scholarly journals Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes

2020 ◽  
Vol 8 (7) ◽  
pp. 1001
Author(s):  
Daniel Vieira ◽  
Soraia Esteves ◽  
Carolina Santiago ◽  
Eduardo Conde-Sousa ◽  
Ticiana Fernandes ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Yeast Species ◽  
Phenotypic Diversity ◽  
Population Analysis ◽  
Nuclear Genome ◽  
Reference Sequence ◽  
Evolutionary Analysis ◽  
Novel Approach ◽  
History Of ◽  
First Time

The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between the two, mainly regarding strains’ technological uses and/or geographical distribution. In the current work, we proposed a new method to align and analyze yeast mitogenomes, overcoming current difficulties that make it impossible to obtain comparable mitogenomes for a large number of isolates. To this end, 12,016 mitogenomes were considered, and we developed a novel approach consisting of the design of a reference sequence intended to be comparable between all mitogenomes. Subsequently, the population structure of 6646 Saccharomyces cerevisiae mitogenomes was assessed. Results revealed the existence of particular clusters associated with the technological use of the strains, in particular regarding clinical isolates, laboratory strains, and yeasts used for wine-associated activities. As far as we know, this is the first time that a positive concordance between nuclear and mitogenomes has been reported for S. cerevisiae, in terms of strains’ technological applications. The results obtained highlighted the importance of including the mtDNA genome in evolutionary analysis, in order to clarify the origin and history of yeast species.

scholarly journals On processes of coloniality and decoloniality of knowledge: notions for analysing the international history of mathematics teaching

ZDM ◽  
2021 ◽  
Author(s):  
Gert Schubring
Keyword(s):  
General Education ◽  
Mathematics Teaching ◽  
History Of Mathematics ◽  
Educational Systems ◽  
Political Processes ◽  
Local Structures ◽  
Novel Approach ◽  
History Of ◽  
Global And Local ◽  
First Time

AbstractThe aspiration of this paper is to develop a novel approach towards investigating the socio-political history of mathematics teaching in educational systems. Traditionally, historical studies are confined to just one country, the author’s country. Broader approaches address international developments by confronting and comparing global and local aspects—revealing general patterns and more specific ‘local’ structures and characteristics. Yet, already in antiquity and medieval times, the specific characteristic of mathematics teaching, namely to operate at the crossroads of general education and vocational training, proved to be intimately tied to the functioning of the particular political system. In pre-modern times, however, a truly international pattern emerged for the first time: European powers conquered, occupied and colonised overseas regions. Given that educational systems were emerging at the same time within these states, they often transmitted elements of these structures to their colonies. This phenomenon included mathematics, and the history of its teaching is analysed here as a part of coloniality. It is shown that this was not a uniform process, and the differences between the various colonial powers are discussed. The involvement of mathematics in the process of decolonisation is addressed, as well as its role in the tension between continued coloniality and movements of decoloniality. Finally, the general framework provided for studying socio-political processes connected with establishing mathematics teaching within public educational systems is applied, in order to analyse recent coloniality practices effected by international achievement studies.

scholarly journals AlphaFold at CASP13

2019 ◽  
Vol 35 (22) ◽  
pp. 4862-4865 ◽  
Author(s):  
Mohammed AlQuraishi
Keyword(s):  
Protein Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Computational Prediction ◽  
Data Bank ◽  
Academic Community ◽  
Physical Contact ◽  
Evolutionary Analysis ◽  
History Of ◽  
First Time

Abstract Summary: Computational prediction of protein structure from sequence is broadly viewed as a foundational problem of biochemistry and one of the most difficult challenges in bioinformatics. Once every two years the Critical Assessment of protein Structure Prediction (CASP) experiments are held to assess the state of the art in the field in a blind fashion, by presenting predictor groups with protein sequences whose structures have been solved but have not yet been made publicly available. The first CASP was organized in 1994, and the latest, CASP13, took place last December, when for the first time the industrial laboratory DeepMind entered the competition. DeepMind's entry, AlphaFold, placed first in the Free Modeling (FM) category, which assesses methods on their ability to predict novel protein folds (the Zhang group placed first in the Template-Based Modeling (TBM) category, which assess methods on predicting proteins whose folds are related to ones already in the Protein Data Bank.) DeepMind's success generated significant public interest. Their approach builds on two ideas developed in the academic community during the preceding decade: (i) the use of co-evolutionary analysis to map residue co-variation in protein sequence to physical contact in protein structure, and (ii) the application of deep neural networks to robustly identify patterns in protein sequence and co-evolutionary couplings and convert them into contact maps. In this Letter, we contextualize the significance of DeepMind's entry within the broader history of CASP, relate AlphaFold's methodological advances to prior work, and speculate on the future of this important problem.

scholarly journals Functional Biodiversity of Yeasts Isolated from Colombian Fermented and Dry Cocoa Beans

2020 ◽  
Vol 8 (7) ◽  
pp. 1086 ◽  
Author(s):  
Johannes Delgado-Ospina ◽  
Samantha Triboletti ◽  
Valentina Alessandria ◽  
Annalisa Serio ◽  
Manuel Sergi ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Fermentation Process ◽  
Yeast Species ◽  
Degradation Products ◽  
Microbial Community Composition ◽  
Functional Biodiversity ◽  
Cocoa Beans ◽  
Pichia Kudriavzevii ◽  
First Time ◽  
Cocoa Fermentation

Yeasts play an important role in the cocoa fermentation process. Although the most relevant function is the degradation of sugars and the production of ethanol, there is little understanding of the enzyme activities and attributes that allow them to survive even after drying. The present study explored the functional biodiversity of yeasts associated with Criollo Colombian cocoa fermented beans, able to survive after drying. Twelve species belonging to 10 genera of osmo-, acid-, thermo-, and desiccation-tolerant yeasts were isolated and identified from fermented and dry cocoa beans, with Pichia kudriavzevii and Saccharomyces cerevisiae standing out as the most frequent. For the first time, we reported the presence of Zygosaccharomyces bisporus in cocoa fermented beans. It was found that resistance to desiccation is related to the different degradation capacities of fermentation substrates, which suggests that associative relationships may exist between the different yeast species and their degradation products. Besides, the increased thermotolerance of some species was related to the presence of polyphenols in the medium, which might play a fundamental role in shaping the microbial community composition.

scholarly journals Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Safia Zeghbib ◽  
Róbert Herczeg ◽  
Gábor Kemenesi ◽  
Brigitta Zana ◽  
Kornélia Kurucz ◽  
...  
Keyword(s):  
Geographical Location ◽  
Data Sets ◽  
Evolutionary Analysis ◽  
Evolutionary Patterns ◽  
Host Genus ◽  
Evolution Analysis ◽  
Zoonotic Viruses ◽  
History Of ◽  
First Time

Abstract Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.

scholarly journals Impact of transposable elements on genome structure and evolution in bread wheat

2018 ◽  
Author(s):  
Thomas Wicker ◽  
Heidrun Gundlach ◽  
Manuel Spannagl ◽  
Cristobal Uauy ◽  
Philippa Borrill ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Bread Wheat ◽  
Genome Structure ◽  
Reference Sequence ◽  
Structural Level ◽  
Gene Promoters ◽  
Genome Wide ◽  
Intergenic Regions ◽  
History Of ◽  
First Time

AbstractBackgroundTransposable elements (TEs) are ubiquitous components of genomes and they are the main contributors to genome evolution. The reference sequence of the hexaploid bread wheat (Triticum aestivum L.) genome enabled for the first time a comprehensive genome-wide view of the dynamics of TEs that have massively proliferated in the A, B, and D subgenomes.ResultsTEs represent 85% of the genome. We traced back TE amplification dynamics in the evolutionary history of wheat and did not find large bursts in the wake of either the tetra- or the hexaploidization. Despite the massive turnover of TEs since A, B, and D diverged, 76% of TE families are present in similar proportions in the three subgenomes. Moreover, spacing between homeologous genes was also conserved. TE content around genes is very different from the TE space comprising large intergenic regions and families that are enriched or depleted from gene promoters are the same in the three subgenomes.ConclusionsThe chromosome-scale assembly of the wheat genome provided an unprecedented genome-wide view of the organization and impact of TEs in such a complex genome. Our results suggest that TEs play a role at the structural level and that the overall chromatin structure is likely under selection pressure.

Adam Zalužanský’s “De sexu plantarum” (1592): an early pioneering chapter on plant sexuality

2013 ◽  
Vol 40 (2) ◽  
pp. 244-256 ◽  
Author(s):  
Holger Funk
Keyword(s):  
Nineteenth Century ◽  
English Translation ◽  
History Of Botany ◽  
Main Work ◽  
Botanical History ◽  
History Of ◽  
The University ◽  
First Time

In the history of botany, Adam Zalužanský (d. 1613), a Bohemian physician, apothecary, botanist and professor at the University of Prague, is a little-known personality. Linnaeus's first biographers, for example, only knew Zalužanský from hearsay and suspected he was a native of Poland. This ignorance still pervades botanical history. Zalužanský is mentioned only peripherally or not at all. As late as the nineteenth century, a researcher would be unaware that Zalužanský’s main work Methodi herbariae libri tres actually existed in two editions from two different publishers (1592, Prague; 1604, Frankfurt). This paper introduces the life and work of Zalužanský. Special attention is paid to the chapter “De sexu plantarum” of Zalužanský’s Methodus, in which, more than one hundred years before the well-known De sexu plantarum epistola of R. J. Camerarius, the sexuality of plants is suggested. Additionally, for the first time, an English translation of Zalužanský’s chapter on plant sexuality is provided.

A Confrontation between Two Doctrines: The Birth of Struggle for Hegemony in Hebrew Children's Literature during the 1930s and 1940s

2008 ◽  
Vol 1 (2) ◽  
pp. 139-155 ◽  
Author(s):  
YAEL DARR
Keyword(s):  
Children's Literature ◽  
Educational System ◽  
Single Channel ◽  
Children’S Literature ◽  
The Political ◽  
Literary Creation ◽  
History Of ◽  
High Level ◽  
First Time ◽  
Literary Quality

This article describes a crucial and fundamental stage in the transformation of Hebrew children's literature, during the late 1930s and 1940s, from a single channel of expression to a multi-layered polyphony of models and voices. It claims that for the first time in the history of Hebrew children's literature there took place a doctrinal confrontation between two groups of taste-makers. The article outlines the pedagogical and ideological designs of traditionalist Zionist educators, and suggests how these were challenged by a group of prominent writers of adult poetry, members of the Modernist movement. These writers, it is argued, advocated autonomous literary creation, and insisted on a high level of literary quality. Their intervention not only dramatically changed the repertoire of Hebrew children's literature, but also the rules of literary discourse. The article suggests that, through the Modernists’ polemical efforts, Hebrew children's literature was able to free itself from its position as an apparatus controlled by the political-educational system and to become a dynamic and multi-layered field.

Digging the history. Absolute chronology of the settlement complex at Czermno-Cherven’ (eastern Poland). Research status and perspectives

2020 ◽  
Vol 72 (2) ◽  
Author(s):  
Tomasz Dzieńkowski ◽  
Marcin Wołoszyn ◽  
Iwona Florkiewicz ◽  
Radosław Dobrowolski ◽  
Jan Rodzik ◽  
...  
Keyword(s):  
Interdisciplinary Research ◽  
Qualitative Change ◽  
Archaeological Research ◽  
Research Status ◽  
History Of ◽  
Absolute Dating ◽  
First Time ◽  
Radiocarbon Datings

The article discusses the results of the latest interdisciplinary research of Czermno stronghold and its immediate surroundings. The site is mentioned in chroniclers’ entries referring to the stronghold Cherven’ (Tale of Bygone Years, first mention under the year 981) and the so-called Cherven’ Towns. Given the scarcity of written records regarding the history of today’s Eastern Poland, Ukraine, and Belarus in the 10th and 11th centuries, recent archaeological research, supported by geoenvironmental analyses and absolute dating, brought a significant qualitative change. In 2014 and 2015, the remains of the oldest rampart of the stronghold were uncovered for the first time. A series of radiocarbon datings allows us to refer the erection of the stronghold to the second half/late 10th century. The results of several years’ interdisciplinary research (2012-2020) introduce qualitatively new data to the issue of the Cherven’ Towns, which both change current considerations and confirm the extraordinary research potential in the archeology of the discussed region.

A Well-Ordered Thing

2018 ◽  
Author(s):  
Michael D. Gordin
Keyword(s):  
Nineteenth Century ◽  
History Of Science ◽  
Periodic Table ◽  
The Arctic ◽  
Classic Work ◽  
Hot Air ◽  
History Of ◽  
First Time

Dmitrii Mendeleev (1834–1907) is a name we recognize, but perhaps only as the creator of the periodic table of elements. Generally, little else has been known about him. This book is an authoritative biography of Mendeleev that draws a multifaceted portrait of his life for the first time. As the book reveals, Mendeleev was not only a luminary in the history of science, he was also an astonishingly wide-ranging political and cultural figure. From his attack on Spiritualism to his failed voyage to the Arctic and his near-mythical hot-air balloon trip, this is the story of an extraordinary maverick. The ideals that shaped his work outside science also led Mendeleev to order the elements and, eventually, to engineer one of the most fascinating scientific developments of the nineteenth century. This book is a classic work that tells the story of one of the world's most important minds.

Victorian Pain

2017 ◽  
Author(s):  
Rachel Ablow
Keyword(s):  
Nineteenth Century ◽  
Victorian Literature ◽  
Social Life ◽  
Charles Darwin ◽  
Harriet Martineau ◽  
The Status ◽  
History Of ◽  
The Individual ◽  
Natural Philosophers ◽  
First Time

The nineteenth century introduced developments in science and medicine that made the eradication of pain conceivable for the first time. This new understanding of pain brought with it a complex set of moral and philosophical dilemmas. If pain serves no obvious purpose, how do we reconcile its existence with a well-ordered universe? Examining how writers of the day engaged with such questions, this book offers a compelling new literary and philosophical history of modern pain. The book provides close readings of novelists Charlotte Brontë and Thomas Hardy and political and natural philosophers John Stuart Mill, Harriet Martineau, and Charles Darwin, as well as a variety of medical, scientific, and popular writers of the Victorian age. The book explores how discussions of pain served as investigations into the status of persons and the nature and parameters of social life. No longer conceivable as divine trial or punishment, pain in the nineteenth century came to seem instead like a historical accident suggesting little or nothing about the individual who suffers. A landmark study of Victorian literature and the history of pain, the book shows how these writers came to see pain as a social as well as a personal problem. Rather than simply self-evident to the sufferer and unknowable to anyone else, pain was also understood to be produced between persons—and even, perhaps, by the fictions they read.

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