Preservação celular de especializacões musculoesqueléticas no pássaro Confuciusornis do Cretáceo

quarta-feira, março 22, 2017

Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis

Baoyu Jiang, Tao Zhao, Sophie Regnault, Nicholas P. Edwards, Simon C. Kohn, Zhiheng Li, Roy A. Wogelius, Michael J. Benton & John R. Hutchinson

Nature Communications 8, Article number: 14779 (2017)


Biomechanics Palaeontology

Received: 14 January 2016 Accepted: 02 February 2017 Published online: 22 March 2017



Abstract

The hindlimb of theropod dinosaurs changed appreciably in the lineage leading to extant birds, becoming more ‘crouched’ in association with changes to body shape and gait dynamics. This postural evolution included anatomical changes of the foot and ankle, altering the moment arms and control of the muscles that manipulated the tarsometatarsus and digits, but the timing of these changes is unknown. Here, we report cellular-level preservation of tendon- and cartilage-like tissues from the lower hindlimb of Early Cretaceous Confuciusornis. The digital flexor tendons passed through cartilages, cartilaginous cristae and ridges on the plantar side of the distal tibiotarsus and proximal tarsometatarsus, as in extant birds. In particular, fibrocartilaginous and cartilaginous structures on the plantar surface of the ankle joint of Confuciusornis may indicate a more crouched hindlimb posture. Recognition of these specialized soft tissues in Confuciusornis is enabled by our combination of imaging and chemical analyses applied to an exceptionally preserved fossil.

Acknowledgements

We thank Zhonghe Zhou, Jin Meng, Junfeng Ji, Xiancai Lu, Julia Clarke and Maria McNamara for discussions, and Yan Fang, Wuping Li, Tong He, H. Jones, M. Hethke, M. Hill, A. Davidson, Junying Ding and Huan Liu for laboratory assistance. This work was supported by the National Science Foundation of China (41672010, 41688103) and State Key Laboratory of Palaeobiology and Stratigraphy (Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences) (153104) to B.J., as well as a Royal Society Leverhulme Trust senior research fellowship, Leverhulme Trust research Grant Number RPG-2013-108 and Natural Environment Research Council Grant Number NE/K004751/1 to J.R.H. We thank the staff at the Diamond Light Source, beamline I18 (beam allocation SP9488). We also thank Nick Lockyer for discussions about the ToF–SIMS data.

Author information

Affiliations

School of Earth Sciences and Engineering, Nanjing University, Nanjing 210023, China

Baoyu Jiang & Tao Zhao

State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China

Baoyu Jiang

Structure and Motion Laboratory, Department of Comparative Biomedical Sciences, The Royal Veterinary College, University of London, Hatfield, Hertfordshire AL9 7TA, UK

Sophie Regnault & John R. Hutchinson

School of Earth and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK

Nicholas P. Edwards & Roy A. Wogelius

School of Earth Sciences, University of Bristol, Bristol BS8 1TH, UK

Simon C. Kohn & Michael J. Benton

Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China

Zhiheng Li

Contributions

B.J. and J.R.H. designed the research, B.J. and T.Z. studied the histology (including SEM) of the fossils, S.R. and J.R.H. made the histological comparisons between fossils and extant birds, N.P.E. and R.A.W. carried out the synchrotron rapid-scanning X-ray fluorescence and X-ray absorption near-edge structure spectroscopies, B.J. did the ToF–SIMS analysis, M.J.B. and S.C.K. did the FTIR analysis, Z.L. and S.R. did the microCT reconstructions, and B.J., R.A.W., M.J.B. and J.R.H. wrote the paper; all authors approved the final draft of the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Baoyu Jiang or John R. Hutchinson.


1.

Supplementary Information

Supplementary Figures, Supplementary Table and Supplementary References

2.

Peer Review File

Origem da vida sem fosfato! Pode isso, Arnaldo? A regra química é clara: Não! Mas...

Remnants of an Ancient Metabolism without Phosphate

Joshua E. Goldford, Hyman Hartman, Temple F. Smith, Daniel Segrè5

5Lead Contact: Daniel Segrè

Published Online: March 02, 2017


Article Info

Publication History

Published: March 2, 2017 Accepted: January 31, 2017 Received in revised form: December 16, 2016 Received: September 12, 2016

User License

Creative Commons Attribution – NonCommercial – NoDerivs (CC BY-NC-ND 4.0)



Highlights

• We computationally test the plausibility of an ancient metabolism without phosphate

• A phosphate-independent network exists within biosphere-level metabolism

• This network displays hallmarks of prebiotic chemistry, e.g., iron-sulfur cofactors

• This could represent a “metabolic fossil” of early thioester-driven biochemistry

Summary

Phosphate is essential for all living systems, serving as a building block of genetic and metabolic machinery. However, it is unclear how phosphate could have assumed these central roles on primordial Earth, given its poor geochemical accessibility. We used systems biology approaches to explore the alternative hypothesis that a protometabolism could have emerged prior to the incorporation of phosphate. Surprisingly, we identified a cryptic phosphate-independent core metabolism producible from simple prebiotic compounds. This network is predicted to support the biosynthesis of a broad category of key biomolecules. Its enrichment for enzymes utilizing iron-sulfur clusters, and the fact that thermodynamic bottlenecks are more readily overcome by thioester rather than phosphate couplings, suggest that this network may constitute a “metabolic fossil” of an early phosphate-free nonenzymatic biochemistry. Our results corroborate and expand previous proposals that a putative thioester-based metabolism could have predated the incorporation of phosphate and an RNA-based genetic system.

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Denis Noble, da Universidade Oxford defende “revisão fundamental” no “neodarwinismo reducionista...” E a teoria da evolução não sofre crise epistêmica???

Denis Noble, da Universidade Oxford defende uma “Revisão Fundamental” no “Neodarwinismo reducionista...”

David Klinghoffer | @d_klinghofferMarch 18, 2017, 2:00 AM – Vide aqui. 


Eis o novo livro de Denis Noble, biólogo da Universidade Oxford, Dance to the Tune of Life: Biological RelativityEle é um dos proponentes do Third Way of Evolution [Terceira Via da Evolução], e não defende o Design Inteligente.

Leia agora este comentário no livro, de Jos de Mul da Universidade Erasmus, em Roterdã, Holanda. Ele também não é proponent do DI:

"Neste livro pessoal e elegantemente escrito, o mundialmente renomado fisiologista e biólogo de sistemas, Denis Noble argumenta eficientemente a favor de uma revisão fundamental da teoria da evolução. Contra a abordagem reducionista, fundamentada nos genes do Neodarwinismo, que tem dominado a biologia por mais de um século, Noble apela veementemente a favor de uma abordagem mais integrada. Massivamente apoiado por recentes pesquisas empíricas pós-genômicas epigenéticas, o livro Dance to the Tune of Life aprofunda e sintetiza as ideias que Noble desenvolveu anteriormente no livro The Music of Life: Biology Beyond the Genome (2006) e em subsequentes escritos. Assim como a física newtoniana sofreu uma grande transformação no começo do século 20 devido à teoria geral da relatividade de Einstein, as ciências da vida estão enfrentando uma transformação não menos fundamental. O livro de Noble é uma leitura obrigatória para quem quer que queira entender essa transformação.

Isso é uma linguagem forte — uma “revisão fundamental” na teoria evolucionária, contra o “neodarwinismo reducionista…”, e comparável a como a “física newtoniana sofreu uma grande transformação no começo do século 20.” Enquanto isso as notícias de falsa ciência que saem da Grande Mídia e do National Center for Science Education [Centro Nacional para a Educação da Ciência] nos asseguram que o pensamento evolucionário está estabelecido tão firmemente quanto os Pilares de Hércules.

O livro foi publicado em janeiro de 2017 pela Cambridge University Press. Você não me acredita? Está lá na página da Amazon. Noble foi um dos organizadores e participantes do encontro da Royal Society em Londres que nós falamos tanto aqui.

A biologia evolucionária está em um estado à beira de fermentação, e em alguns círculos, de rebelião aberta. Não permita que os defensores de Darwin lhe digam o contrário.

Foto: Denis Noble, courtesia de Denis Noble [Copyright livre uso], via Wikimedia Commons.  

Sugestão: Günter Bechly.

Marcadores

Método de fluorescência geoquímica revela tecido mole de fóssil de Anchiornis. Será?

terça-feira, março 21, 2017

Basal paravian functional anatomy illuminated by high-detail body outline

Xiaoli Wang, Michael Pittman, Xiaoting Zheng, Thomas G. Kaye, Amanda R. Falk, Scott A. Hartman & Xing Xu

Nature Communications 8, Article number: 14576 (2017)


Download Citation

Palaeontology

Received: 28 September 2016 Accepted: 13 January 2017 Published online: 01 March 2017



Abstract

Body shape is a fundamental expression of organismal biology, but its quantitative reconstruction in fossil vertebrates is rare. Due to the absence of fossilized soft tissue evidence, the functional consequences of basal paravian body shape and its implications for the origins of avians and flight are not yet fully understood. Here we reconstruct the quantitative body outline of a fossil paravian Anchiornis based on high-definition images of soft tissues revealed by laser-stimulated fluorescence. This body outline confirms patagia-bearing arms, drumstick-shaped legs and a slender tail, features that were probably widespread among paravians. Finely preserved details also reveal similarities in propatagial and footpad form between basal paravians and modern birds, extending their record to the Late Jurassic. The body outline and soft tissue details suggest significant functional decoupling between the legs and tail in at least some basal paravians. The number of seemingly modern propatagial traits hint that feathering was a significant factor in how basal paravians utilized arm, leg and tail function for aerodynamic benefit.

Acknowledgements

This study was supported by the Dr Stephen S.F. Hui Trust Fund (201403173007), the Research Grant Council of Hong Kong’s General Research Fund (17103315), The Faculty of Science of the University of Hong Kong and the National Science Foundation of China (41688103, 41372014 and 41472023). Rui Pei is thanked for discussions about Supplementary Table 1.

Author information

Author notes

Xiaoli Wang & Michael Pittman

These authors contributed equally to this work

Affiliations

Institute of Geology and Paleontology, Linyi University, Linyi City, Shandong 276005, China

Xiaoli Wang & Xiaoting Zheng

Vertebrate Palaeontology Laboratory, Department of Earth Sciences, University of Hong Kong, Pokfulam, Hong Kong, China

Michael Pittman

Shandong Tianyu Museum of Nature, Pingyi, Shandong 273300, China

Xiaoting Zheng

Foundation for Scientific Advancement, 7023 Alhambra Drive, Sierra Vista, Arizona 85650, USA

Thomas G. Kaye

Department of Biology, Centre College, 600 West Walnut Street, Danville, Kentucky 40422, USA

Amanda R. Falk

Department of Geoscience, University of Wisconsin-Madison, Lewis G. Weeks Hall for Geological Sciences, 1215 West Dayton Street, Madison, Wisconsin 53706-1692, USA

Scott A. Hartman

Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China

Xing Xu

Contributions

X.W., M.P., X.Z., T.G.K., A.R.F. and X.X. designed the project. All authors performed the research. M.P., T.G.K., X.W. and X.X. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Xiaoli Wang or Michael Pittman.

Não é DNA "lixo": O Paramecium tetraurelia organiza a transcrição de segmentos de DNA removidos em RNAs, com função reguladora!

Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs

Sarah E. Allen, Iris Hug, Sylwia Pabian, Iwona Rzeszutek, Cristina Hoehener, Mariusz Nowacki2

2Lead Contact

Open Access



Open access funded by European Research Council

Article Info

Publication History

Published: March 9, 2017 Accepted: February 9, 2017 Received in revised form: January 10, 2017 Received: November 21, 2016

User License

Creative Commons Attribution – NonCommercial – NoDerivs (CC BY-NC-ND 4.0)


Highlights

• In Paramecium, pieces of deleted DNA are transcribed to form regulatory RNAs

• Ultra-short DNA segments are concatenated and circularized, allowing transcription

• This concatenation is carried out by Ligase IV, which also repairs DNA ends

• Concatenation is random, which leads to diversity in the resulting sRNA population

Summary

In the ciliated protozoan Paramecium tetraurelia, Piwi-associated small RNAs are generated upon the elimination of tens of thousands of short transposon-derived DNA segments as part of development. These RNAs then target complementary DNA for elimination in a positive feedback process, contributing to germline defense and genome stability. In this work, we investigate the formation of these RNAs, which we show to be transcribed directly from the short (length mode 27 bp) excised DNA segments. Our data support a mechanism whereby the concatenation and circularization of excised DNA segments provides a template for RNA production. This process allows the generation of a double-stranded RNA for Dicer-like protein cleavage to give rise to a population of small regulatory RNAs that precisely match the excised DNA sequences.

Keywords: small RNA, transcription, DNA concatemers, circular DNA, Ligase IV, Dicer, DNA elimination, DNA repair, transposable elements, Piwi-interacting RNA, ciliates, Paramecium

Received: November 21, 2016; Received in revised form: January 10, 2017; Accepted: February 9, 2017; Published: March 9, 2017

© 2017 The Author(s). Published by Elsevier Inc.

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Origem da vida? Simples auto-organização mineral biomimética de nascente de águas ricas em sílica. Será?

Biomimetic mineral self-organization from silica-rich spring waters

Juan Manuel García-Ruiz1,*, Elias Nakouzi2, Electra Kotopoulou1, Leonardo Tamborrino1,† and Oliver Steinbock2

+ See all authors and affiliations

Science Advances 17 Mar 2017:

Vol. 3, no. 3, e1602285


Fig. 3 Silica gardens

Abstract

Purely inorganic reactions of silica, metal carbonates, and metal hydroxides can produce self-organized complex structures that mimic the texture of biominerals, the morphology of primitive organisms, and that catalyze prebiotic reactions. To date, these fascinating structures have only been synthesized using model solutions. We report that mineral self-assembly can be also obtained from natural alkaline silica-rich water deriving from serpentinization. Specifically, we demonstrate three main types of mineral self-assembly: (i) nanocrystalline biomorphs of barium carbonate and silica, (ii) mesocrystals and crystal aggregates of calcium carbonate with complex biomimetic textures, and (iii) osmosis-driven metal silicate hydrate membranes that form compartmentalized, hollow structures. Our results suggest that silica-induced mineral self-assembly could have been a common phenomenon in alkaline environments of early Earth and Earth-like planets.

Keywords Silica Biomorphs Chemical Gardens self-organization Calcite witherite nano composites Life detection Prebiotic chemistry Aqua de Ney

Copyright © 2017, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

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Tardígrados usam proteínas desordenadas intrinsecamente para sobreviver à dessecação

segunda-feira, março 20, 2017

Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation

Thomas C. Boothby 6, Thomas C. BoothbyEmail the author Thomas C. Boothby, Hugo Tapia, Alexandra H. Brozena, Samantha Piszkiewicz, Austin E. Smith, Ilaria Giovannini, Lorena Rebecchi, Gary J. Pielak, Doug Koshland, Bob Goldstein

6 Lead Contact


Article Information

Publication History

Published: March 16, 2017 Accepted: February 16, 2017 Received in revised form: December 14, 2016 

Received: July 26, 2016

Source/Fonte: The New York Times

Highlights

• Tardigrade intrinsically disordered proteins (TDPs) are enriched during desiccation

• TDPs are required for tardigrades to survive desiccation

• Expression of TDPs increases desiccation tolerance in heterologous systems

• TDPs vitrify, and this vitrified state mirrors their protective capabilities

Summary

Tardigrades are microscopic animals that survive a remarkable array of stresses, including desiccation. How tardigrades survive desiccation has remained a mystery for more than 250 years. Trehalose, a disaccharide essential for several organisms to survive drying, is detected at low levels or not at all in some tardigrade species, indicating that tardigrades possess potentially novel mechanisms for surviving desiccation. Here we show that tardigrade-specific intrinsically disordered proteins (TDPs) are essential for desiccation tolerance. TDP genes are constitutively expressed at high levels or induced during desiccation in multiple tardigrade species. TDPs are required for tardigrade desiccation tolerance, and these genes are sufficient to increase desiccation tolerance when expressed in heterologous systems. TDPs form non-crystalline amorphous solids (vitrify) upon desiccation, and this vitrified state mirrors their protective capabilities. Our study identifies TDPs as functional mediators of tardigrade desiccation tolerance, expanding our knowledge of the roles and diversity of disordered proteins involved in stress tolerance.

Author Contributions

Conceptualization, (Lead) T.C.B. (supporting) B.G., G.J.P.; Investigation, T.C.B., H.T., A.H.B., S.P., A.E.S., I.G.; Resources, I.G., L.R., H.T., D.K.; Writing – Original Draft, T.C.B., S.P., G.J.P.; Writing – Review & Editing, T.C.B., H.T., A.H.B, S.P., A.E.S., I.G., L.R., G.J.P., D.K., B.G., Supervision, T.C.B., L.R., D.K., B.G., G.J.P.

Acknowledgments

This work was supported by NASA ( NNX15AB44G to T.C.B.) and the National Science Foundation ( MCB 1410854 and CHE 1607359 to G.J.P., IOS 1557432 and 1257320 to B.G.). L.R. and I.G. were supported by Young Researchers International Mobility of the University of Modena and Reggio Emilia and Fondo di Ateneo per la Ricerca (2015). We acknowledge the Harold and Leila Y. Mathers Charitable Foundation for supporting H.T. and the Simons Foundation of the Life Sciences Research Foundation for supporting T.C.B.

Received: July 26, 2016; Received in revised form: December 14, 2016; Accepted: February 16, 2017; Published: March 16, 2017

© 2017 Elsevier Inc.

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Sinais de inteligência em um carro inteligente, mas na célula não?

sábado, março 18, 2017

Design of an intelligent car

Yongyi Na1,a)View Affiliations

AIP Conference Proceedings 1820, 070003 (2017); 




ABSTRACT

The design of simple intelligent car, using AT89S52 single chip microcomputer as the car detection and control core; The metal sensor TL - Q5MC induction to iron, to detect the way to send feedback to the signal of single chip microcomputer, make SCM according to the scheduled work mode to control the car in the area according to the predetermined speed, and the operation mode of the microcontroller choose different also can control the car driving along s-shaped iron; Use A44E hall element to detect the car speeds; Adopts 1602 LCD display time of car driving, driving the car to stop, take turns to show the car driving time, distance, average speed and the speed of time. This design has simple structure and is easy to implement, but are highly intelligent, humane, to a certain extent reflects the intelligence.

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+++++

DESTAQUE DESTE BLOGGER: Bruce Alberts, foi presidente da Academia Nacional de Ciências dos Estados Unidos, certa vez comparou a célula como uma fábrica...


Source/Fonte: azquotes.com


Carro inteligente com sinais de inteligência, mas célula com sinais de inteligência é ilusão? Pode isso, Arnaldo? A regra é clara, se os sinais de inteligência são detectados empiricamente, negá-los somente por razões ideológicas, científicas, não!

Polêmica à vista: toda a Biologia é Biologia Computacional

sexta-feira, março 17, 2017

All biology is computational biology

Florian Markowetz 


Source/Fonte: Shutterstock

Abstract

Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science.

Citation: Markowetz F (2017) All biology is computational biology. PLoS Biol 15(3): e2002050. doi: 10.1371/journal.pbio.2002050

Published: March 9, 2017

Copyright: © 2017 Florian Markowetz. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: Cancer Research UK http://www.cancerresearchuk.org/ (grant number C14303/A17197). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Provenance: Commissioned; not externally peer reviewed

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Teoremas fundamentais da evolução

Fundamental Theorems of Evolution

David C. Queller*

Department of Biology, Washington University in St. Louis, St. Louis, Missouri

*E-mail: queller@wustl.edu.


SUBMITTED: Nov 07, 2016 ACCEPTED: Nov 23, 2016 ONLINE: Feb 28, 2017


Source/Fonte: Quora

Abstract

Evolutionary biology is undergirded by an extensive and impressive set of mathematical models. Yet only one result, Fisher’s theorem about selection and fitness, is generally accorded the status of a fundamental theorem. I argue that although its fundamental status is justified by its simplicity and scope, there are additional results that seem similarly fundamental. I suggest that the most fundamental theorem of evolution is the Price equation, both because of its simplicity and broad scope and because it can be used to derive four other familiar results that are similarly fundamental: Fisher’s average-excess equation, Robertson’s secondary theorem of natural selection, the breeder’s equation, and Fisher’s fundamental theorem. These derivations clarify both the relationships behind these results and their assumptions. Slightly less fundamental results include those for multivariate evolution and social selection. A key feature of fundamental theorems is that they have great simplicity and scope, which are often achieved by sacrificing perfect accuracy. Quantitative genetics has been more productive of fundamental theorems than population genetics, probably because its empirical focus on unknown genotypes freed it from the tyranny of detail and allowed it to focus on general issues.

Keywords: fundamental theorem, evolution, Price equation, breeder’s equation, average excess.

FREE PDF GRATIS: The American Naturalist

Ciclo de Krebs livre de enzimas pode ter sido um passo fundamental na origem da vida na Terra

quinta-feira, março 16, 2017

Sulfate radicals enable a non-enzymatic Krebs cycle precursor

Markus A. Keller, Domen Kampjut, Stuart A. Harrison & Markus Ralser

Nature Ecology & Evolution 1, Article number: 0083 (2017)


Evolutionary theory Chemical origin of life

Received: 13 August 2016 Accepted: 13 January 2017

Published online: 13 March 2017


Abstract

The evolutionary origins of the Krebs cycle (tricarboxylic acid cycle) are not currently clear. Despite the existence of a simple non-enzymatic Krebs cycle catalyst being dismissed only a few years ago as ‘an appeal to magic’, citrate and other intermediates have since been discovered on a carbonaceous meteorite and do interconvert non-enzymatically. To identify a metabolism-like non-enzymatic Krebs cycle catalyst, we used combinatorial, quantitative high-throughput metabolomics to systematically screen iron and sulfate compounds in a reaction mixture that orients on the typical components of Archaean sediment. Krebs cycle intermediates were found to be stable in water and in the presence of most molecule species, including simple iron sulfate minerals. However, in the presence of sulfate radicals generated from peroxydisulfate, the intermediates underwent 24 interconversion reactions. These non-enzymatic reactions covered the critical topology of the oxidative Krebs cycle, the glyoxylate shunt and the succinic-semialdehyde pathway. Assembled in a chemical network, the reactions achieved over 90% carbon recovery. Our results show that a non-enzymatic precursor of the Krebs cycle is biologically sensible, efficient, and forms spontaneously in the presence of sulfate radicals.

The tricarboxylic acid (TCA) cycle, or Krebs cycle, is a central metabolic pathway, typically of oxidative function. This metabolic pathway provides precursors for the biosynthesis of amino acids, and plays an essential role in fatty-acid breakdown, cellular respiration, and energy and redox metabolism 1. The widespread occurrence of at least its oxidative reactions 2,3 indicates that at least parts of the Krebs cycle originated at a very early stage in evolution; perhaps dating back to the origin of life4,​5,​6. A frequently discussed hypothesis proposes that the Krebs cycle obtained its structural topology by Darwinian selection principles that were enabled by the ‘ribonucleic acid (RNA) world’. A post-genetic origin implies that pathway topologies are subject to progressive change, implying that the modern Krebs cycle could differ substantially from its early precursors 7. However, a post-genetic origin of metabolism struggles to explain how multiple, structurally complex enzymes came into being initially; enzymes themselves are made-up from the metabolic products of the Krebs cycle. Second, a Darwinian origin for the metabolic network topology has difficulties in explaining the high number of reactions that recur between kingdoms despite a lack of enzyme sequence conservation 8. An alternative hypothesis thus proposes that at least the key metabolic reactions originated from environmental chemistry. In this scenario, inorganic catalysis determines the basic structure of metabolism 9,​10,​11,​12.

As enzymatic mechanisms of the Krebs cycle have limited resemblance to inorganic catalysis, the idea of a non-enzymatic origin was received sceptically by many 5,13. For instance, Leslie Orgel, a leading scientist in shaping the RNA world hypothesis, dismissed the possibility that a simple inorganic catalyst that could replace a series set of TCA-like reactions as ‘an appeal to magic’ 5. However, despite the fact that a simple catalyst was indeed missing, others have argued that several Krebs cycle metabolites form in organic chemical reactions 9,10. Meanwhile, the presence of a series of TCA intermediates has been confirmed on a carbonaceous meteorite 14. Furthermore, citrate and other TCA intermediates undergo highly efficient reductive interconversion reactions on semiconductor particles when exposed to strong ultraviolet light15. A non-enzymatic precursor to the Krebs cycle is therefore catalytically possible. Moreover, the existence of a unifying, simple catalyst has become plausible. Non-enzymatic reactions that replicate two other metabolic pathways, glycolysis and the pentose phosphate pathway, are united in their common dependence on ferrous iron as the catalyst and co-substrate 16,17. Fe(II) is abundant in typical Archaean sediments 18,19, implying that general chemical environments, rather than niche conditions, may have been key to shaping the structure of metabolic pathways.

We chose a systematic screening strategy whereby ~4,850 absolute quantitative experiments were performed to examine the reactivity of TCA intermediates in the presence of typical Archaean sediment constituents, as well as related iron and sulfur species. We found that the TCA intermediates were unreactive in the presence of the majority of iron and sulfate combinations, including the simple mineral, ferrous sulfide (FeS). However, in the presence of the radical donor peroxydisulfate, we detected 24 non-enzymatic interconversion reactions. These reactions resemble the isomerization and oxidative reactions of the enzymatic Krebs cycle, the glyoxylate shunt and the succinic semialdehyde pathway, so that their critical topologies are covered. A chemical network assembled from these reactions achieves more than 90% carbon recovery, forming a plausible non-enzymatic precursor for the origin of the early Krebs cycle.

Acknowledgements

We thank G. Averill and T. Littmann for helping with experiments. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001134), the UK Medical Research Council (FC001134) and the Wellcome Trust (FC001134). M.R. is supported by a Wellcome Trust grant, RG 093735/Z/10/Z, and a European Research Council Starting Grant, 260809. M.A.K. is supported by an Erwin Schrödinger postdoctoral fellowship (FWF, Austria, J3341). D.K. is supported by an Ad Futura studentship (Slovene Scholarship Fund).

Author information

Affiliations

Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK

Markus A. Keller, Domen Kampjut, Stuart A. Harrison & Markus Ralser

Division of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria

Markus A. Keller

Division of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Straße 1, 6020 Innsbruck, Austria

Markus A. Keller

The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK

Markus Ralser

Contributions

M.A.K. and M.R. designed the research. M.A.K., D.K. and S.A.H. performed the research. M.A.K. and M.R. wrote the first draft of the paper, and all authors contributed to finalizing the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Markus Ralser.

FREE PDF GRATIS: Nature Ecology and Evolution Sup. Info. Excel files 1, 2, 3, 4, 5

Paleovirologia: inferir a evolução viral a partir dos dados da sequência do genoma do hospedeiro

Paleovirology: inferring viral evolution from host genome sequence data

Aris Katzourakis

Published 12 August 2013.DOI: 10.1098/rstb.2012.0493

Source/Fonte: Bioinformatics ***** Site

1. Introduction

Paleovirology is the study of ancient viruses, typically over prehistoric or geological timescales. There is no physical ‘fossil record’ of viruses; virions persist for short time periods, and rapidly degrade leaving no direct trace of their existence. Many viruses can enter the genomes of their hosts—some, such as retroviruses, do so as an obligate step during their replication process, and others can occasionally do so, either by accident or as a latent part of their life cycle. When viral integrations occur in the germline of their host, they can be passed on to the next generation, potentially fixing in the host population. When this occurs, the integrated endogenous virus genomes evolve at host rates of mutation, and their sequence is relatively stably preserved. The study of this genomic ‘fossil record’ has led to the burgeoning field of paleovirology, which uses these endogenous viruses to disentangle the long-term evolutionary history of virus–host interactions.

Viruses are a pervasive feature of both eukaryotic and prokaryotic life, and offer some of the best-studied examples of evolution in action due to their rapid rates of evolution. We have observed the diversification of HIV into distinct subtypes over the past six decades, variously prevalent in different patient risk groups and geographical locations, as well as the selection of drug and immune escape mutations within the course of single infections [1]. Rates of viral evolution are so rapid that viruses are among the few organisms which can be used to validate the tools used to reconstruct molecular phylogenies [2]. However, at the same time, perhaps more so than for other biological entities, the long-term evolutionary history of viruses is far less well understood. This is, in part, because the rapid mutation rates that enable the study of their short-term evolution erode the signal of molecular evolution in nucleotide sequences [3], but also due to their physical fragility. Thus, the genomic fossil record is the only way to study viral evolutionary history on timescales spanning millions of years.

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Origem marinha de retrovírus no início da Era Paleozóica

Marine origin of retroviruses in the early Palaeozoic Era

Pakorn Aiewsakun & Aris Katzourakis

Nature Communications 8, Article number: 13954 (2017)


Phylogenetics Retrovirus

Received: 13 May 2016 Accepted: 16 November 2016 Published online: 10 January 2017


Abstract

Very little is known about the ancient origin of retroviruses, but owing to the discovery of their ancient endogenous viral counterparts, their early history is beginning to unfold. Here we report 36 lineages of basal amphibian and fish foamy-like endogenous retroviruses (FLERVs). Phylogenetic analyses reveal that ray-finned fish FLERVs exhibit an overall co-speciation pattern with their hosts, while amphibian FLERVs might not. We also observe several possible ancient viral cross-class transmissions, involving lobe-finned fish, shark and frog FLERVs. Sequence examination and analyses reveal two major lineages of ray-finned fish FLERVs, one of which had gained two novel accessory genes within their extraordinarily large genomes. Our phylogenetic analyses suggest that this major retroviral lineage, and therefore retroviruses as a whole, have an ancient marine origin and originated together with, if not before, their jawed vertebrate hosts >450 million years ago in the Ordovician period, early Palaeozoic Era.

Acknowledgements

P.A. is funded by the Royal Thai Government, A.K. is funded by the Royal Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. We thank members of the research group for constructive comments and discussions.

Author information

Affiliations

Department of Zoology, University of Oxford, Oxford OX1 3PS, UK

Pakorn Aiewsakun & Aris Katzourakis

Contributions

P.A. and A.K. conceived the project, performed the analyses, interpreted the results and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Aris Katzourakis.