scholarly journals Genomic perspectives on the birth and spread of plastids

2015 ◽  
Vol 112 (33) ◽  
pp. 10147-10153 ◽  
Author(s):  
John M. Archibald
Keyword(s):  
Gene Transfer ◽  
Deep Structure ◽  
The Other ◽  
Endosymbiotic Gene Transfer ◽  
Microbial Eukaryotes ◽  
Eukaryotic Genes ◽  
History Of ◽  
Potential Impact ◽  
Cyanobacterial Genes ◽  
Endosymbiotic Origin

The endosymbiotic origin of plastids from cyanobacteria was a landmark event in the history of eukaryotic life. Subsequent to the evolution of primary plastids, photosynthesis spread from red and green algae to unrelated eukaryotes by secondary and tertiary endosymbiosis. Although the movement of cyanobacterial genes from endosymbiont to host is well studied, less is known about the migration of eukaryotic genes from one nucleus to the other in the context of serial endosymbiosis. Here I explore the magnitude and potential impact of nucleus-to-nucleus endosymbiotic gene transfer in the evolution of complex algae, and the extent to which such transfers compromise our ability to infer the deep structure of the eukaryotic tree of life. In addition to endosymbiotic gene transfer, horizontal gene transfer events occurring before, during, and after endosymbioses further confound our efforts to reconstruct the ancient mergers that forged multiple lines of photosynthetic microbial eukaryotes.

scholarly journals Endosymbiotic Gene Transfer in Tertiary Plastid-Containing Dinoflagellates

2013 ◽  
Vol 13 (2) ◽  
pp. 246-255 ◽  
Author(s):  
Fabien Burki ◽  
Behzad Imanian ◽  
Elisabeth Hehenberger ◽  
Yoshihisa Hirakawa ◽  
Shinichiro Maruyama ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Host Genome ◽  
Data Sets ◽  
Transcriptome Data ◽  
Endosymbiotic Gene Transfer ◽  
Low Level ◽  
Long Period ◽  
Host Nucleus ◽  
Endosymbiotic Origin

ABSTRACTPlastid establishment involves the transfer of endosymbiotic genes to the host nucleus, a process known as endosymbiotic gene transfer (EGT). Large amounts of EGT have been shown in several photosynthetic lineages but also in present-day plastid-lacking organisms, supporting the notion that endosymbiotic genes leave a substantial genetic footprint in the host nucleus. Yet the extent of this genetic relocation remains debated, largely because the long period that has passed since most plastids originated has erased many of the clues to how this process unfolded. Among the dinoflagellates, however, the ancestral peridinin-containing plastid has been replaced by tertiary plastids on several more recent occasions, giving us a less ancient window to examine plastid origins. In this study, we evaluated the endosymbiotic contribution to the host genome in two dinoflagellate lineages with tertiary plastids. We generated the first nuclear transcriptome data sets for the “dinotoms,” which harbor diatom-derived plastids, and analyzed these data in combination with the available transcriptomes for kareniaceans, which harbor haptophyte-derived plastids. We found low level of detectable EGT in both dinoflagellate lineages, with only 9 genes and 90 genes of possible tertiary endosymbiotic origin in dinotoms and kareniaceans, respectively, suggesting that tertiary endosymbioses did not heavily impact the host dinoflagellate genomes.

scholarly journals Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

2015 ◽  
Vol 112 (33) ◽  
pp. 10139-10146 ◽  
Author(s):  
Chuan Ku ◽  
Shijulal Nelson-Sathi ◽  
Mayo Roettger ◽  
Sriram Garg ◽  
Einat Hazkani-Covo ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Single Gene ◽  
Gene Tree ◽  
Eukaryotic Cell ◽  
Specific Gene ◽  
Gene Trees ◽  
Endosymbiotic Gene Transfer ◽  
Evolutionary Innovation ◽  
Eukaryotic Genes ◽  
A Genome

Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners—the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)—and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic—and plant and algal—lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller’s ratchet—the origin of eukaryotic recombination, or sex—might have required surprisingly little evolutionary innovation.

scholarly journals Gene transfers, like fossils, can date the Tree of Life

2017 ◽  
Author(s):  
Adrián A. Davín ◽  
Eric Tannier ◽  
Tom A. Williams ◽  
Bastien Boussau ◽  
Vincent Daubin ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Gene Families ◽  
Tree Of Life ◽  
Molecular Clocks ◽  
Geological Record ◽  
Microbial Eukaryotes ◽  
Phylogenetic Methods ◽  
History Of ◽  
Source Of Information

Biodiversity has always been predominantly microbial and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here we show that patterns of lateral gene transfer deduced from the analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use new phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukaryotes. An inspection of discrepancies between transfers and clocks and a comparison with mammal fossils show that gene transfer in microbes is potentially as informative for dating the tree of life as the geological record in macroorganisms.

Thomas More and the Master Tropes: The deep structure of A Dialogue Concerning Heresies and Giambattista Vico

Moreana ◽  
2001 ◽  
Vol 38 (Number 147- (3-4) ◽  
pp. 4-24
Author(s):  
John D. Schaeffer
Keyword(s):  
Deep Structure ◽  
The Other ◽  
Thomas More ◽  
Giambattista Vico ◽  
History Of ◽  
Hayden White ◽  
Religiously Based ◽  
Sensus Communis ◽  
Language And Law ◽  
Desperate Attempt

More’s Dialogue Concerning Heresies (1529) has furnished many of his contemporary critics with evidence of his manipulative rhetoric and his rigid orthodoxy. A careful reading of the work, however, reveals its structure to depend upon the four master trop es: metaphor, metonymy, synecdoche, and irony, arranged in a dialectic that Giambattista Vico called “the poetic logic.” Hayden White found this same poetic logic underlying the structure of Michel Foucault’s account of the history of discourse. Vico and Foucault were writing at the end of the dialectic age, in the age of irony. More, on the other hand, was writing at the end of the metonymie stage, when a coherent sensus communis begins to collapse into plurality of competing world views. Viewed against the background of the poetic logic, A Dialogue Concerning Heresies was not merely a defense of religious orthodoxy, but a desperate attempt to maintain a coherent, religiously-based sensus communis, one that underwrote the intelligibility of language and law, against what More perceived as a tide of relativism and solipsism.

scholarly journals Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist

2015 ◽  
Vol 370 (1678) ◽  
pp. 20140324 ◽  
Author(s):  
Laura A. Katz
Keyword(s):  
Gene Transfer ◽  
Single Gene ◽  
Gene Trees ◽  
Phylogenetic Information ◽  
Endosymbiotic Gene Transfer ◽  
Phylogenetic Methods ◽  
Photosynthetic Eukaryotes ◽  
History Of ◽  
The Impact

While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages.

scholarly journals Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs

Biology ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 386
Author(s):  
Miroslav Oborník
Keyword(s):  
Gene Transfer ◽  
Evolutionary History ◽  
Porphobilinogen Deaminase ◽  
Endosymbiotic Gene Transfer ◽  
Heme Synthesis ◽  
Primary Plastid ◽  
Phylogenetic Affiliation ◽  
History Of

In most eukaryotic phototrophs, the entire heme synthesis is localized to the plastid, and enzymes of cyanobacterial origin dominate the pathway. Despite that, porphobilinogen deaminase (PBGD), the enzyme responsible for the synthesis of hydroxymethybilane in the plastid, shows phylogenetic affiliation to α-proteobacteria, the supposed ancestor of mitochondria. Surprisingly, no PBGD of such origin is found in the heme pathway of the supposed partners of the primary plastid endosymbiosis, a primarily heterotrophic eukaryote, and a cyanobacterium. It appears that α-proteobacterial PBGD is absent from glaucophytes but is present in rhodophytes, chlorophytes, plants, and most algae with complex plastids. This may suggest that in eukaryotic phototrophs, except for glaucophytes, either the gene from the mitochondrial ancestor was retained while the cyanobacterial and eukaryotic pseudoparalogs were lost in evolution, or the gene was acquired by non-endosymbiotic gene transfer from an unspecified α-proteobacterium and functionally replaced its cyanobacterial and eukaryotic counterparts.

Theodor W. Adorno

2018 ◽  
Author(s):  
Colby Dickinson
Keyword(s):  
The Other ◽  
History Of Thought ◽  
History Of ◽  
The One

In his somewhat controversial book Remnants of Auschwitz, Agamben makes brief reference to Theodor Adorno’s apparently contradictory remarks on perceptions of death post-Auschwitz, positions that Adorno had taken concerning Nazi genocidal actions that had seemed also to reflect something horribly errant in the history of thought itself. There was within such murderous acts, he had claimed, a particular degradation of death itself, a perpetration of our humanity bound in some way to affect our perception of reason itself. The contradictions regarding Auschwitz that Agamben senses to be latent within Adorno’s remarks involve the intuition ‘on the one hand, of having realized the unconditional triumph of death against life; on the other, of having degraded and debased death. Neither of these charges – perhaps like every charge, which is always a genuinely legal gesture – succeed in exhausting Auschwitz’s offense, in defining its case in point’ (RA 81). And this is the stance that Agamben wishes to hammer home quite emphatically vis-à-vis Adorno’s limitations, ones that, I would only add, seem to linger within Agamben’s own formulations in ways that he has still not come to reckon with entirely: ‘This oscillation’, he affirms, ‘betrays reason’s incapacity to identify the specific crime of Auschwitz with certainty’ (RA 81).

The World after the End of the World

2017 ◽  
Vol 39 (2) ◽  
pp. 265-276 ◽  
Author(s):  
Kas Saghafi
Keyword(s):  
The Other ◽  
The World ◽  
History Of ◽  
The Absolute ◽  
End Of The World

In several late texts, Derrida meditated on Paul Celan's poem ‘Grosse, Glühende Wölbung’, in which the departure of the world is announced. Delving into the ‘origin’ and ‘history’ of the ‘conception’ of the world, this paper suggests that, for Derrida, the end of the world is determined by and from death—the death of the other. The death of the other marks, each and every time, the absolute end of the world.

Med. Dr. Adalbert Wraný (1836–1902) – doctor of medicine, mineral collector and donor to the National Museum in Prague

2019 ◽  
Vol 188 (1) ◽  
pp. 95-146
Author(s):  
Martin Bohatý ◽  
Dalibor Velebil
Keyword(s):  
Natural Science ◽  
Natural Sciences ◽  
The Other ◽  
National Museum ◽  
Industrial Chemistry ◽  
Pediatric Pathology ◽  
Geological Institute ◽  
History Of ◽  
Precious Stones

Adalbert Wraný (*1836, †1902) was a doctor of medicine, with his primary specialization in pediatric pathology, and was also one of the founders of microscopic and chemical diagnostics. He was interested in natural sciences, chemistry, botany, paleontology and above all mineralogy. He wrote two books, one on the development of mineralogical research in Bohemia (1896), and the other on the history of industrial chemistry in Bohemia (1902). Wraný also assembled several natural science collections. During his lifetime, he gave to the National Museum large collections of rocks, a collection of cut precious stones and his library. He donated a collection of fossils to the Geological Institute of the Czech University (now Charles University). He was an inspector of the mineralogical collection of the National Museum. After his death, he bequeathed to the National Museum his collection of minerals and the rest of the gemstone collection. He donated paintings to the Prague City Museum, and other property to the Klar Institute of the Blind in Prague. The National Museum’s collection currently contains 4 325 samples of minerals, as well as 21 meteorites and several hundred cut precious stones from Wraný’s collection.

La ética del Otro: una introducción al pensamiento de Emmanuel Lévinas

2019 ◽  
Vol 1 (1) ◽  
pp. 5-14
Author(s):  
Carlos Alvaréz Teijeiro
Keyword(s):  
Interpersonal Relationships ◽  
Emmanuel Levinas ◽  
Radical Change ◽  
The Other ◽  
Western Philosophy ◽  
Ethical Implications ◽  
Essential Question ◽  
History Of ◽  
The Relationship ◽  
First Philosophy

Emmanuel Lévinas, the philosopher of ethics par excellence in the twentieth century, and by own merit one of the most important ethical philosophers in the history of western philosophy, is also the philosopher of the Other. Thereby, it can be said that no thought has deepened like his in the ups and downs of the ethical relationship between subject and otherness. The general objective of this work is to expose in a simple and understandable way some ideas that tend to be quite dark in the philosophical work of the author, since his profuse religious production will not be analyzed here. It is expected to show that his ideas about the being and the Other are relevant to better understand interpersonal relationships in times of 4.0 (re)evolution. As specific objectives, this work aims to expose in chronological order the main works of the thinker, with special emphasis on his ethical implications: Of the evasion (1935), The time and the Other (1947), From the existence to the existent (1947), Totality and infinity: An essay on exteriority (1961) and, last, Otherwise than being, or beyond essence (1974). In the judgment of Lévinas, history of western philosophy starting with Greece, has shown an unusual concern for the Being, this is, it has basically been an ontology and, accordingly, it has relegated ethics to a second or third plane. On the other hand and in a clear going against the tide movement, our author supports that ethics should be considered the first philosophy and more, even previous to the proper philosophize. This novel approach implies, as it is supposed, that the essential question of the philosophy slows down its origin around the Being in order to inquire about the Other: it is a philosophy in first person. Such a radical change of perspective generates an underlying change in how we conceive interpersonal relationships, the complex framework of meanings around the relationship Me and You, which also philosopher Martin Buber had already spoken of. As Lévinas postulates that ethics is the first philosophy, this involves that the Other claims all our attention, intellectual and emotional, to the point of considering that the relationship with the Other is one of the measures of our identity. Thus, “natural” attitude –husserlian word not used by Lévinas- would be to be in permanent disposition regarding to the meeting with the Other, to be in permanent opening state to let ourselves be questioned by him. Ontology, as the author says, being worried about the Being, has been likewise concerned about the Existence, when the matter is to concern about the particular Existent that every otherness supposes for us. In conclusion it can be affirmed that levinasian ethics of the meeting with the Other, particular Face, irreducible to the assumption, can contribute with an innovative looking to (re)evolving the interpersonal relationships in a 4.0 context.

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