Princípio de redução unificado para a evolução da mutação, migração, e recombinação

sexta-feira, março 24, 2017

Unified reduction principle for the evolution of mutation, migration, and recombination

Lee Altenberg a,b,1, Uri Liberman c,1, and Marcus W. Feldman d,1,2

Author Affiliations

aInformation and Computer Sciences, University of Hawaii at Mānoa, Honolulu, HI 96822;

bKonrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria A3400;

cSchool of Mathematical Sciences, Tel Aviv University, Tel Aviv 69978, Israel;

dDepartment of Biology, Stanford University, Stanford, CA 94305-5020

Contributed by Marcus W. Feldman, January 31, 2017 (sent for review November 29, 2016; reviewed by Reinhard Burger, Yoh Iwasa, and Hamish G. Spencer)

Significance

Evolution by Darwinian natural selection can not only shape how organisms survive and reproduce, but also affect transmission of genetic and other information between generations. Modifier-gene models for the evolution of information transmission have revealed a universal tendency for more faithful transmission to evolve in populations at equilibrium where natural selection is balanced by errors in information transmission. This is shown to be a very general property of models that include mutation and migration under selection and recombination under selection on diploids. The breadth of this reduction principle focuses attention on the departures from its mathematical assumptions, which may explain those biological phenomena of information transmission between generations for which the reduction principle fails.




Abstract

Modifier-gene models for the evolution of genetic information transmission between generations of organisms exhibit the reduction principle: Selection favors reduction in the rate of variation production in populations near equilibrium under a balance of constant viability selection and variation production. Whereas this outcome has been proven for a variety of genetic models, it has not been proven in general for multiallelic genetic models of mutation, migration, and recombination modification with arbitrary linkage between the modifier and major genes under viability selection. We show that the reduction principle holds for all of these cases by developing a unifying mathematical framework that characterizes all of these evolutionary models.

mutation recombination dispersal modifier genes external stability

Footnotes

1L.A., U.L., and M.W.F. contributed equally to this work.

2To whom correspondence should be addressed. Email: mfeldman@stanford.edu.

Author contributions: L.A., U.L., and M.W.F. designed research, performed research, analyzed data, and wrote the paper.

Reviewers: R.B., University of Vienna; Y.I., Kyushu University; and H.G.S., University of Otago.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1619655114/-/DCSupplemental.

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Aumento maciço no alcance visual precedeu a origem dos vertebrados terrestres

Massive increase in visual range preceded the origin of terrestrial vertebrates

Malcolm A. MacIver a,b,c,1, Lars Schmitz d,e,1, Ugurcan Mugan c, Todd D. Murphey b, and Curtis D. Mobley f

Author Affiliations

aThe Neuroscience and Robotics Laboratory, Northwestern University, Evanston, IL 60208;

bDepartment of Mechanical Engineering, Northwestern University, Evanston, IL 60208;

cDepartment of Biomedical Engineering, Northwestern University, Evanston, IL 60208;

dW. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711;

eDinosaur Institute, Natural History Museum of Los Angeles County, Los Angeles, CA 90007;

fSection for Optical Oceanography, Sequoia Scientific, Inc., Bellevue, WA 98005

Edited by Neil H. Shubin, The University of Chicago, Chicago, IL, and approved January 24, 2017 (received for review September 17, 2016)


Significance

Starting 385 million years ago, certain fish slowly evolved into legged animals living on land. We show that eyes tripled in size and shifted from the sides to the top of the head long before fish modified their fins into limbs for land. Before permanent life on land, these animals probably hunted like crocodiles, looking at prey from just above the water line, where the vastly higher transparency of air enabled long-distance vision and selected for larger eyes. The “buena vista” hypothesis that our study forwards is that seeing opportunities far away provided an informational zip line to the bounty of invertebrate prey on land, aiding selection for limbs—first for brief forays onto land and eventually, for life there.

Abstract

The evolution of terrestrial vertebrates, starting around 385 million years ago, is an iconic moment in evolution that brings to mind images of fish transforming into four-legged animals. Here, we show that this radical change in body shape was preceded by an equally dramatic change in sensory abilities akin to transitioning from seeing over short distances in a dense fog to seeing over long distances on a clear day. Measurements of eye sockets and simulations of their evolution show that eyes nearly tripled in size just before vertebrates began living on land. Computational simulations of these animal’s visual ecology show that for viewing objects through water, the increase in eye size provided a negligible increase in performance. However, when viewing objects through air, the increase in eye size provided a large increase in performance. The jump in eye size was, therefore, unlikely to have arisen for seeing through water and instead points to an unexpected hybrid of seeing through air while still primarily inhabiting water. Our results and several anatomical innovations arising at the same time suggest lifestyle similarity to crocodiles. The consequent combination of the increase in eye size and vision through air would have conferred a 1 million-fold increase in the amount of space within which objects could be seen. The “buena vista” hypothesis that our data suggest is that seeing opportunities from afar played a role in the subsequent evolution of fully terrestrial limbs as well as the emergence of elaborated action sequences through planning circuits in the nervous system.

fish–tetrapod transition vision visual ecology terrestriality prospective cognition

Footnotes

1To whom correspondence may be addressed. Email: maciver@northwestern.edu or lschmitz@kecksci.claremont.edu.

Author contributions: M.A.M. and L.S. designed research; M.A.M. and L.S. performed research; T.D.M. contributed new reagents/analytic tools; M.A.M., L.S., U.M., and C.D.M. analyzed data; and M.A.M. and L.S. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: Code and data to reproduce these results is available at https://doi.org/10.5281/zenodo.321923.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1615563114/-/DCSupplemental.

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Modelos de expressão global de gene definem os principais domínios de tipo de célula e identidade de tecidos

Models of global gene expression define major domains of cell type and tissue identity

Andrew P. Hutchins Zhongzhou Yang Yuhao Li Fangfang He Xiuling Fu Xiaoshan Wang Dongwei Li Kairong Liu Jiangping He Yong Wang ... Show more

Nucleic Acids Res (2017) 45 (5): 2354-2367. 


Published: 30 January 2017 

Article history

Received: 07 December 2016 Revision Received: 16 January 2017 Accepted: 22 January 2017


Abstract

The current classification of cells in an organism is largely based on their anatomic and developmental origin. Cells types and tissues are traditionally classified into those that arise from the three embryonic germ layers, the ectoderm, mesoderm and endoderm, but this model does not take into account the organization of cell type-specific patterns of gene expression. Here, we present computational models for cell type and tissue specification derived from a collection of 921 RNA-sequencing samples from 272 distinct mouse cell types or tissues. In an unbiased fashion, this analysis accurately predicts the three known germ layers. Unexpectedly, this analysis also suggests that in total there are eight major domains of cell type-specification, corresponding to the neurectoderm, neural crest, surface ectoderm, endoderm, mesoderm, blood mesoderm, germ cells and the embryonic domain. Further, we identify putative genes responsible for specifying the domain and the cell type. This model has implications for understanding trans-lineage differentiation for stem cells, developmental cell biology and regenerative medicine.

Topic: gene expression mesoderm endoderm computer simulation ectoderm embryo genes germ cells neural crest mice

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Ressacas de equinodermas paleozóicos: despertando no Triássico

Paleozoic echinoderm hangovers: Waking up in the Triassic

Ben Thuy1, Hans Hagdorn2 and Andy S. Gale3

- Author Affiliations

1Natural History Museum Luxembourg, Department of Palaeontology, 24 rue Münster, Luxembourg 2160, Luxembourg

2Muschelkalkmuseum Ingelfingen, Schlossstrasse 11, 74653 Ingelfingen, Germany

3School of Earth and Environmental Sciences, University of Portsmouth, Burnaby Building, Burnaby Road, Portsmouth PO1 3QL, Great Britain


Abstract

Echinoderms are among the marine invertebrates that underwent the most severe losses at the end-Permian extinction. The prevailing paradigm claims an extreme bottleneck with only very few, if not single, holdovers ("hangovers" herein) sparking the post-Paleozoic radiation. Here we identify previously overlooked Triassic echinoids, ophiuroids, and asteroids as unambiguous members of Paleozoic stem groups. These echinoderm hangovers occurred almost worldwide and had spread into a wide range of paleoenvironments by the Late Triassic. Our discovery challenges fundamentals of echinoderm evolution with respect to end-Permian survival and sheds new light on the early evolution of the modern clades, in particular on Triassic ghost lineages (i.e., inferred but undocumented fossil record) of the crown-group look-alikes of the Paleozoic hangovers.

Received 21 December 2016. Revision received 3 February 2017. Accepted 11 February 2017.

©The Authors

Gold Open Access: This paper is published under the terms of the CC-BY license.

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Cientistas revelam estrutura cromossômica escondida no genoma da bactéria Mycoplasma pneumoniae

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Marie Trussart, Eva Yus, Sira Martinez, Davide Baù, Yuhei O. Tahara, Thomas Pengo, Michael Widjaja, Simon Kretschmer, Jim Swoger, Steven Djordjevic, Lynne Turnbull, Cynthia Whitchurch, Makoto Miyata, Marc A. Marti-Renom, Maria Lluch-Senar & Luís Serrano

Nature Communications 8, Article number: 14665 (2017)


Download Citation

Chromosomes Computational models Molecular modelling

Received: 04 November 2016 Accepted: 20 January 2017 Published online: 08 March 2017

Figure 6: Models of bacterial chromosome organization.
Models of nucleoid organization with Ori and Ter represented by red and purple circles. (a) Model of the E. coli genome with the four macro-domains Ori, Ter, left, right, represented by circles in red, purple, pink and blue, respectively. (b) Model of the B. subtilis genome adapted from ref. 52. (c) 3D models of the M. pneumoniae genome conformation.

Abstract

DNA-binding proteins are central regulators of chromosome organization; however, in genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of such bacteria adopt defined three-dimensional structures remains unexplored. Here we combine Hi-C and super-resolution microscopy to determine the structure of the Mycoplasma pneumoniae chromosome at a 10 kb resolution. We find a defined structure, with a global symmetry between two arms that connect opposite poles, one bearing the chromosomal Ori and the other the midpoint. Analysis of local structures at a 3 kb resolution indicates that the chromosome is organized into domains ranging from 15 to 33 kb. We provide evidence that genes within the same domain tend to be co-regulated, suggesting that chromosome organization influences transcriptional regulation, and that supercoiling regulates local organization. This study extends the current understanding of bacterial genome organization and demonstrates that a defined chromosomal structure is a universal feature of living systems.

Acknowledgements

We thank Dr Besray Ünal and Dr Ivan Junier for providing the co-expression data, and Dr Ivan Junier and Dr François Serra for helpful suggestions. We are also grateful to Dr Jae-Seong Yang for fruitful discussions and Tony Ferrar for critical manuscript revision and language editing (http://www.theeditorsite.com). The research leading to these results was funded by the European Union Seventh Framework Programme (FP7/2007-2013 to L.S.), through the European Research Council, under grant agreement 232913 to L.S. and 609989 to M.A.M-R., the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 634942 to L.S, the Fundación Botín to L.S., the Spanish Ministry of Economy and Competitiveness (BIO2007-61762 to L.S. and BFU2013–47736-P to M.A.M.-R., the National Plan of R+D+i, the ISCIII-Subdirección General de Evaluación y Fomento de la Investigación- (PI10/01702 to L.S.), the Human Frontiers Science Program (RGP0044 to M.A.M.-R.), the ERASynBio/MINECO Grant PCIN-2015-125 to L.S, and the European Regional Development Fund (ERDF) to L.S. We acknowledge support from the Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’ (SEV-2012-0208). We acknowledge the support of the CERCA Programme / Generalitat de Catalunya. This paper reflects only the authorś views and the Union is not liable for any use that may be made of the information contained therein. Library preparation and sequencing was done in the CRG Genomics Unit and high resolution light microscopy analysis in the CRG microscopy unit.

Author information

Affiliations

EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain

Marie Trussart, Eva Yus, Sira Martinez, Thomas Pengo, Jim Swoger, Maria Lluch-Senar & Luís Serrano

Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain

Marie Trussart, Eva Yus, Jim Swoger, Marc A. Marti-Renom, Maria Lluch-Senar & Luís Serrano

Gene Regulation, Stem Cells and Cancer Program. Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain

Davide Baù & Marc A. Marti-Renom

CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain

Davide Baù & Marc A. Marti-Renom

Department of Biology, Graduate School of Science, Osaka City University, 558-8585 Osaka, Japan

Yuhei O. Tahara & Makoto Miyata

OCU Advanced Research Institute for Natural Science and Technology (OCARNA), Osaka City University, 558-8585 Osaka, Japan

Yuhei O. Tahara & Makoto Miyata

Advanced Light Microscopy Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain

Thomas Pengo

The ithree Institute, The University of Technology Sydney, Sydney, New South Wales 2007, Australia

Michael Widjaja, Steven Djordjevic, Lynne Turnbull & Cynthia Whitchurch

Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany

Simon Kretschmer

Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain

Marc A. Marti-Renom & Luís Serrano

Contributions

M.T. performed super-resolution imaging experiments, DAPI and EM experiments, collected and analysed the data and wrote the manuscript; E.Y. designed, optimized and performed Hi-C experiments, obtained the gene expression data and reviewed the manuscript; C.M. performed Hi-C experiments and the FISH for super-resolution imaging experiments. D.B. implemented the simulation of 3D models and reviewed the manuscript. Y.O.T. performed EM experiments. T.P. designed a pipeline to analyse super-resolution images. MW cultured M. pneumoniae and performed the 3D-SIM experiments. S.K. performed initial Hi-C experiments and reviewed the manuscript. J.S. performed 3D reconstruction from EM images; SPD designed and supervised the mycoplasma imaging experiments and reviewed the manuscript. LT imaged the slides on the OMX microscope. MW, SPD, LT and CBW analysed the 3D-SIM data and generated the 3D models for the chromosome volume measurements. M.M. designed and supervised EM experiments and reviewed the manuscript. M.A.M.-R. supervised the computational 3D modelling and reviewed the manuscript. M.L.-S. designed and supervised super-resolution imaging experiments and reviewed the manuscript. and L.S. supervised the study and reviewed the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Marc A. Marti-Renom or Maria Lluch-Senar or Luís Serrano.

Dois códigos genéticos: sintaxe repetitiva para RNAs não codificantes; sintaxe não repetitiva para arquivos de DNA

quinta-feira, março 23, 2017

Communicative & Integrative Biology 
Volume 10, 2017 - Issue 2

Two genetic codes: Repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives


Article: e1297352 | Received 14 Feb 2017, Accepted 16 Feb 2017, Published online: 15 Mar 2017




ABSTRACT

Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share—as main characteristics—a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are coherent with the differences of the functions they represent. Interestingly, these 2 genetic codes resemble the function of all natural languages, i.e., the repetitive non-coding sequences serve as appropriate tool for organization, coordination and regulation of group behavior, and the non-repetitive coding sequences are for conservation of instrumental constructions, plans, blueprints for complex protein-body architecture. This differentiation may help to better understand RNA group behavioral motifs.

KEYWORDS: DNA, Repetitive sequences, RNA stem loops, RNA group identities, RNA

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

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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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