Hasil untuk "Genealogy"

A. Atkinson, A. Brandolini

K. Jolley, C. Bliss, Julia S. Bennett et al.

No single genealogical reconstruction or typing method currently encompasses all levels of bacterial diversity, from domain to strain. We propose ribosomal multilocus sequence typing (rMLST), an approach which indexes variation of the 53 genes encoding the bacterial ribosome protein subunits (rps genes), as a means of integrating microbial genealogy and typing. As with multilocus sequence typing (MLST), rMLST employs curated reference sequences to identify gene variants efficiently and rapidly. The rps loci are ideal targets for a universal characterization scheme as they are: (i) present in all bacteria; (ii) distributed around the chromosome; and (iii) encode proteins which are under stabilizing selection for functional conservation. Collectively, the rps loci exhibit variation that resolves bacteria into groups at all taxonomic and most typing levels, providing significantly more resolution than 16S small subunit rRNA gene phylogenies. A web-accessible expandable database, comprising whole-genome data from more than 1900 bacterial isolates, including 28 draft genomes assembled de novo from the European Bioinformatics Institute (EBI) sequence read archive, has been assembled. The rps gene variation catalogued in this database permits rapid and computationally non-intensive identification of the phylogenetic position of any bacterial sequence at the domain, phylum, class, order, family, genus, species and strain levels. The groupings generated with rMLST data are consistent with current nomenclature schemes and independent of the clustering algorithm used. This approach is applicable to the other domains of life, potentially providing a rational and universal approach to the classification of life that is based on one of its fundamental features, the translation mechanism.

Stuart Hall

A. Cockburn

P. Underhill, G. Passarino, A. A. Lin et al.

G. Kendall, G. Wickham

J. Pickles

M. Kuhner

Brian C. Zhang, Arjun Biddanda, Á. F. Gunnarsson et al.

ARG-Needle is a method to infer genome-wide genealogies from large-scale genotyping data that can be used in association analyses. Applied to UK Biobank data, genealogy-based testing finds more trait associations than using imputed genotypes. Genome-wide genealogies compactly represent the evolutionary history of a set of genomes and inferring them from genetic data has the potential to facilitate a wide range of analyses. We introduce a method, ARG-Needle, for accurately inferring biobank-scale genealogies from sequencing or genotyping array data, as well as strategies to utilize genealogies to perform association and other complex trait analyses. We use these methods to build genome-wide genealogies using genotyping data for 337,464 UK Biobank individuals and test for association across seven complex traits. Genealogy-based association detects more rare and ultra-rare signals ( N  = 134, frequency range 0.0007−0.1%) than genotype imputation using ~65,000 sequenced haplotypes ( N  = 64). In a subset of 138,039 exome sequencing samples, these associations strongly tag (average r  = 0.72) underlying sequencing variants enriched (4.8×) for loss-of-function variation. These results demonstrate that inferred genome-wide genealogies may be leveraged in the analysis of complex traits, complementing approaches that require the availability of large, population-specific sequencing panels.

R. Munck

Тихонов Сергей Семенович

Автор рассматривает процесс сложения одного из позднесредневековых археологических микрорайонов (АМР), сформированного русскими первопроходцами в среднем течении р. Томь. Первыми здесь, на левобережье Томи между устьями рек Мунгат и Уньга, поселились крестьяне – выходцы из деревень, расположенных к северу от Кузнецкой крепости. В 1715 г. для их охраны был поставлен Мунгатский острог, тем самым было завершено освоение русскими первопроходцами всего течения Томи. Примерно в конце первой трети XVIII в. все земли на указанном участке были освоены и началось уплотнение сложившейся системы расселения за счет организации деревень в среднем и верхнем течении небольших левых притоков Томи, а также освоения правого берега реки. По мнению автора, каждую из этих деревень можно считать первичным археологическим микрорайоном, т.к. они занимали ограниченную территорию и отстояли от ближайших деревень на расстояние 10 и более километров, а вокруг них формируются хозяйственные территории. Одна из них – Крапивино, которая находилась в непосредственной близости от Мунгатского острога. На примере этой деревни автор рассматривает формирование АМР и усложнение его структуры. Близ каждого из этих двух населенных пунктов формируются кладбища (даже несколько), появляются храмы, возникают местные дороги, ведущие от острога к деревне, и от них на места ведения хозяйства – пашни, покосы, места заготовки древесины, рыболовные угодья и т.д. В первой трети XX в. острог и деревня слились в единый населенный пункт с несколькими кладбищами, окруженными хозяйственными и промысловыми сооружениями: мельницами, пасеками, летними станами на покосах, местами заготовки камней для изготовления точил и жерновов и т.д. Возможными границами этого комплекса были пороги на р. Томь, а острог и деревню разделяли колки (небольшие лесные массивы) и выпасы, часть из которых использовались как аэродромы в 1940–1960 гг.

Jason Hockaday

Previous research has shown that Appalachian Studies as a field, by drawing upon Appalachian Studies scholars and activists such as Harry Caudill, Helen Lewis, and Chris Irwin, misapplied the colonialism model to whites in the region, which resulted in clear remnants of self-Indigenization in the field. I show through a rhetorical analysis of recent (2020–2023) editions of the <i>Journal of Appalachian Studies</i> that these critiques have been left largely unaddressed in the field. In reviewing these issues, a tenet of Appalachian Studies is to employ “Appalachian” as an identity (rather than as solely a regional analytic) that is claimable by whites as distinct from other white settler colonizer identities. Applying the peoplehood matrix, which is a theory of that which imbues Indigenous peoples with Indigeneity and sovereignty, I reveal that white Appalachia often rhetorically presents itself as a colonized Indigenous people—though not necessarily as American Indians.

J. Carrette, R. King

Luciana Ballestrin

The aim of this article is to present the history and thought of the Modernity/Coloniality (M/C) Group, from its split away from subaltern - Latin Americans and Indians - , cultural and postcolonial studies in the late 90s. The group made ​​a crucial epistemological move for critical and utopian renewal of social sciences in Latin America in the 21st century: the radicalization of the post-colonial argument through the ideia of "decolonial turn." At first, we draw a brief genealogy of postcolonialism. Subsequently, we present the establishment of the M/C group and some central concepts created and shared by its main exponents. The paper intends to invite the reader to this unfamiliar debate in social science and political theory in Brazil.

J. Kaplanis, Assaf Gordon, T. Shor et al.

Surmani Huidrom, Surmani Huidrom, Ng Ngashangva et al.

Lactiplantibacillus plantarum BRD3A was isolated from Atingba, a traditional fermented rice-based beverage of Manipur. Its genomic sequence has 13 contigs and its genome size is 3,320,817 bp with a guanine–cytosine (GC) ratio of 44.6%. It comprises 3185 genes including 3112 coding sequences (CDSs), 73 RNAs (including 66 tRNAs and others), and one clustered regularly interspaced short palindromic repeat (CRISPR) array. A comparative and phylogenetic analysis with the Lp. plantarum genome shows that this strain has close similarity with other Lp. plantarum strains and about 99% average nucleotide identity. Functional annotation using evolutionary genealogy of genes—non-supervised orthologous groups (EggNOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) reveals genes associated with various biological processes such as metabolism, genetic information processing, and transport functions. Furthermore, the strain harbors bacteriocins like plantaricin E, Plantaricin F, and Enterocin X categorized under class IIb by the BAGEL4 database, indicating its potential antimicrobial properties. Additionally, AntiSMASH web server predicted four secondary regions—T3PKS, terpene, cyclic lactone inducer, and ribosomally synthesized and post-translationally modified peptide (RiPP)—suggesting an even higher antimicrobial potential. We validated the antimicrobial activity of Lp. plantarum BRD3A through in vitro experiments in which it exhibited promising bactericidal effects on methicillin-resistant Staphylococcus aureus, inhibiting their biofilm growth. These findings indicate the potential of Lp. plantarum BRD3A to be used as an alternative to conventional antibiotics.

Niklas Kant, Jonas Magnusson

Den här artikeln är en påbyggnad på den ganska omfattande kunskapsbas som redan finns tillgänglig kring släkten Sondell. Den innehåller ny information om stamfadern Nils Eriksson Sundelius ursprung. Därtill kompletterar, och i något fall rättar, vi vedertagna uppgifter om efterföljande släktled. Vår ambition har varit att där tidigare arbeten lutat sig mot andrahandskällor, för det mesta litteratur i form av äldre herdaminnen, har vi i stället försökt att uppsöka och referera till primärkällorna. Artikeln har avgränsats till att i släkttabellen omfatta fyra generationer, inklusive stamfader Nils Eriksson Sundelius, vilket i stora drag spänner över tidsperioden 1630–1820. I de fall där döttrar Sondell har gift in sig i andra släkter har vi inte redovisat deras avkommor. Som ett bidrag till kunskapen kring metodik har vi införlivat ett avsnitt där vi genom några exempel kopplad till den här artikeln visar på värdet av avhandlingar som källa för släktskapsuppgifter.

N. Ray, M. Currat, L. Excoffier

Topalović Milica

The work covers a wide field of origin, development, but also the current state of higher education and science in the Republic of Albania. In all post-communist countries, higher education is a mirror of the entire society and the political-economic state of the country, and in Albania, too, a long evolutionary process of turmoil between conservative and more liberal higher education policies can be observed, which resulted in a decline in the quality of education and scientific research. On this path of harmonization with world and European standards in the field of higher education and science, the paper investigates the role of the French Republic, which gives rise to the research question: At what level are the bilateral relations between the Republic of Albania and the French Republic in the field of higher education and science, bearing in mind that is the Republic of Albania a permanent member of the francophone organization, as well as the fact that the share of the Albanian francophone population is significant? The work will especially take into account the mobility of Albanian students, programs and projects implemented at Albanian universities with the help of the Government of France, universities, cities and regions, and private companies, but will also include the problems of excessive outflow of educated and able-bodied population. The author's conclusion is that the presence of France is not negligible, but still insufficient considering the traditionally friendly relations of these two countries. Of particular importance will be the use of the method of document analysis, genealogy, as well as analytical-descriptive methods.

Hermie C. van Zyl

No abstract available.