Relevant bibliographies by topics / Evolution of the archaea

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Academic literature on the topic 'Evolution of the archaea'

Author: Grafiati
Published: 25 May 2024

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Journal articles on the topic "Evolution of the archaea"

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Kellner, Siri, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, and Tom A. Williams. "Genome size evolution in the Archaea." Emerging Topics in Life Sciences 2, no. 4 (November 14, 2018): 595–605. http://dx.doi.org/10.1042/etls20180021.

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What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.
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Ngcobo, Phelelani Erick, Bridget Valeria Zinhle Nkosi, Wanping Chen, David R. Nelson, and Khajamohiddin Syed. "Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea." International Journal of Molecular Sciences 24, no. 4 (February 19, 2023): 4161. http://dx.doi.org/10.3390/ijms24044161.

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Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study’s results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.
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Rafiq, Muhammad, Noor Hassan, Maliha Rehman, Muhammad Hayat, Gullasht Nadeem, Farwa Hassan, Naveed Iqbal, et al. "Challenges and Approaches of Culturing the Unculturable Archaea." Biology 12, no. 12 (December 7, 2023): 1499. http://dx.doi.org/10.3390/biology12121499.

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Since Carl Woese’s discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.
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Gribaldo, Simonetta, and Celine Brochier-Armanet. "The origin and evolution of Archaea: a state of the art." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1470 (May 9, 2006): 1007–22. http://dx.doi.org/10.1098/rstb.2006.1841.

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Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 °C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components of different molecular systems are highlighting a core of mainly vertically inherited genes in Archaea. This allows recovering a globally well-resolved picture of archaeal evolution, as opposed to what is observed for Bacteria and Eukarya. This may be due to the fact that no rapid divergence occurred at the emergence of present-day archaeal lineages. This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life. Nanoarchaea may not represent a third and ancestral archaeal phylum, but a fast-evolving euryarchaeal lineage. Methanogenesis seems to have appeared only once and early in the evolution of Euryarchaeota. Filling up this picture of archaeal evolution by adding presently uncultivated species, and placing it back in geological time remain two essential goals for the future.
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Williams, Tom A., Gergely J. Szöllősi, Anja Spang, Peter G. Foster, Sarah E. Heaps, Bastien Boussau, Thijs J. G. Ettema, and T. Martin Embley. "Integrative modeling of gene and genome evolution roots the archaeal tree of life." Proceedings of the National Academy of Sciences 114, no. 23 (May 22, 2017): E4602—E4611. http://dx.doi.org/10.1073/pnas.1618463114.

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A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.
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Forterre, Patrick. "The Common Ancestor of Archaea and Eukarya Was Not an Archaeon." Archaea 2013 (2013): 1–18. http://dx.doi.org/10.1155/2013/372396.

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It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.
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VERHEES, Corné H., Servé W. M. KENGEN, Judith E. TUININGA, Gerrit J. SCHUT, Michael W. W. ADAMS, Willem M. de VOS, and John van der OOST. "The unique features of glycolytic pathways in Archaea." Biochemical Journal 375, no. 2 (October 15, 2003): 231–46. http://dx.doi.org/10.1042/bj20021472.

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An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved, variant pathways have developed in Archaea involving several novel enzymes with a distinct control. A spectacular example of convergent evolution concerns the glucose-degrading pathways of saccharolytic archaea. The identification, characterization and comparison of the glycolytic enzymes of a variety of phylogenetic lineages have revealed a mosaic of canonical and novel enzymes in the archaeal variants of the Embden–Meyerhof and the Entner–Doudoroff pathways. By means of integrating results from biochemical and genetic studies with recently obtained comparative and functional genomics data, the structure and function of the archaeal glycolytic routes, the participating enzymes and their regulation are re-evaluated.
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Zhu, Pengfei, Jialin Hou, Yixuan Xiong, Ruize Xie, Yinzhao Wang, and Fengping Wang. "Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis." Microorganisms 12, no. 4 (March 30, 2024): 707. http://dx.doi.org/10.3390/microorganisms12040707.

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Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA’s enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.
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Tamarit, Daniel, Eva F. Caceres, Mart Krupovic, Reindert Nijland, Laura Eme, Nicholas P. Robinson, and Thijs J. G. Ettema. "A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses." Nature Microbiology 7, no. 7 (June 27, 2022): 948–52. http://dx.doi.org/10.1038/s41564-022-01122-y.

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AbstractAsgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled and closed the chromosome of Candidatus Odinarchaeum yellowstonii LCB_4, through long-range PCR, revealing CRISPR spacers targeting viral contigs. We found related viruses in the genomes of diverse prokaryotes from geothermal environments, including other Asgard archaea. These viruses open research avenues into the ecology and evolution of Asgard archaea.
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Fouqueau, Thomas, Fabian Blombach, Gwenny Cackett, Alice E. Carty, Dorota M. Matelska, Sapir Ofer, Simona Pilotto, Duy Khanh Phung, and Finn Werner. "The cutting edge of archaeal transcription." Emerging Topics in Life Sciences 2, no. 4 (November 14, 2018): 517–33. http://dx.doi.org/10.1042/etls20180014.

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The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP and ultimately gene expression. This review focusses on recent progress in our understanding of (i) the structure, function and molecular mechanisms of known and less characterized factors including Elf1 (Elongation factor 1), NusA (N-utilization substance A), TFS4, RIP and Eta, and (ii) their evolution and phylogenetic distribution across the expanding tree of Archaea.
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Dissertations / Theses on the topic "Evolution of the archaea"

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Cossu, Matteo. "Genomic evolution of archaea thermococcales." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLS028.

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L'objectif principal de mon projet de doctorat est d'étudier l'évolution génomique de l'ordre des Archaea Thermococcales. Je me suis intéressé à comprendre les mécanismes des éléments mobiles génétiques (MGE) pouvant influencer l'évolution des génomes. En utilisant une approche multidisciplinaire, nous avons pu explorer les différents aspects de ce phénomène in silico, in vitro et in vivo. Grâce à des analyses in silico de tous les génomes de Thermococcales complètement séquencés disponibles, nous avons montré que cet ordre affiche un niveau élevé de réarrangements pouvant perturber les modèles d'expression génique. Dans une première approche, nous avons étudié l'existence de l'organisation chromosomique. L'inefficacité dans la prédiction de l'origine et de la terminaison de la réplication sur la seule base de la composition de l'ADN chromosomique ou skew, nous a motivé à utiliser une approche différente basée sur des séquences biologiquement pertinentes. Nous avons donc déterminé la position de l'origine de la réplication (oriC) dans tous les 21 génomes séquencés Thermococcales. La position potentielle de la terminaison a été prédite dans 19 génomes à ou près du site dif, où les dimères chromosomiques sont résolus avant la ségrégation de l'ADN. Le calcul du génome central a révélé un certain nombre de grappes de gènes essentiels avec une position chromosomique remarquablement stable à travers les espèces, en utilisant oriC comme référence. D'autre part, les régions core-free semblent correspondre à des éléments mobiles intégrés putatifs. Ces observations indiquent qu'un degré remarquable d ' «ordre» a été maintenu à travers les Thermococcales, même s'ils présentent des chromosomes fortement brouillés, les inversions étant particulièrement fréquentes. La découverte et la caractérisation d'un nouvel organisme, Thermococcus nautili nous ont permis de mieux comprendre le mécanisme sous-jacent causant ces inversions. En effet, le séquençage et l'analyse in silico de son génome ont fortement suggéré l'implication d'une nouvelle classe de tyrosine recombinases dans la plasticité génomique. Le plasmide pTN3 de T. nautili, qui est intégré dans le chromosome et auto-réplicable, code une intégrase appartenant à la classe des tyrosine recombinases. Des plasmides similaires ont également été trouvés intégrés dans le chromosome d'autres séquences de Thermococcales (par exemple TKV4 dans T. kodakarensis). Afin de tester son activité enzymatique, l’integrase codée par le plasmide pTN3 a été surproduite et purifiée. Les expériences in vitro ont d'abord permis de déterminer le segment de séquence minimal requis pour l'activité de l'intégrase et optimisé la réaction enzymatique in vitro. Ces résultats nous ont permis, en suite, de démontrer la réaction d'excision / d'intégration observée avec d'autres recombinases de tyrosine. De plus, l'excision in vivo d'un élément intégré apparenté (TKV4 de T. kodakarensis) par l'intégrase pTN3 a été réalisée au cours de cette étude. Pour cela, le gène IntpTN3 a été clone dans un vecteur de la bactérie E. coli / Thermococcus pour la transformation et l'expression dans T. kodakarensis. Après incubation, les cellules ont montré la présence de l'élément TKV4-intégré dans la forme circulaire libre. Enfin, nous avons pu imiter l'inversion chromosomique in vitro en utilisant des substrats synthétiques contenant des séquences cibles d'intégration. Nous avons également pu montrer que l'intégrase pTN3 possède une activité qui peut intervenir sur des inversions génomiques à grande échelle en utilisant différents sites et donc expliquer les réarrangements observés dans Thermococcales (Cossu et al, in prep)
The main goal of my PhD project is to investigate the genomic evolution of the Archaea Thermococcales order. I am interested in understanding how mobile genetic elements (MGE) can influence the evolution of genomes. Using a multidisciplinary approach, we were able to explore the different aspects of this phenomenon in silico, in vitro and in vivo. Through in silico analyses of all available completely sequenced Thermococcales genomes, we showed that this order displays a characteristic high level of rearrangements potentially disrupting gene expression patterns. In a first approach, we investigated the existence of chromosomal organization. The inefficiency in predicting origin and termination of replication on the sole basis of chromosomal DNA composition or skew, motivated us to use a different approach based on biologically relevant sequences. We determined the position of the origin of replication (oriC) in all 21 sequenced Thermococcales genomes. The potential position of the termination was predicted in 19 genomes at or near the dif site, where chromosome dimers are resolved before DNA segregation. Computation of the core genome uncovered a number of essential gene clusters with a remarkably stable chromosomal position across species, using oriC as reference. On the other hand, core-free regions appear to correspond to putative integrated mobile elements. These observations indicate that a remarkable degree of “order” has been maintained across Thermococcales even if they display highly scrambled chromosomes, with inversions being especially frequent. The discovery and characterization of a new organism, Thermococcus nautili allowed us to better understand the underlying mechanism causing these inversions. The sequencing and in silico analysis of its genome strongly suggested the involvement of a new class of tyrosine recombinases in genomic plasticity. T. nautili pTN3 plasmid, which is found integrated into the chromosome and also self-replicating encodes an integrase belonging to this class. Similar plasmids have also been found integrated in the chromosome of other sequenced Thermococcales (e.g. TKV4 in T. kodakarensis). In order to test its enzymatic activity, we overproduced and purified the integrase encoded by pTN3. In vitro experiments first determined the minimal sequence segment required for integrase activity and optimized the enzymatic reaction in vitro. Due to this early results, we were able to demonstrate the excision/integration reaction observed with other tyrosine recombinases. Additionally, the in vivo excision of a related integrated element (TKV4 from T. kodakarensis) by the pTN3 integrase was performed during this study. The IntpTN3 gene has been cloned into an E. coli/Thermococcus shuttle vector for transformation and expression in T. kodakarensis. After incubation, cells showed the presence of the TKV4-integrated element in free circular form. Finally, we were able to mimic in vitro chromosomal inversion using synthetic substrates containing integration target sequences. We were also able to show that pTN3 integrase possesses an activity which can mediate large scale genomic inversions using different sites and therefore explain the rearrangements observed in Thermococcales)
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Aouad, Monique. "Phylogenomic study of the evolutionary history of the Archaea and their link with eukaryogenesis." Thesis, Lyon, 2018. http://www.theses.fr/2018LYSE1246.

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L'explosion des données de séquençage a permis de résoudre la plupart des relations phylogénétiques chez les archées. Néanmoins, de nombreuses questions restent à résoudre à l'échelle du domaine des archées et à l'échelle des trois domaines du vivant. Parmi elles, les relations phylogénétiques au sein du cluster II, notamment la position des archées halophiles extrêmes qui ont été placées à différentes positions dans l'arbre en fonction des marqueurs et des modèles de reconstruction utilisés, ainsi que la position de la racine des archées et la position des eucaryotes à la lumière des lignées d'archées nouvellement séquencées. Au cours de ma thèse, j'ai contribué à (i) affiner la phylogénie du domaine des Archaea en se concentrant sur les relations phylogénétiques au sein du cluster II, en particulier les positions des lignées halophiles extrêmes par rapport aux méthanogènes à travers des analyses dédiées à cette partie spécifique de l'arbre, et (ii) établir une phylogénie globale des archées afin de comprendre leur histoire évolutive ancienne et leur lien avec les eucaryotes à travers une analyse phylogénomique en deux étapes à l'échelle des trois domaines du vivant. D'abord, en utilisant des approches de génomique comparée sur 155 génomes complets appartenant aux Halobacteria, Nanohaloarchaea, méthanogènes de classe II, Archaeoglobales et Diaforarchaea, j'ai identifié 258 protéines portant un signal phylogénétique fiable pour étudier les relations de parente au sein du cluster II. En combinant différentes approches limitant l'impact du signal non phylogénétique sur l'inférence phylogénétique (comme la méthode Slow-Fast et le recodage des acides aminés), j'ai montré que les Nanohaloarchaea branchent avec les Methanocellales et les Halobacteria branchent avec les Methanomicrobiales. Ce jeu de données a ensuite été utilisé pour étudier la position d'une troisième lignée halophile extrême, les Methanonatronarchaeia, qui se positionnent entre les Archaeoglobales et les Diaforarchaea. Ces résultats suggèrent que l'adaptation à la salinité extrême serait apparue au moins trois fois de manière indépendante chez les archées et que les similitudes phénotypiques observées chez les Nanohaloarchaea, Halobacteria et Methanonatronarchaeia résulteraient d'une convergence évolutive, éventuellement accompagnée de transferts de gènes horizontaux. Enfin, ces résultats suggèrent que le groupement basal des Nanohaloarchaea avec d'autres lignées des DPANN serait la conséquence d'un artefact de reconstruction. Pour la deuxième partie de ma thèse, j'ai appliqué une stratégie consistant à analyser séparément les trois domaines du vivant considérés deux à deux, en mettant à jour 72 familles protéiques précédemment identifiées par Raymann et ses collègues (2015) pour inclure toutes les nouvelles lignées d'archées séquencées depuis la publication de cette étude comme les Asgard, les DPANN, les Stygia, les Acherontia, etc. Au total, mon échantillonnage taxonomique comprend 435 archées, 18 eucaryotes et 67 bactéries. Les résultats des analyses par la méthode Slow-Fast soutiennent une racine des Archaea située entre le superphylum basal des DPANN et le reste des archées séparées en deux groupes monophylétiques : les cluster I et cluster II, comme décrits par Raymann et ses collègues (2015), et montrent que la monophylie des Euryarchaeota est liée aux positions évoluant vite. Mes résultats placent les eucaryotes en tant que groupe frère du superphylum des TACK et montrent que leur regroupement avec les Asgard est lié aux positions évoluant vite. Ces résultats ont des implications majeures sur les inférences de la nature du dernier ancêtre commun des archées et sur l'histoire évolutive de ce domaine qui a conduit à l'apparition de la première cellule eucaryote
The burst of sequencing data has helped disentangling most of the phylogenetic relationships in Archaea. Nevertheless, many questions remain to be addressed both at the level of the archaeal domain and at the level of the three domains of life. Among them, the phylogenetic relationships inside the cluster II, in particular the position of extreme halophilic archaeal lineages relatively to the methanogens which have been placed at different positions in the tree based on the different markers and reconstruction models used, as well as the position of the root of the Archaea and the position of the eukaryotes in the light of the newly sequenced archaeal lineages. During my thesis, I have contributed to (i) refine the phylogeny of the archaeal domain by focusing on the phylogenetic relationships among the cluster II Archaea, in particular the positions of the extreme halophilic lineages through dedicated analyses focusing on this specific part of the archaeal tree, and (ii) establish a global phylogeny of the Archaea to understand their early evolutionary history and their link with the eukaryotes through a large-scale two-step phylogenomic analysis at the level of the three domains of life. First, using comparative genomics approaches on 155 complete genomes belonging to the Halobacteria, Nanohaloarchaea, methanogens class II, Archaeoglobales, and Diaforarchaea, I have identified 258 proteins carrying a reliable phylogenetic signal to investigate the position of the extreme halophilic lineages in Archaea. By combining different approaches limiting the impact of non-phylogenetic signal on phylogenetic inference (like the Slow Fast method and the recoding of amino acids), I showed that the Nanohaloarchaea branch with Methanocellales, and Halobacteria branch with Methanomicrobiales. This dataset has been subsequently used to investigate the position of a third extreme halophilic lineage, the Methanonatronarchaeia, which I showed to branch in between the Archaeoglobales and Diaforarchaea. These results suggest that adaption to high salinity emerged at least three times independently in Archaea, and that the phenotypic similarities observed in Nanohaloarchaea, Halobacteria, and Methanonatronarchaeia likely result from convergent evolution, possibly accompanied by horizontal gene transfers. Finally, these results suggest that the basal grouping of Nanohaloarchaea with other DPANN lineages is likely the consequence of a tree reconstruction artefact. For the second part of my thesis, I have applied a strategy consisting in separately analyzing the three domains of life two by two, by updating 72 protein families previously identified by Raymann and colleagues (2015) to include all novel archaeal lineages that were sequenced since the publication of this study like the Asgard, the DPANN, the Stygia, the Acherontia, etc. In total, my taxonomic sampling includes 435 archaea, 18 eukaryotes, and 67 bacteria. The results of the Slow-Fast method supported a root of the Archaea lying between a basal DPANN superphylum and the rest of the Archaea separated into two monophyletic groups: the cluster I and cluster II as described by Raymann and colleagues (2015), and showed that the monophyly of the Euryarchaeota is supported only by the fast-evolving sites. My results also placed the eukaryotes as the sister group to the TACK superphylum and showed that their sister grouping with the Asgard is linked to the fast-evolving sites. These results have major implications on the inferences of the nature of the last common archaeal ancestor and the subsequent evolutionary history of this domain that led to the rise of the first eukaryotic cell
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Berthon, Jonathan. "Etude de la réplication de l'ADN chez les Archaea." Phd thesis, Université Paris Sud - Paris XI, 2008. http://tel.archives-ouvertes.fr/tel-00344124.

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Les organismes cellulaires appartiennent à l'un des trois domaines du vivant : Archaea, Bacteria, Eucarya. Les Archaea sont des organismes unicellulaires avec un phénotype bactérien mais qui possèdent de nombreux caractères moléculaires eucaryotes. En particulier, la machinerie de réplication archéenne est une version homologue et simplifiée de celle des eucaryotes. Au cours de cette thèse, j'ai étudié la réplication de l'ADN chez les Archaea en combinant des approches in vitro et in silico.
Premièrement, j'ai essayé de purifier la protéine initiatrice de la réplication Cdc6/Orc1, sous une forme native, dans l'espoir de mettre au point le premier système de réplication de l'ADN in vitro chez les Archaea. Malheureusement, cette approche a été infructueuse en raison de l'instabilité et des propriétés d'agrégation de la protéine.
Deuxièmement, j'ai réalisé une analyse comparative du contexte génomique des gènes de réplication dans les génomes d'Archaea. Cette analyse nous a permis d'identifier une association très conservée entre des gènes de la réplication et des gènes liés au ribosome. Cette organisation suggère l'existence d'un mécanisme de couplage entre la réplication de l'ADN et la traduction. De manière remarquable, des données expérimentales obtenues chez des modèles bactériens et eucaryotes appuient cette idée. J'ai ensuite mis au point des outils expérimentaux qui permettront d'éprouver la pertinence biologique de certaines des prédictions effectuées.
Finalement, j'ai examiné la distribution taxonomique des gènes de la réplication dans les génomes d'Archaea afin de prédire la composition probable de la machinerie de réplication de l'ADN chez le dernier ancêtre commun des Archaea. Dans leur ensemble, les profils phylétiques des gènes de la réplication suggèrent que la machinerie ancestrale était plus complexe que celle des organismes archéens contemporains.
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Petitjean, Celine. "Phylogénie et évolution des Archaea, une approche phylogénomique." Phd thesis, Université Paris Sud - Paris XI, 2013. http://tel.archives-ouvertes.fr/tel-01070633.

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En 1977, Carl Woese sépare les procaryotes en deux grands groupes en proposant une nouvelle classification basée sur des critères phylogénétiques. Les Archaea deviennent ainsi un domaine à part entière aux cotés des Bacteria et des Eucarya. Depuis, la compréhension de ce nouveau groupe et de ses relations avec les deux autres domaines, essentielles pour comprendre l'évolution ancienne du vivant, est largement passée par l'étude de leur phylogénie. Presque 40 ans de recherche sur les archées ont permis de faire évoluer leur image : de bactéries vivant dans des milieux spécialisés, souvent extrêmes, on est passé à un domaine indépendant, très diversifié aussi bien génétiquement, métaboliquement ou encore écologiquement. Ces dernières années la barre symbolique de cent génomes complets d'archées séquencés a été franchie et, parallèlement, les projets génomiques et métagénomiques sur des groupes peu caractérisés ou de nouvelles lignées de haut rang taxonomique (e.g. Nanohaloarchaea, Thaumarchaeota, ARMAN, Aigarchaeota, groupe MGC, groupe II des Euryarchaeota, etc.) se sont multipliés. Tout ceci apporte un matériel sans précédent pour l'étude de l'histoire évolutive et de la diversité des Archaea. Les protéines ribosomiques ont été utilisées de façon courante pour inférer la position phylogénétique des nouvelles lignées d'Archaea. Néanmoins, les phylogénies résultantes ne sont pas complètement résolues, laissant des interrogations concernant d'importantes relations de parenté. La recherche de nouveaux marqueurs est donc cruciale et c'est dans ce contexte que mon projet de thèse s'inscrit. À partir de l'analyse des génomes de deux Thaumarchaeota et d'une Aigarchaeota, nous avons identifié 200 protéines conservées et bien représentées dans les différents phyla d'archées. Ces protéines sont impliquées dans de nombreux processus cellulaires, ce qui peut apporter un signal phylogénétique complémentaire à celui des marqueurs de type informationnel utilisés par le passé. En plus de confirmer la plupart des relations phylogénétiques inférées à partir de ces derniers (i.e., protéines ribosomiques et sous unités de l'ARN polymérase), l'analyse phylogénétique de ces nouveaux marqueurs apporte un signal permettant une meilleure résolution de la phylogénie des archées et la clarification de certaines relations jusqu'ici confuses. Un certain nombre de ces nouveaux marqueurs sont aussi présents chez les bactéries. Les relations entre les grands phyla d'archées restant encore non résolues, nous avons utilisé ces protéines pour essayer de placer la racine de l'arbre des Archaea en utilisant comme groupe extérieur les bactéries. Nous avons ainsi pu identifier 38 protéines, parmi les 200 sélectionnées précédemment, ayant un signal phylogénétique suffisamment fiable pour cette étude, auxquelles nous avons ajouté 32 protéines ribosomiques universelles. L'utilisation conjointe de ces données nous a permis de placer la racine entre les Euryarchaeota, d'une part, et un groupe rassemblant les Thaumarchaeota, les Aigarchaeota, les Korarchaeota et les Crenarchaeota, d'autre part. Ce nouvel éclairage sur l'évolution ancienne des archées nous a amené à proposer une révision de leur taxonomie avec, principalement, la création du nouveau phylum "Proteoarchaeota" contenant les quatre phyla actuels que nous proposons de rétrograder en classes : Thaumarchaea, Aigarchaea, Korarchaea et Crenarchaea.Finalement, l'analyse des protéines codées dans les trois génomes qui ont servi de point de départ de ma thèse nous a permis de générer une masse considérable de données qui ont révélé des traits particuliers ou encore des histoires évolutives inattendues. Un exemple est l'histoire du complexe formé par la chaperonne DnaK et de ses co-chaperonnes GrpE, DnaJ, et DnaJ-Fer chez les Thaumarchaeota, impliquant plusieurs transferts horizontaux entre les trois domaines du vivant.
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Hepp, Benjamin. "Characterization of IntpTN3 : A suicidal integrase capable of in vitro homologous recombination." Electronic Thesis or Diss., université Paris-Saclay, 2023. http://www.theses.fr/2023UPASL151.

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Les organismes hyperthermophiles sont des microorganismes qui prospèrent de manière optimale à des températures de 85 °C ou plus. On les trouve couramment dans des environnements extrêmes tels que les sources chaudes, les puits de pétrole et les fosses océaniques près des évents hydrothermaux, tels que les fumeurs noirs. Ces organismes sont devenus des ressources précieuses pour les applications biotechnologiques en raison de leur production d'enzymes thermostables, notamment les polymérases utilisées dans la PCR (réaction de polymérase en chaîne) et les enzymes utilisées dans l'industrie des détergents pour dégrader les biomolécules à haute température. Au sein de l'archée hyperthermophile Thermococcus nautili, nous avons découvert une enzyme capable de catalyser la recombinaison de l'ADN avec pratiquement n'importe quelle molécule d'ADN. Cette enzyme présente un immense potentiel en tant qu'outil biotechnologique robuste pour les chercheurs, permettant l'assemblage in vitro de molécules d'ADN et facilitant les processus de modification de l'ADN. Ces découvertes prometteuses nous ont conduits à déposer une déclaration d'invention pour notre enzyme, reconnaissant sa valeur significative dans l'avancement de la biologie moléculaire et de l'ingénierie génétique
Hyperthermophilic organisms are microorganisms that thrive optimally at temperatures of 85°C or higher. They are commonly found in extreme environments such as hot springs, oil wells, and oceanic trenches near hydrothermal vents, such as black smokers. These organisms have emerged as valuable resources for biotechnological applications due to their production of thermostable enzymes, including polymerases used in PCR (Polymerase Chain Reaction) and enzymes employed in the detergent industry for breaking down biomolecules at high temperatures. Within the hyperthermophilic archaea Thermococcus nautili, we have discovered an enzyme capable of catalyzing DNA recombination with virtually any DNA molecule. This enzyme holds immense potential as a robust biotechnological tool for researchers, enabling the in vitro assembly of DNA molecules and facilitating DNA modification processes. These promising findings have led us to file an invention disclosure statement for our enzyme, recognizing its significant value in advancing molecular biology and genetic engineering
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Li, Jun, and 李俊. "Molecular evolution and phylogeny of methanogenic archael genomes." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208152.

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Methane (CH4) is the major chemical component of natural gas, as well as a particularly potent greenhouse gas. Methanogens are the archaeal organisms that produce methane and play a key role in biological methanogenesis. A total of six taxonomic orders of archaeal methanogens have been discovered and almost all previous phylogenetics studies have confirmed that these methanogens are genetically diversified and do not belong to a phylogenetically monophyletic group. To date, the relationships between methanogens and closely related non-methanogen species at the taxonomic order level remain unresolved and different studies have often produced contradictory results based on different gene markers. These studies suggest the complicated and distinct evolutionary histories between different genes in these genomes. In this thesis, 74 fully sequenced archaeal genomes, including 41 methanogens, were collected and used in a comprehensive comparative genomics and evolutionary analysis. First, numerous phylogenomic trees were reconstructed based on various datasets using several methods and the results show that Methanopyrales is close to Methanobacteriales (or Methanopyrales) in the statistically best species tree. In addition, Methnocellales and Methanosarcinales, and as well as Methanomicrobiales and Halobacteriales are sister clades in the best species tree, but the confidence level is low. Further incongruence tests among the phylogenetic forest, which is composed of 3,694 ortholog gene families, reveal that the archaeal core genes have much stronger consistent vertical evolutionary signals than other genes, but these core genes are not topologically fully congruent with each other. Secondly, a series of weighted network analyses were implemented to decompose the hierarchical structure and to reveal the co-evolved gene modules, global and local features in the archaeal methanogen phylogenetic forest. The results show that this co-evolution network contains 7 statistical robust modules, and the module with the highest average node strength includes the majority of the core genes located in the central position of the network. Further in-depth evolutionary analysis reveals that the modularized evolution in the archaeal phylogenetic forest is closely related to the time of origin, HGT rate and ubiquitous vertical inheritance in gene families. Lastly, to investigate the causes for and factors related to the pervasive topology incongruence in the phylogenetic forest, in-depth clanistics analysis and HGT detection were carried out. These results show that (1) about 63% of gene families experienced at least 1 HGT event in their whole history; (2) core genes are not immune to HGT but they do have much lower HGT rates than other genes; (3) methanogens have distinct trends of HGTs from non-methanogen species; and (4) highly frequent inter-order HGTs, even for core genes, in methanogen genomes lead to their scrambled phylogenetic relationships. Further clanistics analysis screened out 119 candidate genes related to methanogenic pathways adaptation and most of these gene families have experienced at least one HGT. In conclusion, a complex evolutionary scenario for methanogenic archaeal species was described in this thesis as a combination of complicated vertical and non-vertical evolutionary processes in a modularized phylogenetic forest.
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Biological Sciences
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Doctor of Philosophy
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Archibald, John M. "Studies on the evolution of archaeal and eukaryotic chaperonins." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2001. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp05/NQ66656.pdf.

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Robertson, S. "Late Archaean crustal evolution in the Ivisartoq region, southern west Greenland." Thesis, University of Exeter, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.353048.

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Dougherty-Page, Jon Stanley. "The evolution of the Archaean continental crust of Northern Zimbabwe." Thesis, Open University, 1994. http://oro.open.ac.uk/54877/.

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Granitoid clasts preserved in Late Archaean conglomerates indicate the presence of continental crust in Northern Zimbabwe prior to the ≈ 2.7 to ≈ 2.6Ga "event" which terminated with the stabilisation of the Zimbabwe Craton. The "Kober Technique" (Kober, 1986, 1987) of direct thermal ionisation of zircons has been set up in order to investigate the geochronological record preserved in such clasts. Conglomerates were sampled from two localities, Shamva, within the central part of Northern Zimbabwe, and Chinhoyi, at the north-western boundary of the craton. The results from both localities demonstrate the presence of continental crust in Northern Zimbabwe with a long and complex history prior to the Late Archaean "event". The minimum age of continental crust in the Shamva region is 3.34 Ga (Sm-Nd model age),with further episodes of granitiod intrusion indicated by zircon crystallisation at 3/197 ± 10 Ma, 2,925 ± 10 Ma, and 2,800 ± 20 Ma (Pb-Pb zircon). The Chinhoyi region has a shorter, simpler history, with the earliest recorded continental crust at 2,875 ± 3 Ma and later intrusions of granitoids at 2/800 ± 20 Ma, and2,720 ± 6 Ma (Pb-Pb zircon). Chemically, the early crust was dominated by sodic, Tonalite Trondhjemite-Granodiorite granitoids, whose formation may be modelled by the partial melting of metabasalts with residual hornblende and/or garnet. By contrast, the granitoids formed during the Late Archaean "event" which culminated in the stabilisation of the craton, dominantly follow calc-alkalinetrends, and their formation may be modelled by the fractionation of basaltic magmas (combined with assimilation- of pre-existing continental material) or intra-crustal remelting. This major switch in the origins (and hence chemistry) of granitoids may be attributed to mantle plume activity, the onset of which is recorded by the presence of greens tone belt volcanics derived from anomalously hot mantle, dated at' 2,713 ± 15 Ma (U-Pb zircon Jelsma, 1993).
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Ticak, Tomislav. "Anoxic quaternary amine utilization by archaea and bacteria through a non-L-pyrrolysine methyltransferase; insights into global ecology, human health, and evolution of anaerobic systems." Miami University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=miami1429897518.

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Books on the topic "Evolution of the archaea"

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1943-, Garrett Roger A., and Klenk Hans-Peter, eds. Archaea: Evolution, physiology, and molecular biology. Malden, MA: Blackwell Pub., 2007.

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Kurup, Ravikumar, and Parameswaran Achutha Kurup. The third element: Actinidic archaea, digoxin, and the biological universe. Hauppauge, N.Y: Nova Science Publishers, 2011.

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C, Condie Kent, ed. Archean crustal evolution. Amsterdam: Elsevier, 1994.

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D, Ayres L., ed. Evolution of Archean supracrustal sequences. [St. John, Nfld.]: Geological Association of Canada, 1985.

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Dilek, Yildirim, and Harald Furnes, eds. Evolution of Archean Crust and Early Life. Dordrecht: Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-007-7615-9.

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Hickman, Arthur H. Archean Evolution of the Pilbara Craton and Fortescue Basin. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-18007-1.

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Cavicchioli, Ricardo, ed. Archaea. Washington, DC, USA: ASM Press, 2007. http://dx.doi.org/10.1128/9781555815516.

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Ferreira-Cerca, Sébastien, ed. Archaea. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2445-6.

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Garrett, Roger A., and Hans-Peter Klenk, eds. Archaea. Malden, MA, USA: Blackwell Publishing Ltd, 2006. http://dx.doi.org/10.1002/9780470750865.

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Margulis, Lynn. Symbiosis in cell evolution: Microbial communities in the Archean and Proterozoic eons. 2nd ed. New York: Freeman, 1993.

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Book chapters on the topic "Evolution of the archaea"

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Boucher, Yan. "Lipids: Biosynthesis, Function, and Evolution." In Archaea, 341–53. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815516.ch15.

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Forterre, Patrick, Yvan Zivanovic, and Simonetta Gribaldo. "Structure and Evolution of Genomes." In Archaea, 411–33. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815516.ch19.

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Woese, Carl R. "The Archaea: an Invitation to Evolution†." In Archaea, 1–13. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815516.ch1.

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Grogan, Dennis W. "Mechanisms of Genome Stability and Evolution†." In Archaea, 120–38. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815516.ch5.

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Gil, Rosario, Amparo Latorre, and Andrés Moya. "Evolution of Prokaryote-Animal Endosymbiosis from a Genomics Perspective." In (Endo)symbiotic Methanogenic Archaea, 223–55. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-98836-8_11.

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Gil, Rosario, Amparo Latorre, and Andrés Moya. "Evolution of Prokaryote-Animal Symbiosis from a Genomics Perspective." In (Endo)symbiotic Methanogenic Archaea, 207–33. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-13615-3_11.

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Spradlin, Savannah, Lori Cobani, Christian Brininger, and Caryn Evilia. "Archaea Were Trailblazers in Signaling Evolution: Protein Adaptation and Structural Fluidity as a Form of Intracellular Communication." In Biocommunication of Archaea, 195–211. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-65536-9_12.

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Frye, Roy A. "Evolution of Sirtuins From Archaea to Vertebrates." In Histone Deacetylases, 183–202. Totowa, NJ: Humana Press, 2006. http://dx.doi.org/10.1385/1-59745-024-3:183.

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Bertrand, Jean-Claude, Pierre Caumette, Philippe Normand, Bernard Ollivier, and Télesphore Sime-Ngando. "Prokaryote/Eukaryote Dichotomy and Bacteria/Archaea/Eukarya Domains: Two Inseparable Concepts." In Prokaryotes and Evolution, 1–21. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-99784-1_1.

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Tripp, Vanessa, and Lennart Randau. "Evolution of C/D Box sRNAs." In RNA Metabolism and Gene Expression in Archaea, 201–24. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-65795-0_9.

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Conference papers on the topic "Evolution of the archaea"

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Pikuta, Elena V., Dragana Tankosic, and Rob Sheldon. "Evolution of Archaea in 3D modeling." In SPIE Optical Engineering + Applications, edited by Richard B. Hoover, Gilbert V. Levin, and Alexei Y. Rozanov. SPIE, 2012. http://dx.doi.org/10.1117/12.929945.

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Jain, Prem. "Architecture evolution and evaluation (ArchEE) capability." In 2011 6th International Conference on System of Systems Engineering (SoSE). IEEE, 2011. http://dx.doi.org/10.1109/sysose.2011.5966581.

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Raju, Perumala, and Rajat Mazumder. "THE GEOLOGICAL EVOLUTION OF THE ARCHEAN DHARWAR-CRATON." In GSA Connects 2021 in Portland, Oregon. Geological Society of America, 2021. http://dx.doi.org/10.1130/abs/2021am-364281.

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Zhao, S., L. Zhou, X. Sun, Z. Gao, Y. Zhou, N. Wang, Y. Wang, J. Chen, L. Xing, and R. Bao. "Temperature Controls on Dynamics and Evolution of Archaeal Lipid Distribution." In IMOG 2023. European Association of Geoscientists & Engineers, 2023. http://dx.doi.org/10.3997/2214-4609.202333092.

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Durgalakshmi, Durgalakshmi, Ian Williams, and Sajeev Krishnan. "Petrogenesis and evolution of charnockites formed at the Archaean-Proterozoic boundary." In Goldschmidt2022. France: European Association of Geochemistry, 2022. http://dx.doi.org/10.46427/gold2022.9850.

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Brown, Michael, Christopher L. Kirkland, Tim E. Johnson, and Phil Sutton. "GIANT IMPACTS AND THE ORIGIN AND EVOLUTION OF ARCHEAN CRATONS." In GSA Connects 2023 Meeting in Pittsburgh, Pennsylvania. Geological Society of America, 2023. http://dx.doi.org/10.1130/abs/2023am-391877.

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Brown, Michael, Christopher Kirkland, Tim Johnson, and Phil Sutton. "Giant impacts and the origin and evolution of Archean cratons." In Goldschmidt2023. France: European Association of Geochemistry, 2023. http://dx.doi.org/10.7185/gold2023.16192.

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Gillespie, Jack, Pete Kinny, Chris Kirkland, Laure Martin, Alexander Nemchin, Aaron J. Cavosie, and Derrick Hasterok. "Isotopic modelling of Archean crustal evolution from comagmatic zircon--apatite pairs." In Goldschmidt2021. France: European Association of Geochemistry, 2021. http://dx.doi.org/10.7185/gold2021.5488.

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Fenu, Luigi, and Giuseppe C. Marano. "Steel Truss-Type Arches Optimization Under Multi-Load Cases." In IABSE Congress, New York, New York 2019: The Evolving Metropolis. Zurich, Switzerland: International Association for Bridge and Structural Engineering (IABSE), 2019. http://dx.doi.org/10.2749/newyork.2019.1338.

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<p>Structural optimization of arches under multi-load cases is faced. For this aim, truss-type arches are to be considered because, under different load cases, bending effects unavoidably occur in single-rib arches shaped under one load case only. An effective procedure for simultaneous topology, shape and size optimization of truss-arches under multi-load cases is proposed. For this aim, shape, size and topology variables are assembled in a unique set of variables that are simultaneously optimised by the optimization algorithm. For given Pratt-type brace pattern, different topologies have been considered by varying the node number, whereas Cubic Rational Bézier curves have been used to shape the arch chords. Optimum diameter and thickness of the circular hollow section members was also obtained. Optimization was performed in MATLAB environment, by applying a modified Differential Evolution (DE) algorithm implemented with a Constraint Domination Selection (CDS) criterion. For each design variable vector, a FEM analysis of the resulting model has been carried out by SAP2000 to evaluate the objective function value (volume) feasibility of each design variable vector in terms of structural performance. Optimal solutions have been found and compared, providing useful suggestions to consider as guidelines in truss-arche design.</p>
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Menon, Swathi Sivakumar, and Vinod Balakrishnan. "Language Evolution: An NCT and Conlang Framework." In GLOCAL Conference on Asian Linguistic Anthropology 2022. The GLOCAL Unit, SOAS University of London, 2023. http://dx.doi.org/10.47298/cala2022.7-4.

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Decades of scholarly work have displaced previously accepted assumptions of the separation of the cognitive and the cultural as two separate entities. Notably, interventions of scholars such as Bouchard, Arbib, and Odling-Smee, have effectively positioned this older and more archaic thinking. In this paper, we posit that the propensity for constructivism in human languages has not been sufficiently studied. To this end, we propose Niche Construction Theory, a framework with which to address this gap. We also juxtapose natlangs (natural languages) with conlangs (constructed languages) in order to clarify the effectiveness of each. To facilitate this discussion, we propose the following points: Conlang origins are well-known, the study of conlangs has tangible evidence of manipulation of language elements, and the study of conlangs can further our understanding of natlangs. We draw on multiple fields to effect this anthropological study. Our literature in this paper has invited our use of Bouchard’s concept of offline base systems (OBS) to respond to questions of the characteristics and mechanics of language vis-à-vis ethnological work. For this, we turn to issues of embodiment, to then extend this to other consequences of and motives for developing conlangs and hence language evolution, such as language disabilities and impairments, a field which is still in its infancy. A focus on language construction using conlangs to test OBS promises another avenue to explore language evolution.
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Reports on the topic "Evolution of the archaea"

1

Skulski, T., J. A. Percival, and R. A. Stern. Archean crustal evolution in the central Minto block, northern Quebec. Natural Resources Canada/ESS/Scientific and Technical Publishing Services, 1996. http://dx.doi.org/10.4095/207760.

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Lucas, S. B., and M. R. St-Onge. Evolution of Archean and Early Proterozoic Magmatic Arcs in northeastern Ungava Peninsula, Quebec. Natural Resources Canada/ESS/Scientific and Technical Publishing Services, 1991. http://dx.doi.org/10.4095/132566.

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Gregersen, U., P. C. Knutz, G. K. Pedersen, H. Nøhr-Hansen, J. R. Ineson, L. M. Larsen, J R Hopper, et al. Stratigraphy of the West Greenland Margin. Natural Resources Canada/CMSS/Information Management, 2022. http://dx.doi.org/10.4095/321849.

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The stratigraphy and the geological evolution of the West Greenland margin from the Labrador Sea to Baffin Bay in both the onshore and offshore areas are described. The primary data sets include seismic reflection surveys, wells, and outcrops. In addition, seabed samples, seismic refraction and magnetic data, onshore and offshore maps, and stratigraphic compilations were used. The basins of the West Greenland continental margin are described in three regions from the south to the north: southern West Greenland basins, central West Greenland basins, and northern West Greenland basins. Each region includes a description of the stratigraphy and evolution from the Archean to the Quaternary, divided into six phases: pre-rift and early extension, early rift, subsidence and rifting, late rift, drift, and post-drift. Finally, the regions are correlated and described in a tectonostratigraphic context together with analogues from the Canadian conjugate margin.
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Trent, J. D., H. K. Kagawa, and N. J. Zaluzec. Chaperonin polymers in archaea: The cytoskeleton of prokaryotes? Office of Scientific and Technical Information (OSTI), July 1997. http://dx.doi.org/10.2172/505321.

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Kelly, R. M. Bioenergetic and physiological studies of hyperthermophilic archaea. Final report. Office of Scientific and Technical Information (OSTI), March 1999. http://dx.doi.org/10.2172/325744.

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Davis, W. J., J. J. Ryan, H. A. Sandeman, and S. Tella. A Paleoproterozoic detrital zircon age for a key conglomeratic horizon within the Rankin Inlet area, Kivalliq Region, Nunavut: implications for Archean and Proterozoic evolution of the area. Natural Resources Canada/ESS/Scientific and Technical Publishing Services, 2008. http://dx.doi.org/10.4095/225479.

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Schuster, Gadi, and David Stern. Integration of phosphorus and chloroplast mRNA metabolism through regulated ribonucleases. United States Department of Agriculture, August 2008. http://dx.doi.org/10.32747/2008.7695859.bard.

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Abstract:
New potential for engineering chloroplasts to express novel traits has stimulated research into relevant techniques and genetic processes, including plastid transformation and gene regulation. This proposal continued our long time BARD-funded collaboration research into mechanisms that influence chloroplast RNA accumulation, and thus gene expression. Previous work on cpRNA catabolism has elucidated a pathway initiated by endonucleolytic cleavage, followed by polyadenylation and exonucleolytic degradation. A major player in this process is the nucleus-encoded exoribonuclease/polymerasepolynucleotidephoshorylase (PNPase). Biochemical characterization of PNPase has revealed a modular structure that controls its RNA synthesis and degradation activities, which in turn are responsive to the phosphate (P) concentration. However, the in vivo roles and regulation of these opposing activities are poorly understood. The objectives of this project were to define how PNPase is controlled by P and nucleotides, using in vitro assays; To make use of both null and site-directed mutations in the PNPgene to study why PNPase appears to be required for photosynthesis; and to analyze plants defective in P sensing for effects on chloroplast gene expression, to address one aspect of how adaptation is integrated throughout the organism. Our new data show that P deprivation reduces cpRNA decay rates in vivo in a PNPasedependent manner, suggesting that PNPase is part of an organismal P limitation response chain that includes the chloroplast. As an essential component of macromolecules, P availability often limits plant growth, and particularly impacts photosynthesis. Although plants have evolved sophisticated scavenging mechanisms these have yet to be exploited, hence P is the most important fertilizer input for crop plants. cpRNA metabolism was found to be regulated by P concentrations through a global sensing pathway in which PNPase is a central player. In addition several additional discoveries were revealed during the course of this research program. The human mitochondria PNPase was explored and a possible role in maintaining mitochondria homeostasis was outlined. As polyadenylation was found to be a common mechanism that is present in almost all organisms, the few examples of organisms that metabolize RNA with no polyadenylation were analyzed and described. Our experiment shaded new insights into how nutrient stress signals affect yield by influencing photosynthesis and other chloroplast processes, suggesting strategies for improving agriculturally-important plants or plants with novel introduced traits. Our studies illuminated the poorly understood linkage of chloroplast gene expression to environmental influences other than light quality and quantity. Finely, our finding significantly advanced the knowledge about polyadenylation of RNA, the evolution of this process and its function in different organisms including bacteria, archaea, chloroplasts, mitochondria and the eukaryotic cell. These new insights into chloroplast gene regulation will ultimately support plant improvement for agriculture
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Luthey-Schulten, Zaida. Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea. Office of Scientific and Technical Information (OSTI), January 2017. http://dx.doi.org/10.2172/1337955.

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Eichler, Jerry. Protein Glycosylation in Archaea: A Post-Translational Modification to Enhance Extremophilic Protein Stability. Fort Belvoir, VA: Defense Technical Information Center, January 2010. http://dx.doi.org/10.21236/ada515568.

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Martin, Maurice. Grid Evolution and Attack Evolution. Office of Scientific and Technical Information (OSTI), April 2018. http://dx.doi.org/10.2172/1434234.

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