A dinâmica da rede turbulenta da evolução microbiana e a Árvore da Vida estatística

J Mol Evol (2015) 80:244–250

DOI 10.1007/s00239-015-9679-7

The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life

Eugene V. Koonin 1

Received: 18 March 2015 / Accepted: 8 April 2015 / Published online: 18 April 2015

The Author(s) 2015. This article is published with open access at Springerlink.com

Source/Fonte: Seed

Abstract 

The wide spread and high rate of gene exchange and loss in the prokaryotic world translate into ‘‘network genomics’’. The rates of gene gain and loss are comparable with the rate of point mutations but are substantially greater than the duplication rate. Thus, evolution of prokaryotes is primarily shaped by gene gain and loss. These processes are essential to prevent mutational meltdown of microbial populations by stopping Muller’s ratchet and appear to trigger emergence of major novel clades by opening up new ecological niches. At least some bacteria and archaea seem to have evolved dedicated devices for gene transfer. Despite the dominance of gene gain and loss, evolution of genes is intrinsically tree-like. The significant coherence between the topologies of numerous gene trees, particularly those for (nearly) universal genes, is compatible with the concept of a statistical tree of life, which forms the framework for reconstruction of the evolutionary processes in the prokaryotic world.

Keywords Microbial evolution Phylogenetic trees Horizontal gene transfer Muller’s ratchet Evolvability

FREE PDF GRATIS: Journal of Molecular Evolution

Como os genes são regulados - fatores de transcrição. Mero acaso, fortuita necessidade ou design inteligente?

Uma nova pesquisa rastreia "a ascensão dos gigantes do oceano."

The rise of ocean giants: maximum body size in Cenozoic marine mammals as an indicator for productivity in the Pacific and Atlantic Oceans

Nicholas D. Pyenson, Geerat J. Vermeij

Published 5 July 2016.DOI: 10.1098/rsbl.2016.0186

Fig. 1. (a,b) Maximal body size in North Pacific and North Atlantic marine mammal herbivores, and (c,d) similarly for mammalian filter-feeders, during the Cenozoic. PhyloPics of herbivores, except Hydrodamalis, by Steven Traver.

Abstract

Large consumers have ecological influence disproportionate to their abundance, although this influence in food webs depends directly on productivity. Evolutionary patterns at geologic timescales inform expectations about the relationship between consumers and productivity, but it is very difficult to track productivity through time with direct, quantitative measures. Based on previous work that used the maximum body size of Cenozoic marine invertebrate assemblages as a proxy for benthic productivity, we investigated how the maximum body size of Cenozoic marine mammals, in two feeding guilds, evolved over comparable temporal and geographical scales. First, maximal size in marine herbivores remains mostly stable and occupied by two different groups (desmostylians and sirenians) over separate timeframes in the North Pacific Ocean, while sirenians exclusively dominated this ecological mode in the North Atlantic. Second, mysticete whales, which are the largest Cenozoic consumers in the filter-feeding guild, remained in the same size range until a Mio-Pliocene onset of cetacean gigantism. Both vertebrate guilds achieved very large size only recently, suggesting that different trophic mechanisms promoting gigantism in the oceans have operated in the Cenozoic than in previous eras.

Data accessibility

All additional data are in the electronic supplementary material file.

Authors' contributions

N.D.P collected the data. N.D.P. and G.J.V. analysed the data, wrote the manuscript, approved the final draft of the manuscript and agree to be held accountable for the content herein.

Competing interests

We have no competing interests.

Funding

N.D.P. is supported by the Smithsonian Institution, its Remington Kellogg Fund, and the Basis Foundation. All figures are our own.

Acknowledgements

We thank J. Vélez-Juarbe for help with data collection and four anonymous reviewers along with A. H. Fleming, J. A. Goldbogen, A. O'Dea, J. F. Parham, C. M. Peredo and J. Vélez-Juarbe for helpful comments.

Received March 3, 2016. Accepted June 13, 2016.

© 2016 The Authors.

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

FREE PDF GRATIS: Biology Letters

Nova pesquisa desafia hipótese evolucionista antiga sobre o voo das aves

The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents

Evolutionary Studies Paleontology

T. Alexander Dececchi​1, Hans C.E. Larsson2, Michael B. Habib3,4

July 7, 2016

Source/Fonte:
“Dinosaur into Bird” artwork by paleoartist Mark Hallett, part of “The Dinosaur Postcard Book” (1987) from Running Press.

Abstract

Background: Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping.

Methods: Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground truthed using extant avians we seek to test if an incipient flight stroke may have contributed sufficient force to permit flap running, WAIR, or leaping takeoff along the phylogenetic lineage from Coelurosauria to birds.

Results: None of these behaviours were found to meet the biomechanical threshold requirements before Paraves. Neither was there a continuous trend of refinement for any of these biomechanical performances across phylogeny nor a signal of universal applicability near the origin of birds. None of these flap-based locomotory models appear to have been a major influence on pre-flight character acquisition such as pennaceous feathers, suggesting non-locomotory behaviours, and less stringent locomotory behaviours such as balancing and braking, played a role in the evolution of the maniraptoran wing and nascent flight stroke. We find no support for widespread prevalence of WAIR in non-avian theropods, but can’t reject its presence in large winged, small-bodied taxa like Microraptor and Archaeopteryx.

Discussion: Using our first principles approach we find that “near flight” locomotor behaviors are most sensitive to wing area, and that non-locomotory related selection regimes likely expanded wing area well before WAIR and other such behaviors were possible in derived avians. These results suggest that investigations of the drivers for wing expansion and feather elongation in theropods need not be intrinsically linked to locomotory adaptations, and this separation is critical for our understanding of the origin of powered flight and avian evolution.

Cite this as

Dececchi TA, Larsson HCE, Habib MB. (2016) The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents. PeerJ 4:e2159 https://doi.org/10.7717/peerj.2159

FREE PDF GRATIS: PeerJ

Base de dados de literatura de Física de Alta Energia

High-Energy Physics Literature Database

Sobre a estratégia da natureza em atribuir multiplicidade ao código genético

On Nature’s Strategy for Assigning Genetic Code Multiplicity

Simone Gardini, Sara Cheli, Silvia Baroni, Gabriele Di Lascio, Guido Mangiavacchi, Nicholas Micheletti, Carmen Luigia Monaco, Lorenzo Savini, Davide Alocci, Stefano Mangani, Neri Niccolai 

Published: February 5, 2016 http://dx.doi.org/10.1371/journal.pone.0148174

Abstract

Genetic code redundancy would yield, on the average, the assignment of three codons for each of the natural amino acids. The fact that this number is observed only for incorporating Ile and to stop RNA translation still waits for an overall explanation. Through a Structural Bioinformatics approach, the wealth of information stored in the Protein Data Bank has been used here to look for unambiguous clues to decipher the rationale of standard genetic code (SGC) in assigning from one to six different codons for amino acid translation. Leu and Arg, both protected from translational errors by six codons, offer the clearest clue by appearing as the most abundant amino acids in protein-protein and protein-nucleic acid interfaces. Other SGC hidden messages have been sought by analyzing, in a protein structure framework, the roles of over- and under-protected amino acids.

Citation: Gardini S, Cheli S, Baroni S, Di Lascio G, Mangiavacchi G, Micheletti N, et al. (2016) On Nature’s Strategy for Assigning Genetic Code Multiplicity. PLoS ONE 11(2): e0148174. doi:10.1371/journal.pone.0148174

Editor: Denis Dupuy, Inserm U869, FRANCE

Received: October 7, 2015; Accepted: January 13, 2016; Published: February 5, 2016

Copyright: © 2016 Gardini et al. 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.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: The authors have no support or funding to report.

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

FREE PDF GRATIS: PLoS One

A distinção espectral em animais daltônicos através de aberração cromática e formato de pupila

Spectral discrimination in color blind animals via chromatic aberration and pupil shape

Alexander L. Stubbs a,b,1,2 and Christopher W. Stubbs c,d,2

Author Affiliations

aMuseum of Vertebrate Zoology, University of California, Berkeley, CA 94720;

bDepartment of Integrative Biology, University of California, Berkeley, CA 94720;

cDepartment of Physics, Harvard University, Cambridge, MA 02138;

dDepartment of Astronomy, Harvard University, Cambridge, MA 02138

Edited by John Mollon, University of Cambridge, Cambridge, United Kingdom, and accepted by Editorial Board Member Jeremy Nathans May 23, 2016 (received for review December 13, 2015)

Significance

We describe a means of obtaining spectral information using the principles of physical optics and an off-axis pupil shape without requiring spectrally distinct photoreceptor classes. The mechanism described here offers a possible solution to a long-standing puzzle in marine animals: cephalopods dramatically change color for both producing chromatically matched camouflage and signaling to conspecifics, despite having a single photoreceptor channel. The ability of these animals to achieve such excellent color matching to their surroundings, despite being “color blind” in the traditional sense, can be understood if they exploit chromatic aberration to deduce spectral information. The bizarre off-axis pupils of these animals can be understood as an adaptation that maximizes spectral information, even at the expense of image acuity.

Abstract

We present a mechanism by which organisms with only a single photoreceptor, which have a monochromatic view of the world, can achieve color discrimination. An off-axis pupil and the principle of chromatic aberration (where different wavelengths come to focus at different distances behind a lens) can combine to provide “color-blind” animals with a way to distinguish colors. As a specific example, we constructed a computer model of the visual system of cephalopods (octopus, squid, and cuttlefish) that have a single unfiltered photoreceptor type. We compute a quantitative image quality budget for this visual system and show how chromatic blurring dominates the visual acuity in these animals in shallow water. We quantitatively show, through numerical simulations, how chromatic aberration can be exploited to obtain spectral information, especially through nonaxial pupils that are characteristic of coleoid cephalopods. We have also assessed the inherent ambiguity between range and color that is a consequence of the chromatic variation of best focus with wavelength. This proposed mechanism is consistent with the extensive suite of visual/behavioral and physiological data that has been obtained from cephalopod studies and offers a possible solution to the apparent paradox of vivid chromatic behaviors in color blind animals. Moreover, this proposed mechanism has potential applicability in organisms with limited photoreceptor complements, such as spiders and dolphins.

spectral discrimination chromatic aberration color vision pupil shape cephalopod

FREE PDF GRATIS: PNAS

Espaço, Tempo e Matéria (e como eles importam): discussão sobre alguns insights metafísicos fornecidos por nossas melhores teorias físicas

Space, Time, and (how they) Matter: a Discussion about some Metaphysical Insights Provided by our Best Fundamental Physical Theories

Allori, Valia (2017) Space, Time, and (how they) Matter: a Discussion about some Metaphysical Insights Provided by our Best Fundamental Physical Theories. [Preprint]

Abstract

This paper is a brief (and hopelessly incomplete) non-standard introduction to the philosophy of space and time. It is an introduction because I plan to give an overview of what I consider some of the main questions about space and time: Is space a substance over and above matter? How many dimensions does it have? Is space-time fundamental or emergent? Does time have a direction? Does time even exist? Nonetheless, this introduction is not standard because I conclude the discussion by presenting the material with an original spin, guided by a particular understanding of fundamental physical theories, the so-called primitive ontology approach.

Keywords: space, time, space-time, substantivalism, relationism, wave function realism, primitive ontology,string theory, dualities, quantum gravity, emergence, unreality of time

Allori, Valia vallori@niu.edu 

FREE PDF GRATIS: PhilSci

Uma 'ponte' de carbono entre os tecidos nervosos

3D meshes of carbon nanotubes guide functional reconnection of segregated spinal explants

Sadaf Usmani1,*, Emily Rose Aurand2,*, Manuela Medelin2, Alessandra Fabbro2, Denis Scaini2,3, Jummi Laishram2, Federica B. Rosselli1, Alessio Ansuini1, Davide Zoccolan1, Manuela Scarselli4, Maurizio De Crescenzi4, Susanna Bosi5, Maurizio Prato5,6,7,† and Laura Ballerini1,†

+ Author Affiliations

↵†Corresponding author. Email: laura.ballerini@sissa.it (L.B.); prato@units.it (M.P.)

↵* These authors contributed equally to this work.

Science Advances 15 Jul 2016: Vol. 2, no. 7, e1600087

DOI: 10.1126/sciadv.1600087

Abstract

In modern neuroscience, significant progress in developing structural scaffolds integrated with the brain is provided by the increasing use of nanomaterials. We show that a multiwalled carbon nanotube self-standing framework, consisting of a three-dimensional (3D) mesh of interconnected, conductive, pure carbon nanotubes, can guide the formation of neural webs in vitro where the spontaneous regrowth of neurite bundles is molded into a dense random net. This morphology of the fiber regrowth shaped by the 3D structure supports the successful reconnection of segregated spinal cord segments. We further observed in vivo the adaptability of these 3D devices in a healthy physiological environment. Our study shows that 3D artificial scaffolds may drive local rewiring in vitro and hold great potential for the development of future in vivo interfaces.

Keywords Nanomaterials carbon nanotubes organotypic cultures spinal cord microscopy

Copyright © 2016, 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.

FREE PDF GRATIS: Science Advances

Caminhos da demetilação do DNA: insights recentes

DNA Demethylation Pathways: Recent Insights

Submit a Paper

Cong-jun Li

Genetics & Epigenetics 2013:5 43-49

Review

Published on 28 Jul 2013

DOI: 10.4137/GEG.S12143

Source/Fonte: Nature - Epigenetics: Reading the second genomic code

Abstract

DNA methylation is a major epigenetic regulatory mechanism for gene expression and cell differentiation. Until recently, it was still unclear how unmethylated regions in mammalian genomes are protected from de novo methylation and whether or not active demethylating activity is involved. Even the role of molecules and the mechanisms underlying the processes of active demethylation itself is blurred. Emerging sequencing technologies have led to recent insights into the dynamic distribution of DNA methylation during development and the role of this epigenetic mark within a distinct genome context, such as the promoters, exons, or imprinted control regions. This review summarizes recent insights on the dynamic nature of DNA methylation and demethylation, as well as the mechanisms regulating active DNA demethylation in mammalian cells, which have been fundamental research interests in the field of epigenomics.

FREE PDF GRATIS: Genetics and Epigenetics

Lançamento do livro Undeniable: How Biology Confirms Our Intuition That Life Is Designed, de Doug Axe

Tentando desvendar o mistério da replicação do DNA

Template-dependent nucleotide addition in the reverse (3′-5′) direction by Thg1-like protein

Shoko Kimura1,*, Tateki Suzuki1,*, Meirong Chen1, Koji Kato1,2, Jian Yu2, Akiyoshi Nakamura3, Isao Tanaka2 and Min Yao1,2,†

+ Author Affiliations

↵†Corresponding author. E-mail: yao@castor.sci.hokudai.ac.jp

↵* These authors contributed equally to this work.

Science Advances 25 Mar 2016:

Vol. 2, no. 3, e1501397

DOI: 10.1126/sciadv.1501397

Structure of the MaTLP complex with ppptRNAPhe

Abstract

Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner. The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition. Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3′-5′ direction. The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion. When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. That the 3′-5′ elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode.

Keywords biomolecules nucleotides tRNA3′-5′ addition reverse polymerization TLPcrystal structure

Copyright © 2016, 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.

FREE PDF GRATIS: Science Advances

Organismos com códigos genéticos alternativos sem códons de parada dedicados

Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination

Estienne Carl Swart, Valentina Serra, Giulio Petroni, Mariusz Nowackicorrespondenceemail

Publication stage: In Press Corrected Proof

Open Access

DOI: http://dx.doi.org/10.1016/j.cell.2016.06.020

Open access funded by European Research Council

Highlights

• Alternative nuclear genetic codes continue to be discovered in ciliates

• Genetic codes with stops and all their codons encoding standard amino acids exist

• Transcript ends may distinguish stop codons as such in ambiguous genetic codes

• The ability to resolve genetic code ambiguity may enable genetic code evolution

Summary

The prevailing view of the nuclear genetic code is that it is largely frozen and unambiguous. Flexibility in the nuclear genetic code has been demonstrated in ciliates that reassign standard stop codons to amino acids, resulting in seven variant genetic codes, including three previously undescribed ones reported here. Surprisingly, in two of these species, we find efficient translation of all 64 codons as standard amino acids and recognition of either one or all three stop codons. How, therefore, does the translation machinery interpret a “stop” codon? We provide evidence, based on ribosomal profiling and “stop” codon depletion shortly before coding sequence ends, that mRNA 3′ ends may contribute to distinguishing stop from sense in a context-dependent manner. We further propose that such context-dependent termination/readthrough suppression near transcript ends enables genetic code evolution.

Received: August 11, 2015; Received in revised form: April 19, 2016; Accepted: June 6, 2016; Published: July 14, 2016

© 2016 The Author(s). Published by Elsevier Inc.

FREE PDF GRATIS: Cell

Morte celular: como uma proteína conduz as células do sistema imunológico ao suicídio

GSDMD membrane pore formation constitutes the mechanism of pyroptotic cell death

Author affiliations

Lorenzo Sborgi1,†, Sebastian Rühl1,†, Estefania Mulvihill2, Joka Pipercevic1, Rosalie Heilig1, Henning Stahlberg1, Christopher J Farady3, Daniel J Müller2, Petr Broz*,1 and Sebastian Hiller*,1

1Biozentrum, University of Basel, Basel, Switzerland

2Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel, Switzerland

3Novartis Institutes for BioMedical Research Forum 1, Basel, Switzerland

↵* Corresponding author. Tel: +41 6126 72342; E‐mail: petr.broz@unibas.ch

Corresponding author. Tel: +41 6126 72082; E‐mail: sebastian.hiller@unibas.ch

↵† These authors contributed equally to this work

DOI 10.15252/embj.201694696 | Published online 14.07.2016

The EMBO Journal (2016) e201694696

Abstract

Pyroptosis is a lytic type of cell death that is initiated by inflammatory caspases. These caspases are activated within multi‐protein inflammasome complexes that assemble in response to pathogens and endogenous danger signals. Pyroptotic cell death has been proposed to proceed via the formation of a plasma membrane pore, but the underlying molecular mechanism has remained unclear. Recently, gasdermin D (GSDMD), a member of the ill‐characterized gasdermin protein family, was identified as a caspase substrate and an essential mediator of pyroptosis. GSDMD is thus a candidate for pyroptotic pore formation. Here, we characterize GSDMD function in live cells and in vitro. We show that the N‐terminal fragment of caspase‐1‐cleaved GSDMD rapidly targets the membrane fraction of macrophages and that it induces the formation of a plasma membrane pore. In vitro, the N‐terminal fragment of caspase‐1‐cleaved recombinant GSDMD tightly binds liposomes and forms large permeability pores. Visualization of liposome‐inserted GSDMD at nanometer resolution by cryo‐electron and atomic force microscopy shows circular pores with variable ring diameters around 20 nm. Overall, these data demonstrate that GSDMD is the direct and final executor of pyroptotic cell death.

FREE PDF GRATIS: The EMBO Journal

Dinâmica da evolução dental dos dinossauros ornitópodes

Dynamics of dental evolution in ornithopod dinosaurs

Edward Strickson, Albert Prieto-Márquez, Michael J. Benton & Thomas L. Stubbs

Scientific Reports 6, Article number: 28904 (2016)

doi:10.1038/srep28904

Download Citation

Palaeontology

Received: 20 April 2016 Accepted: 10 June 2016 Published online: 14 July 2016

Abstract

Ornithopods were key herbivorous dinosaurs in Mesozoic terrestrial ecosystems, with a variety of tooth morphologies. Several clades, especially the ‘duck-billed’ hadrosaurids, became hugely diverse and abundant almost worldwide. Yet their evolutionary dynamics have been disputed, particularly whether they diversified in response to events in plant evolution. Here we focus on their remarkable dietary adaptations, using tooth and jaw characters to examine changes in dental disparity and evolutionary rate. Ornithopods explored different areas of dental morphospace throughout their evolution, showing a long-term expansion. There were four major evolutionary rate increases, the first among basal iguanodontians in the Middle-Late Jurassic, and the three others among the Hadrosauridae, above and below the split of their two major clades, in the middle of the Late Cretaceous. These evolutionary bursts do not correspond to times of plant diversification, including the radiation of the flowering plants, and suggest that dental innovation rather than coevolution with major plant clades was a major driver in ornithopod evolution.

FREE PDF GRATIS: Scientific Reports

Casal de proteínas sinalizam para as células armazenar e lembrar de informação: mero acaso, fortuita necessidade ou design inteligente?

Protein Dimerization Generates Bistability in Positive Feedback Loops

Chieh Hsu3, Vincent Jaquet3, Mumun Gencoglu, Attila Becskei correspondence email

3Co-first author

Publication stage: In Press Corrected Proof

Open Access

DOI: http://dx.doi.org/10.1016/j.celrep.2016.06.072

Highlights

•RNA stem loops tune translation rates over two orders of magnitude

•Positive feedback loops with reduced translation generate bistable cell fates

•Dimerizing transcription factors generate bistability without cooperative binding

Summary

Bistability plays an important role in cellular memory and cell-fate determination. A positive feedback loop can generate bistability if it contains ultrasensitive molecular reactions. It is often difficult to detect bistability based on such molecular mechanisms due to its intricate interaction with cellular growth. We constructed transcriptional feedback loops in yeast. To eliminate growth alterations, we reduced the protein levels of the transcription factors by tuning the translation rates over two orders of magnitude with designed RNA stem loops. We modulated two ultrasensitive reactions, homodimerization and the cooperative binding of the transcription factor to the promoter. Either of them is sufficient to generate bistability on its own, and when acting together, a particularly robust bistability emerges. This bistability persists even in the presence of a negative feedback loop. Given that protein homodimerization is ubiquitous, it is likely to play a major role in the behavior of regulatory networks.

Received: September 24, 2015; Received in revised form: May 22, 2016; Accepted: June 16, 2016; Published: July 14, 2016

© 2016 The Author(s). Published by Elsevier Inc.

FREE PDF GRATIS: Cell Reports

Os vírus, quem diria, são um condutor dominante de adaptação de proteína em mamíferos

Viruses are a dominant driver of protein adaptation in mammals

David Enard Le Cai Carina Gwennap Dmitri A Petrov

Stanford University, United States

DOI: http://dx.doi.org/10.7554/eLife.12469

Published May 17, 2016

Cite as eLife 2016;5:e12469

Abstract

Viruses interact with hundreds to thousands of proteins in mammals, yet adaptation against viruses has only been studied in a few proteins specialized in antiviral defense. Whether adaptation to viruses typically involves only specialized antiviral proteins or affects a broad array of virus-interacting proteins is unknown. Here, we analyze adaptation in ~1300 virus-interacting proteins manually curated from a set of 9900 proteins conserved in all sequenced mammalian genomes. We show that viruses (i) use the more evolutionarily constrained proteins within the cellular functions they interact with and that (ii) despite this high constraint, virus-interacting proteins account for a high proportion of all protein adaptation in humans and other mammals. Adaptation is elevated in virus-interacting proteins across all functional categories, including both immune and non-immune functions. We conservatively estimate that viruses have driven close to 30% of all adaptive amino acid changes in the part of the human proteome conserved within mammals. Our results suggest that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes.

DOI: http://dx.doi.org/10.7554/eLife.12469.001

eLife digest

When an environmental change occurs, species are able to adapt in response due to mutations in their DNA. Although these mutations occur randomly, by chance some of them make the organism better suited to their new environment. These are known as adaptive mutations.

In the past ten years, evolutionary biologists have discovered a large number of adaptive mutations in a wide variety of locations in the genome – the complete set of DNA – of humans and other mammals. The fact that adaptive mutations are so pervasive is puzzling. What kind of environmental pressure could possibly drive so much adaptation in so many parts of the genome?

Viruses are ideal suspects since they are always present, ever-changing and interact with many different locations of the genome. However, only a few mammalian genes had been studied to see whether they adapt to the presence of viruses. By studying thousands of proteins whose genetic sequence is conserved in all mammalian species, Enard et al. now suggest that viruses explain a substantial part of the total adaptation observed in the genomes of humans and other mammals. For instance, as much as one third of the adaptive mutations that affect human proteins seem to have occurred in response to viruses.

So far, Enard et al. have only studied old adaptations that occurred millions of years ago in humans and other mammals. Further studies will investigate how much of the recent adaptation in the human genome can also be explained by the arms race against viruses.

DOI: http://dx.doi.org/10.7554/eLife.12469.002

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Acesso livre a dados de biodiversidade

Global Biodiversity Information Facility

Free and Open Access to Biodiversity Data/Acesso Livre a Dados de Biodiversidade

Dinossauro predador tinha braços pequeninos como do Tyrannosaurus rex

An Unusual New Theropod with a Didactyl Manus from the Upper Cretaceous of Patagonia, Argentina

Sebastián Apesteguía, Nathan D. Smith, Rubén Juárez Valieri, Peter J. Makovicky 

Published: July 13, 2016 http://dx.doi.org/10.1371/journal.pone.0157793

Abstract

Background

Late Cretaceous terrestrial strata of the Neuquén Basin, northern Patagonia, Argentina have yielded a rich fauna of dinosaurs and other vertebrates. The diversity of saurischian dinosaurs is particularly high, especially in the late Cenomanian-early Turonian Huincul Formation, which has yielded specimens of rebacchisaurid and titanosaurian sauropods, and abelisaurid and carcharodontosaurid theropods. Continued sampling is adding to the known vertebrate diversity of this unit.

Methodology/ Principal Findings

A new, partially articulated mid-sized theropod was found in rocks from the Huincul Formation. It exhibits a unique combination of traits that distinguish it from other known theropods justifying erection of a new taxon, Gualicho shinyae gen. et sp. nov. Gualicho possesses a didactyl manus with the third digit reduced to a metacarpal splint reminiscent of tyrannosaurids, but both phylogenetic and multivariate analyses indicate that didactyly is convergent in these groups. Derived characters of the scapula, femur, and fibula supports the new theropod as the sister taxon of the nearly coeval African theropod Deltadromeus and as a neovenatorid carcharodontosaurian. A number of these features are independently present in ceratosaurs, and Gualicho exhibits an unusual mosaic of ceratosaurian and tetanuran synapomorphies distributed throughout the skeleton.

Conclusions/ Significance

Gualicho shinyae gen. et sp. nov. increases the known theropod diversity of the Huincul Formation and also represents the first likely neovenatorid from this unit. It is the most basal tetatanuran to exhibit common patterns of digit III reduction that evolved independently in a number of other tetanuran lineages. A close relationship with Deltadromaeus from the Kem Kem beds of Niger adds to the already considerable biogeographic similarity between the Huincul Formation and coeval rock units in North Africa.

Citation: Apesteguía S, Smith ND, Juárez Valieri R, Makovicky PJ (2016) An Unusual New Theropod with a Didactyl Manus from the Upper Cretaceous of Patagonia, Argentina. PLoS ONE 11(7): e0157793. doi:10.1371/journal.pone.0157793

Editor: Andrew A. Farke, Raymond M. Alf Museum of Paleontology, UNITED STATES

Received: December 11, 2015; Accepted: June 2, 2016; Published: July 13, 2016

Copyright: © 2016 Apesteguía et al. 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.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: Fieldwork was supported by funding from the Field Museum of Natural History to PJM. PJM and NDS were supported by grants from the US National Science Foundation over the course of this work (EAR 0228607; ANT 0838925; PLR 1246379; and EAR 1349554). SA was supported by the Consejo Nacional de Ciencia y Tecnologia.

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

FREE PDF GRATIS: PLoS One

Pesquisadores "provam" a existência de vórtice gravitacional em buracos negros

A quasi-periodic modulation of the iron line centroid energy in the black hole binary H1743−322

Adam Ingram1,★, Michiel van der Klis1, Matthew Middleton2, Chris Done3, Diego Altamirano4, Lucy Heil1, Phil Uttley1 and Magnus Axelsson5

-Author Affiliations

1Anton Pannekoek Institute for Astronomy, University of Amsterdam, Science Park 904, NL-1098 XH Amsterdam, the Netherlands

2Institute of Astronomy, Cambridge University, Madingley Road, Cambridge CB3 0HA, UK

3Center for Extragalactic Astronomy, Department of Physics, University of Durham, South Road, Durham DH1 3LE, UK

4Department of Physics & Astronomy, University of Southampton, Southampton, Hampshire SO17 1BJ, UK

5Department of Physics, Tokyo Metropolitan University, Minami Osawa 1-1, Hachioji, Tokyo 192-0397, Japan

↵★E-mail: a.r.ingram@uva.nl

Accepted 2016 May 19. Received 2016 May 19. In original form 2016 April 15. First published online May 25, 2016.

Source/Fonte: ESA/ATG medialab via Spaceanswers

Abstract

Accreting stellar-mass black holes often show a ‘Type-C’ quasi-periodic oscillation (QPO) in their X-ray flux and an iron emission line in their X-ray spectrum. The iron line is generated through continuum photons reflecting off the accretion disc, and its shape is distorted by relativistic motion of the orbiting plasma and the gravitational pull of the black hole. The physical origin of the QPO has long been debated, but is often attributed to Lense–Thirring precession, a General Relativistic effect causing the inner flow to precess as the spinning black hole twists up the surrounding space–time. This predicts a characteristic rocking of the iron line between red- and blueshift as the receding and approaching sides of the disc are respectively illuminated. Here we report on XMM–Newton andNuSTAR observations of the black hole binary H1743−322 in which the line energy varies systematically over the ∼4 s QPO cycle (3.70σ significance), as predicted. This provides strong evidence that the QPO is produced by Lense–Thirring precession, constituting the first detection of this effect in the strong gravitation regime. There are however elements of our results harder to explain, with one section of data behaving differently than all the others. Our result enables the future application of tomographic techniques to map the inner regions of black hole accretion discs.

Key words accretion, accretion discs black hole physics relativistic processes X-rays: individual: H1743−322

© 2016 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society

FREE PDF GRATIS: MNRAS

Darwin, mais outra teoria da evolução: uma perspectiva hierárquica!

Evolutionary Theory

A HIERARCHICAL PERSPECTIVE

EDITED BY NILES ELDREDGE, TELMO PIEVANI, EMANUELE SERRELLI, AND ILYA TEMKIN

384 pages | 12 halftones, 15 line drawings, 4 tables | 6 x 9 | © 2016

The natural world is infinitely complex and hierarchically structured, with smaller units forming the components of progressively larger systems: molecules make up cells, cells comprise tissues and organs that are, in turn, parts of individual organisms, which are united into populations and integrated into yet more encompassing ecosystems. In the face of such awe-inspiring complexity, there is a need for a comprehensive, non-reductionist evolutionary theory. Having emerged at the crossroads of paleobiology, genetics, and developmental biology, the hierarchical approach to evolution provides a unifying perspective on the natural world and offers an operational framework for scientists seeking to understand the way complex biological systems work and evolve.

Source/Fonte: The Hierarchy Group

Coedited by one of the founders of hierarchy theory and featuring a diverse and renowned group of contributors, this volume provides an integrated, comprehensive, cutting-edge introduction to the hierarchy theory of evolution. From sweeping historical reviews to philosophical pieces, theoretical essays, and strictly empirical chapters, it reveals hierarchy theory as a vibrant field of scientific enterprise that holds promise for unification across the life sciences and offers new venues of empirical and theoretical research. Stretching from molecules to the biosphere, hierarchy theory aims to provide an all-encompassing understanding of evolution and—with this first collection devoted entirely to the concept—will help make transparent the fundamental patterns that propel living systems.

Introduction The Checkered Career of Hierarchical Thinking in Evolutionary Biology

Niles Eldredge

Part 1 Hierarchy Theory of Evolution

Linking Section General Principles of Biological Hierarchical Systems

Ilya Tëmkin and Emanuele Serrelli

Chapter 1 Pattern versus Process and Hierarchies: Revisiting Eternal Metaphors in Macroevolutionary Theory

Bruce S. Lieberman

Chapter 2 Lineages and Systems: A Conceptual Discontinuity in Biological Hierarchies

Gustavo Caponi

Chapter 3 Biological Organization from a Hierarchical Perspective: Articulation of Concepts and Interlevel Relation

Jon Umerez

Chapter 4 Hierarchy: The Source of Teleology in Evolution

Daniel W. McShea

Chapter 5 Three Approaches to the Teleological and Normative Aspects of Ecological Functions

Gregory J. Cooper, Charbel N. El-Hani, and Nei F. Nunes-Neto

Part 2 Hierarchical Dynamics: Process Integration across Levels

Linking Section Information and Energy in Biological Hierarchical Systems

Ilya Tëmkin and Emanuele Serrelli

Chapter 6 Why Genomics Needs Multilevel Evolutionary Theory

T. Ryan Gregory, Tyler A. Elliott, and Stefan Linquist

Chapter 7 Revisiting the Phenotypic Hierarchy in Hierarchy Theory

Silvia Caianiello

Chapter 8 Multilevel Selection in a Broader Hierarchical Perspective

Telmo Pievani and Andrea Parravicini

Chapter 9 Systems Emergence: The Origin of Individuals in Biological and Biocultural Evolution

Mihaela Pavličev, Richard O. Prum, Gary Tomlinson, and Günter P. Wagner

Part 3 Biological Hierarchies and Macroevolutionary Patterns

Linking Section Ecology and Evolution: Neither Separate nor Merged

Emanuele Serrelli and Ilya Tëmkin

Chapter 10 Unification of Macroevolutionary Theory: Biologic Hierarchies, Consonance, and the Possibility of Connecting the Dots

William Miller III

Chapter 11 Coming to Terms with Tempo and Mode: Speciation, Anagenesis, and Assessing Relative Frequencies in Macroevolution

Warren D. Allmon

Chapter 12 Niche Conservatism, Tracking, and Ecological Stasis: A Hierarchical Perspective

Carlton E. Brett, Andrew Zaffos, and Arnold I. Miller

Chapter 13 The Stability of Ecological Communities as an Agent of Evolutionary Selection: Evidence from the Permian-Triassic Mass Extinction

Peter D. Roopnarine and Kenneth D. Angielczyk

Chapter 14 Hierarchy Theory in the Anthropocene: Biocultural Homogenization, Urban Ecosystems, and Other Emerging Dynamics

Michael L. McKinney

Conclusion Hierarchy Theory and the Extended Synthesis Debate

Telmo Pievani

List of Contributors

Index

+++++

To be published in Sep. 2016/A ser publicado em Set. 2016

The University of Chicago Press