽  
The World ◽  
History Of ◽  
Polish Art ◽  
Set Up

Professor Zdzisław Żygulski Jr. (1921–2015) was one of the most prominent Polish art historians of the second half of the 20th century. He treated the history of art as a broadly understood science of mankind and his artistic achievements. His name was recognised in global research on antique weapons, and among experts on Rembrandt and Leonardo da Vinci. He studied museums and Oriental art. He wrote 35 books, about 200 articles, and numerous essays on art; he wrote for the daily press about his artistic journeys through Europe, Japan and the United States. He illustrated his publications with his own photographs, and had a large set of slides. Żygulski created many exhibitions both at home and abroad presenting Polish art in which armour and oriental elements played an important role. He spent his youth in Lvov, and was expatriated to Cracow in 1945 together with his wife, the pottery artist and painter Eva Voelpel. He studied English philology and history of art at the Jagiellonian University (UJ), and was a student under Adam Bochnak and Vojeslav Molè. He was linked to the Czartoryski Museum in Cracow for his whole life; he worked there from 1949 until 2010, for the great majority of time as curator of the Arms and Armour Section. He devoted his whole life to the world of this museum, and wrote about its history and collections. Together with Prof. Zbigniew Bocheński, he set up the Association of Lovers of Old Armour and Flags, over which he presided from 1972 to 1998. He set up the Polish school of the study of militaria. He was a renowned and charismatic member of the circle of international researchers and lovers of militaria. He wrote the key texts in this field: Broń w dawnej Polsce na tle uzbrojenia Europy i Bliskiego Wschodu [Weapons in old Poland compared to armaments in Europe and the Near East], Stara broń w polskich zbiorach [Old weapons in Polish armouries], Polski mundur wojskowy [Polish military uniforms] (together with H. Wielecki). He was an outstanding researcher on Oriental art to which he dedicated several books: Sztuka turecka [Turkish art], Sztuka perska [Persian art], Sztuka mauretańska i jej echa w Polsce [Moorish art and its echoes in Poland]. Prof. Zdzisław Żygulski Jr. was a prominent educator who enjoyed great respect. He taught costume design and the history of art and interiors at the Academy of Fine Arts in Cracow, as well as Mediterranean culture at the Mediterranean Studies Department and at the Postgraduate Museum Studies at the UJ. His lectures attracted crowds of students, for whose needs he wrote a book Muzea na świecie. Wstęp do muzealnictwa [Museums in the world. Introduction to museum studies]. He also lectured at the Florence Academy of Art and at the New York University. He was active in numerous Polish scientific organisations such as PAU, PAN and SHS, and in international associations such as ICOMAM and ICOM. He represented Polish art history at general ICOM congresses many times. He was also active on diverse museum councils all over Poland.

scholarly journals Evolution of word meanings through metaphorical mapping: Systematicity over the past millennium.

2018 ◽  
Author(s):  
Yang Xu ◽  
Barbara Claire Malt ◽  
Mahesh Srinivasan
Keyword(s):  
Large Scale ◽  
Computational Models ◽  
Compact Set ◽  
Large Set ◽  
Word Meanings ◽  
The Past ◽  
History Of ◽  
Cognitive Principles ◽  
Metaphorical Mapping ◽  
Past Millennium

One way that languages are able to communicate a potentially infinite set of ideas through a finite lexicon is by compressing emerging meanings into words, such that over time, individual words come to express multiple, related senses of meaning. We propose that overarching communicative and cognitive pressures have created systematic directionality in how new metaphorical senses have developed from existing word senses over the history of English. Given a large set of pairs of semantic domains, we used computational models to test which domains have been more commonly the starting points (source domains) and which the ending points (target domains) of metaphorical mappings over the past millennium. We found that a compact set of variables, including externality, embodiment, and valence, explain directionality in the majority of about 5000 metaphorical mappings recorded over the past 1100 years. These results provide the first large-scale historical evidence that metaphorical mapping is systematic, and driven by measurable communicative and cognitive principles.

scholarly journals treeWidget: a BioJS component to visualise phylogenetic trees

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 49 ◽  
Author(s):  
Fabian Schreiber
Keyword(s):  
Phylogenetic Trees ◽  
Protein Domains ◽  
Gene Families ◽  
Sequence Information ◽  
Gene Duplications ◽  
Link Type ◽  
History Of ◽  
Conservation Patterns ◽  
Evolution Of Gene Families ◽  
The Web

Summary: Phylogenetic trees are widely used to represent the evolution of gene families. As the history of gene families can be complex (including lots of gene duplications), its visualisation can become a difficult task. A good/accurate visualisation of phylogenetic trees - especially on the web - allows easier understanding and interpretation of trees to help to reveal the mechanisms that shape the evolution of a specific set of gene/species. Here, I present treeWidget, a modular BioJS component to visualise phylogenetic trees on the web. Through its modularity, treeWidget can be easily customized to allow the display of sequence information, e.g. protein domains and alignment conservation patterns.Availability: http://github.com/biojs/biojs; http://dx.doi.org/10.5281/zenodo.7707

scholarly journals Solution structure of sperm lysin yields novel insights into molecular dynamics of rapid protein evolution

2018 ◽  
Vol 115 (6) ◽  
pp. 1310-1315 ◽  
Author(s):  
Damien B. Wilburn ◽  
Lisa M. Tuttle ◽  
Rachel E. Klevit ◽  
Willie J. Swanson
Keyword(s):  
Protein Evolution ◽  
Solution Structure ◽  
Biochemical Characterization ◽  
Purifying Selection ◽  
Biochemical Properties ◽  
Targeted Mutagenesis ◽  
High Definition ◽  
Binding Interface ◽  
Accelerated Evolution ◽  
Species Specific

Protein evolution is driven by the sum of different physiochemical and genetic processes that usually results in strong purifying selection to maintain biochemical functions. However, proteins that are part of systems under arms race dynamics often evolve at unparalleled rates that can produce atypical biochemical properties. In the marine mollusk abalone, lysin and vitelline envelope receptor for lysin (VERL) are a pair of rapidly coevolving proteins that are essential for species-specific interactions between sperm and egg. Despite extensive biochemical characterization of lysin—including crystal structures of multiple orthologs—it was unclear how sites under positive selection may facilitate recognition of VERL. Using a combination of targeted mutagenesis and multidimensional NMR, we present a high-definition solution structure of sperm lysin from red abalone (Haliotis rufescens). Unapparent from the crystallography data, multiple NMR-based analyses conducted in solution reveal clustering of the N and C termini to form a nexus of 13 positively selected sites that constitute a VERL binding interface. Evolutionary rate was found to be a significant predictor of backbone flexibility, which may be critical for lysin bioactivity and/or accelerated evolution. Flexible, rapidly evolving segments that constitute the VERL binding interface were also the most distorted regions of the crystal structure relative to what was observed in solution. While lysin has been the subject of extensive biochemical and evolutionary analyses for more than 30 years, this study highlights the enhanced insights gained from applying NMR approaches to rapidly evolving proteins.

Introduction

2021 ◽  
pp. 1-27
Author(s):  
Patricia Kitcher
Keyword(s):  
Western Philosophy ◽  
African Philosophy ◽  
Intimate Relation ◽  
History Of ◽  
Striking Contrast

No philosophical dictum is better known than Descartes’s assertion about the intimate relation between thinking and existing. What remains unknown is how we are to understand the “I” who thinks and exists. This book is about the ways that the concept of an “I” or a “self” has been developed and deployed at different times in the history of western philosophy. It also offers a striking contrast case, the “interconnected” self, who appears in some expressions of African philosophy. Appealing to philosophy to illuminate the concept of a “self” may seem unnecessary. Anyone who can read this book is a self, so why ...

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

scholarly journals Discussion on the origin and relationship of the British flora

1935 ◽  
Vol 118 (808) ◽  
pp. 197-241 ◽  
Keyword(s):  
Flowering Plants ◽  
Ice Age ◽  
Glacial Period ◽  
Important Data ◽  
Early Tertiary ◽  
Crucial Problem ◽  
History Of ◽  
Relationship Of ◽  
Geological Background ◽  
Striking Contrast

Professor Seward, in his introductory remarks, referred to the publication in 1899 of Mr. Clement Reid’s “Origin of the British Flora,” and spoke of the more recent researches of Mrs. Reid which have considerably extended our knowledge of British Tertiary floras. He drew attention to the striking contrast between the early Tertiary floras and the present plant population of Britain, and to the changes exhibited by successive floras in geographical relationship and in composition. He emphasized the importance of reconstructing the geological background as well as the botanical features of the series of floras preceding and subsequent to the Glacial period. Reference was made to the more controversial question of the effect of the Ice Age upon the plant-world, and he expressed the hope that the discussion would enable botanists to form a more definite opinion on the crucial problem of survival or extinction of flowering plants when the British area was exposed to the maximum invasion of ice. Professor Seward offered a hearty welcome to Dr. du Reitz of Uppsala, whose work on Scandinavian floras provided particularly important data having a direct bearing upon the history of the Pre-Glacial and Post-Glacial floras of Britain.

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