scholarly journals Ανάπτυξη και εφαρμογή εργαλείων βιοπληροφορικής για τη φυλογενετική ανάλυση και πρόβλεψη της δομής και ρύθμισης της λειτουργίας των πρωτεϊνών

2011 ◽  
Author(s):  
Αθανασία Παυλοπούλου
Keyword(s):  
Evolutionary History ◽  
Inflammatory Diseases ◽  
Structural Features ◽  
Dna Methyltransferases ◽  
The Novel ◽  
Homologous Proteins ◽  
Plant Dna ◽  
History Of ◽  
The Individual ◽  
Encoding Genes

In the present thesis, the availability of an increasing number of complete or almostcomplete genomes, including those that were completed recently, enabled the study ofthe evolutionary history of three functionally important protein families: (a) the plant DNAmethyltransferases and (b) the eukaryotic RNA methyltransferases, which are enzymesthat catalyze the transfer of a methyl group to nucleotide sequences, as well as (c) thekallikrein-related peptidases or KLKs, which are trypsin- or chymotrypsin-like serineproteases. The evolutionary relationships of the already known and the novel proteins ofthe three families that were identified here were investigated using phylogenetic trees.Moreover, the secondary and tertiary structures of the homologous proteins wereanalyzed, as well as the structure of the protein-encoding genes, and diagnostic proteinmotifs were constructed based on the sequences of the three enzyme families. Ourresults led to suggestions pertaining to the biological function of the identified novelproteins. In particular, homologous plant DNA methyltransferases and novel eukaryoticRNA methyltransferases were identified in publicly accessible sequence databases.Detailed phylogenetic analysis of plant DNA methyltransferases identified four alreadyknown families and a novel subfamily in addition (Pavlopoulou and Kossida, 2007).Moreover, five distinct eukaryotic RNA methyltransferase subfamilies were identified;apart from the three already known subfamilies (NOP2, NCL1 and YNL022C), onenovel subfamily (RCMT9) and the FMU which hitherto was considered to existexclusively in prokaryotes were also identified (Pavlopoulou and Kossida, 2009).Furthermore, protein fingerprints were constructed from the generic family of RNAmethyltransferases (and the individual subfamilies), which were deposited in thePRINTS database (http://www.bioinf.man.ac.uk/dbbrowser/PRINTS). We developed the computational program RCMTHMM, in order to discriminate/identify eukaryotic RNAmethyltransferases from other proteins. The RCMTHMM program has been madepublicly available in the URL: http://www.bioacademy.gr/bioinformatics/RCMTHMM.Finally, the evolutionary history of KLKs was reconstructed. Kallikreins are importantproteolytic enzymes which are involved in proteolytic cascade pathways and theirdysregulated expression has been associated with major human pathologies(cardiovascular diseases, neurodegenerative disorders, inflammatory diseases, skindiseases, different cancer types). The prominent feature of the kallikrein family is that itconsists of tandemly and uninterruptedly arrayed genes on a single locus at humanchromosome 19q13.3-13.4. This unique feature was used in order to identify novelKLKs and KLK-like genes/proteins. Previous studies on the evolution of kallikreins wererestricted to mammals and the emergence of the kallikrein genes was suggestedapproximately 150 million years ago. In the present study, homologous novel kallikreinprotein sequences were detected in silico in the genomes of various species. For thefirst time, novel KLK orthologues were identified in reptiles, aves and amphibia, whichallowed us to trace the evolutionary origin of kallikreins 330 million years ago. Inaddition, apart from the 15 already known KLK genes (KLK1-15), three novel memberswere identified (orphan Klks). All the defining structural features which are related to thecatalytic activity of KLKs were found to be conserved in the novel KLK proteinsequences. Of particular interest, the synteny of the KLK-encoding genes was analyzedand it was shown that these genes are co-localized in contiguous, uninterrupted clustersmaintaining the same orientation in all species under investigation. We suggest that aseries of gene duplication and mutation events gave rise to the family of KLK enzymesand KLKs have co-evolved with their specific substrates (Pavlopoulou et al., 2010).

scholarly journals Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’

2014 ◽  
Vol 9 (2) ◽  
pp. 447-460 ◽  
Author(s):  
Noha H Youssef ◽  
Christian Rinke ◽  
Ramunas Stepanauskas ◽  
Ibrahim Farag ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
Evolutionary History ◽  
The Novel ◽  
History Of The Novel ◽  
History Of

scholarly journals Development and characterization of twelve new polymorphic microsatellite loci in the Iberian ribbed newt, Pleurodeles waltl (Caudata: Salamandridae), with data on cross-amplification in P. nebulosus

2014 ◽  
Vol 35 (1) ◽  
pp. 129-134 ◽  
Author(s):  
Jorge Gutiérrez-Rodríguez ◽  
Elena G. Gonzalez ◽  
Íñigo Martínez-Solano
Keyword(s):  
Population Dynamics ◽  
Microsatellite Loci ◽  
Evolutionary History ◽  
The Novel ◽  
Expected Heterozygosity ◽  
History Of ◽  
Southern Iberia ◽  
Polymorphic Microsatellite ◽  
Pleurodeles Waltl

Twelve novel polymorphic microsatellite loci were isolated and characterized for the Iberian ribbed newt, Pleurodeles waltl (Caudata, Salamandridae). The distribution of this newt ranges from central and southern Iberia to northwestern Morocco. Polymorphism of these novel loci was tested in 40 individuals from two Iberian populations and compared with previously published markers. The number of alleles per locus ranged from two to eight. Observed and expected heterozygosity ranged from 0.13 to 0.57 and from 0.21 to 0.64, respectively. Cross-species amplification was tested in Pleurodeles nebulosus, which is listed as Vulnerable by the IUCN. Eight new and seven previously published loci amplified successfully in that species and thus represent a valuable conservation tool. The novel microsatellites will be useful for a better understanding of the population dynamics, demography, genetic structure, and evolutionary history of Pleurodeles waltl and P. nebulosus.

scholarly journals Diverse DNA modification in marine prokaryotic and viral communities

2021 ◽  
Author(s):  
Satoshi Hiraoka ◽  
Tomomi Sumida ◽  
Miho Hirai ◽  
Atsushi Toyoda ◽  
Shinsuke Kawagucci ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Single Molecule ◽  
Evolutionary History ◽  
Defense Mechanism ◽  
Dna Methyltransferases ◽  
Dna Modifications ◽  
History Of ◽  
Viral Communities ◽  
Metagenomic Assembly ◽  
Marine Microbial Communities

Chemical modifications of DNA, including methylation, play an important role in prokaryotes and viruses. However, our knowledge of the modification systems in environmental microbial communities, typically dominated by members not yet cultured, is limited. Here, we conducted 'metaepigenomic' analyses by single-molecule real-time sequencing of marine microbial communities. In total, 233 and 163 metagenomic assembly genomes (MAGs) were constructed from diverse prokaryotes and viruses, respectively, and 220 modified motifs and 276 DNA methyltransferases (MTases) were identified. Most of the MTases were not associated with the defense mechanism. The MTase-motif correspondence found in the MAGs revealed 10 novel pairs, and experimentally confirmed the catalytic specificities of the MTases. We revealed novel alternative motifs in the methylation system that are highly conserved in Alphaproteobacteria, illuminating the co-evolutionary history of the methylation system and host genome. Our findings highlight diverse unexplored DNA modifications that potentially affect the ecology and evolution of prokaryotes and viruses.

New pieces on genetic diversity and evolutionary history of hepatitis B virus: Characterization of the novel subgenotype F6

2017 ◽  
Vol 47 ◽  
pp. 140-142 ◽  
Author(s):  
Laura Noelia Mojsiejczuk ◽  
Carolina Torres ◽  
María Belén Pisano ◽  
Viviana Re ◽  
Rodolfo Héctor Campos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Evolutionary History ◽  
The Novel ◽  
B Virus ◽  
History Of

scholarly journals Foucault’un İktidar Görüşleri Işığında Erdal Öz’ün Yaralısın Romanı / Yaralisin, the Novel by Erdal Oz, in the Light of Foucault’s Power Theory

2017 ◽  
Vol 6 (6) ◽  
pp. 564
Author(s):  
Koray Üstün
Keyword(s):  
Michel Foucault ◽  
Power Structure ◽  
New Order ◽  
The Novel ◽  
Second Person ◽  
Private Space ◽  
Power Theory ◽  
History Of ◽  
The Subject ◽  
The Individual

<p><strong>Abstract</strong></p><p>In the light of the power concepts theorized by Michel Foucault, this article investigates Erdal Oz's novel Yaralisin (You’re Wounded). Foucault’s power structure that systematized in Subject and Power (1961), History of Sexuality (1984), Birth of Prison (1975), The Birth of Biopolitics (2004), has similarities with crime production that the novel reflects. Accordingly, individuals are being standardized in the prison through programs, strategies and technics that the power structure determined. In this process, there is no direct enforcement on the individual. The power structure connects the individual to itself through knowledge and body. In Oz’s novel the subject depending on space changing are being standardized and transformed into the “Nuri” character, as we read in the text. At the base of becoming standard individual through lost of identity, there is crime production. As for crime production, it takes shape in accordance with space. In the novel, space dependent suffering, inflicted on individuals, places the subject on a hierarchical plane, as Foucault has also indicated, and brings an end to existence. The power structure, cutting off the individual from his private space, taking him first into the interrogation room, and then to the prison, has made him a part of the system and has objectified him. The digestive effect of the power structure has become even more concrete with the presence of the second person narrator within the narrative plane; depersonalization has taken place within the new order.</p><p><strong>Öz</strong></p><p>Bu makalede Michel Foucault’un kuramsallaştırdığı iktidar kavramı ışığında Erdal Öz’ün <em>Yaralısın</em> romanı incelenmiştir. Foucault’nun <em>Özne ve İktidar </em>(1961),<em> Cinselliğin Tarihi </em>(1984)<em>, Hapishanenin Doğuşu </em>(1975)<em>, Biyopolitikanın Doğuşu</em> (2004) gibi kitaplarında sistemleştirdiği iktidar, romanda aktarılan suç üretimi ile paralellik taşımaktadır. Bireyler, iktidar tarafından belirlenen program, strateji ve tekniklerle hapishanelerde tek tipleştirilmektedir. Bu süreçte bireyler üzerine doğrudan bir yaptırım uygulanmaz; iktidar, bilgi ve beden yönetimi üzerinden bireyi kendine bağlar. Öz’ün romanında da uzamsal değişimlere bağlı olarak tekil özneler, tek tipleştirilerek metindeki karşılığıyla “Nuri”lere dönüşür. Bireyin kendi kimliğini yitirerek tek tipleşmesinin temelinde suç üretimi vardır. Suç üretimi ise uzama göre şekillenir. Romanda uzama göre değişen çektirilen azaplar, Foucault’un da belirttiği gibi özneyi hiyerarşik düzleme yerleştirir ve varoluşu sona erdirir. İktidar, özneyi kişisel mekânından ayırıp önce sorgu odasına ardından da hapishaneye götürerek onu düzenin bir parçası hâline getirmiş ve nesneleştirmiştir. İktidarın sindirici etkisi, anlatı düzlemindeki ikinci tekil anlatıcının varlığıyla daha da somutlaşmış; kurulan düzen içerisinde özne yitimi gerçekleşmiştir. </p>

scholarly journals Some Endangered Feeling

Daedalus ◽  
2020 ◽  
Vol 150 (01) ◽  
pp. 40-61
Author(s):  
Nancy Armstrong
Keyword(s):  
Recent Trend ◽  
Affect Theory ◽  
The Novel ◽  
Robinson Crusoe ◽  
History Of The Novel ◽  
Human Motivation ◽  
History Of ◽  
To Come ◽  
The Individual ◽  
And Behavior

This essay sees the recent trend in novels that feature damaged, partial, or wayward protagonists as the ascent of a tradition of formal outliers as old as the novel itself to a position of dominance. Rather than formulate a self-contained individual capable of defending itself against whatever forces of nature or society might disperse and refigure it, this other tradition gave into those forces, releasing human subjectivity from the confines of the self-regulating individual. Why now? How does this major turn in the history of the novel contribute to the current reconsideration of human motivation and behavior in light of affect theory? If Robinson Crusoe provided a bellwether for the individual to come, then what can the damaged protagonist of Tom McCarthy's 2005 novel Remainder tell us about the selves we are likely to become?

scholarly journals Between Social Utopia and Totalitarian Reality: “Children of Milky Way” by Dokiia Humenna

2019 ◽  
pp. 73-89
Author(s):  
Vadym Vasylenko
Keyword(s):  
Milky Way ◽  
Traumatic Memory ◽  
The Novel ◽  
Life Strategies ◽  
The World ◽  
Literary Process ◽  
History Of ◽  
The Individual ◽  
And Control ◽  
Social Utopia

The paper considers the novel “Children of Milky Way” by Dokiia Humenna in the context of the postwar Ukrainian diaspora’s literary process. The focus is on the issues of relations between fiction and documentary writing, the individual and collective experiences. The literary Kyiv, being one of the central images in Dokiia Humenna’s novel, appears not only as a page from individual or national histories, a sample of the Kyiv text in the Ukrainian diaspora’s prose, but also as a generalization based on such texts and made due to various forms of intertextuality, which absorb the history and atmosphere of the Kyiv 1920s. The problem of interrelations between the writer and government, art, politic, and ideology is one of the most essential in the novel: Dokia Humenna reveals various aspects of the writer’s life and work in conditions of the totalitarian state and culture – from suicide to madness, from resistance to adaptation and collaboration. A future person and society in “Children of Milky Way” are represented in a commune. The histories of the two characters-antipodes Taras Saragola and Seraphym Carmalita are connected to its progress and decline; in the world of totalitarian repressions and control they choose different life strategies and roles. The memory about Soviet terror and repressions, as well as the Holodomor-genocide, “killing the Ukrainian peasantry as a foundation of the nation and destructing intellectuals as a brain of the nation” is important in the novel. The history of collectivization is related to the traumatic memory of the serfdom times, which affects  the second and third generations and deepens the trauma caused by disintegration of a family, destruction of the patriarchal peasant world. This process was accompanied by desacralization of the Father’s figure as a personification of power, by infantilization of masculinity. The writer associates totalitarian reality with the metaphor of Night, which acquires different ambiguous meanings in the Ukrainian anti-totalitarian discourse.

scholarly journals ASPEN: A methodology for reconstructing protein evolution with improved accuracy using ensemble models

2017 ◽  
Author(s):  
Roman Sloutsky ◽  
Kristen M. Naegle
Keyword(s):  
Protein Evolution ◽  
Protein Function ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Protein Family ◽  
Reconstruction Algorithms ◽  
Protein Families ◽  
Homologous Proteins ◽  
Extant Species ◽  
History Of

AbstractEvolutionary reconstruction algorithms produce models of the evolutionary history of proteins: the order of duplications and speciations that led to extant homologous proteins observed across species. Although they are regularly used to gain insight into protein function, these models are estimates of an unknowable truth according to the underlying assumptions inherent in each algorithm, its objective function, and the input sequences supplied for reconstruction. In practice, the generated models are highly sensitive to the sequence inputs. In this work, we asked whether we could identify stronger phylogenetic signal by capitalizing on the variance introduced by perturbing the input to evolutionary reconstruction to explore a rich space of possible models that could explain protein evolution. We subsampled from available protein orthologs, “same” proteins across multiple extant species, and produced an ensemble of topologies representing the duplication history which produced related proteins (paralogs) for simulated protein families and in a real protein family – the LacI transcription factor family. We found that two very important phenomena arise from this approach. First, the reproducibility of an all-sequence, single-alignment reconstruction, measured by comparing topologies inferred from 90% subsamples, directly correlates with the accuracy of that single-alignment reconstruction, producing a measurable value for something that has been traditionally unknowable. Second, if we take a large ensemble of trees inferred from 50% subsamples and cast the ensemble into a form that represents the distribution of pairwise leaf distances observed across the ensemble, then trees that capture the most frequently observed relationships are also the most accurate. We propose a new methodology, ASPEN, a meta-algorithm that finds and ranks the trees that are most consistent with observations across the ensemble. Top-ranked ASPEN trees are significantly more accurate than the single-alignment tree produced from all available sequences. Importantly, our findings suggest that the true tree is currently inaccessible for most real protein families. Instead, applications that rely on evolutionary models should integrate across many trees that are equally likely to represent the true evolutionary history of a protein family.

‘Always Returning from It’: Neoliberal Capitalism, Retrospect, and Marlon James's A Brief History of Seven Killings

CounterText ◽  
2018 ◽  
Vol 4 (2) ◽  
pp. 169-191
Author(s):  
Sharae Deckard
Keyword(s):  
Latin American ◽  
Structural Adjustment ◽  
State Violence ◽  
Historical Event ◽  
The Novel ◽  
Neoliberal Capitalism ◽  
History Of ◽  
Social Totality ◽  
The Individual ◽  
Structural Adjustment Programmes

This article contemplates the question of the afterwardly through a reading of Marlon James's A Brief History of Seven Killings (2014). I argue that in Brief History, anxieties about the inability to summon a future beyond the present – to know a world beyond neoliberal capitalism – are formally generative, providing the literary and cultural material for experimentation. Far from having exhausted the potential of the literary, the novel instead insists on the vitality of counter-hegemonic representation of the rise of the neoliberal world-system, and the capacity to resurrect the ‘not-known’ social totality of an earlier historical event even as it simultaneously struggles to imagine potentialities of collective agency in the present. James constructs a retrospective history of the aftermath of the 1976 attempted assassination of Bob Marley, reinterpreted from the standpoint of the twenty-first century in order to narrate not only the individual traumas incurred by the event, but in order to rematerialise a collective history of the social, systemic, and inter-state violence perpetrated by the neoliberal turn of capitalist accumulation in the Caribbean. In particular, the novel offers a hemispheric view of the complex historical causality of the political destabilisation of Caribbean and Latin American states through CIA-sponsored drug and arms trafficking, the exploitation of extractivist resource regimes, and the economic imposition of structural adjustment programmes.

scholarly journals Kinetochore microtubule numbers of different sized chromosomes

1979 ◽  
Vol 83 (3) ◽  
pp. 556-561 ◽  
Author(s):  
PB Moens
Keyword(s):  
Evolutionary History ◽  
Spindle Pole ◽  
Mitotic Metaphase ◽  
Robertsonian Fusion ◽  
Metaphase Chromosomes ◽  
History Of ◽  
The Individual ◽  
Kinetochore Region ◽  
Mitosis And Meiosis ◽  
Metaphase I

For three species of grasshoppers the volumes of the largest and the smallest metaphase chromosome differ by a factor of 10, but the microtubules (MTs) attached to the individual kinetochores show no corresponding range in numbers. Locusta mitotic metaphase chromosomes range from 2 to 21 μm, and the average number of MTs per kinetochore is 21 with an SD of 4.6. Locusta meiotic bivalents at late metaphase I range from 4 to 40 μm(3), and the kinetochore regions (= two sister kinetochores facing the same spindle pole) have an average of 25 kinetochore microtubules (kMTs) with an SD of 4.9. Anaphase velocities are the same at mitosis and meiosis I. The smaller mitotic metaphase chromosomes of neopodismopsis are similar in size, 6 to 45 μm(3), to Locusta, but they have an average more kMTs, 33, SD = 9.2. The four large Robertsonian fusion chromosomes of neopodismopsis have an average of 67 MTs per kinetochore, the large number possibly the result of a permanent dicentric condition. Chloealtis has three pairs of Robertsonian fusion chromosomes which, at late meiotic metaphase I, form bivalents of 116, 134, and 152 μm (3) with an average of 67 MTs per kinetochore similar to Locusta bivalents, but with a much higher average of 42 MTs per kinetochore region. It is speculated that, in addition to mechanical demands of force, load, and viscosity, the kMT numbers are governed by cell type and evolutionary history of the karyotype in these grasshoppers.

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