Apresentando o DNA "escuro" - o fenômeno que pode mudar como nós pensamos sobre a evolução

Introducing ‘dark DNA’ – the phenomenon that could change how we think about evolution

Source/Fonte: NIH

Adam Hargreaves

Postdoctoral Research Fellow, University of Oxford

Disclosure statement

Adam Hargreaves does not work for, consult, own shares in or receive funding from any company or organization that would benefit from this article, and has disclosed no relevant affiliations beyond the academic appointment above.

August 24, 2017 6.22am EDT

DNA sequencing technology is helping scientists unravel questions that humans have been asking about animals for centuries. By mapping out animal genomes, we now have a better idea of how the giraffe got its huge neck and why snakes are so long. Genome sequencing allows us to compare and contrast the DNA of different animals and work out how they evolved in their own unique ways.

But in some cases we’re faced with a mystery. Some animal genomes seem to be missing certain genes, ones that appear in other similar species and must be present to keep the animals alive. These apparently missing genes have been dubbed “dark DNA”. And its existence could change the way we think about evolution.

My colleagues and I first encountered this phenomenon when sequencing the genome of the sand rat (Psammomys obesus), a species of gerbil that lives in deserts. In particular we wanted to study the gerbil’s genes related to the production of insulin, to understand why this animal is particularly susceptible to type 2 diabetes.

But when we looked for a gene called Pdx1 that controls the secretion of insulin, we found it was missing, as were 87 other genes surrounding it. Some of these missing genes, including Pdx1, are essential and without them an animal cannot survive. So where are they?

The first clue was that, in several of the sand rat’s body tissues, we found the chemical products that the instructions from the “missing” genes would create. This would only be possible if the genes were present somewhere in the genome, indicating that they weren’t really missing but just hidden.

...

Read more here/Leia mais aqui.

Porque a construção de nicho de desenvolvimento não é construção de nicho seletivo e porque isso importa

Why developmental niche construction is not selective niche construction: and why it matters

Karola Stotz

Published 18 August 2017.DOI: 10.1098/rsfs.2016.0157

Article Figures & Data Info & Metrics eLetters

Source/Fonte

Abstract

In the last decade, niche construction has been heralded as the neglected process in evolution. But niche construction is just one way in which the organism's interaction with and construction of the environment can have potential evolutionary significance. The constructed environment does not just select for, it also produces new variation. Nearly 3 decades ago, and in parallel with Odling-Smee's article ‘Niche-constructing phenotypes', West and King introduced the ‘ontogenetic niche’ to give the phenomena of exogenetic inheritance a formal name. Since then, a range of fields in the life sciences and medicine has amassed evidence that parents influence their offspring by means other than DNA (parental effects), and proposed mechanisms for how heritable variation can be environmentally induced and developmentally regulated. The concept of ‘developmental niche construction’ (DNC) elucidates how a diverse range of mechanisms contributes to the transgenerational transfer of developmental resources. My most central of claims is that whereas the selective niche of niche construction theory is primarily used to explain the active role of the organism in its selective environment, DNC is meant to indicate the active role of the organism in its developmental environment. The paper highlights the differences between the construction of the selective and the developmental niche, and explores the overall significance of DNC for evolutionary theory.

Competing interests

I declare I have no competing interests.

Funding

This publication was made possible through the support of a grant from the Templeton World Charity Foundation, Causal Foundations of Biological Information TWCF0063/AB37.

Disclaimer

The opinions expressed in this publication are those of the author and do not necessarily reflect the views of the Templeton World Charity Foundation.

Acknowledgements

I also want to express gratitude to the helpful comments provided by two reviewers.

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Genomas ampliados: simbiose e evolução

Extended genomes: symbiosis and evolution

Gregory D. D. Hurst

Published 18 August 2017.DOI: 10.1098/rsfs.2017.0001

Article Figures & Data Info & Metrics eLetters PDF

Source/Fonte

Abstract

Many aspects of an individual's biology derive from its interaction with symbiotic microbes, which further define many aspects of the ecology and evolution of the host species. The centrality of microbes in the function of individual organisms has given rise to the concept of the holobiont—that an individual's biology is best understood as a composite of the ‘host organism’ and symbionts within. This concept has been further elaborated to posit the holobiont as a unit of selection. In this review, I critically examine whether it is useful to consider holobionts as a unit of selection. I argue that microbial heredity—the direct passage of microbes from parent to offspring—is a key factor determining the degree to which the holobiont can usefully be considered a level of selection. Where direct vertical transmission (VT) is common, microbes form part of extended genomes whose dynamics can be modelled with simple population genetics, but that nevertheless have subtle quantitative distinctions from the classic mutation/selection model for nuclear genes. Without direct VT, the correlation between microbial fitness and host individual fitness erodes, and microbe fitness becomes associated with host survival only (rather than reproduction). Furthermore, turnover of microbes within a host may lessen associations between microbial fitness with host survival, and in polymicrobial communities, microbial fitness may derive largely from the ability to outcompete other microbes, to avoid host immune clearance and to minimize mortality through phage infection. These competing selection pressures make holobiont fitness a very minor consideration in determining symbiont evolution. Nevertheless, the importance of non-heritable microbes in organismal function is undoubted—and as such the evolutionary and ecological processes giving rise to variation and evolution of the microbes within and between host individuals represent a key research area in biology.

Competing interests

I declare I have no competing interests.

Funding

The work was supported by Leverhulme Trust and NERC grant no. NE/N010434/1.

Acknowledgements

Feedback on drafts of the manuscript was provided by Dr Michael Gerth, Dr David Baltrus and Dr Kayla King, and improved further by comments from Prof. Seth Bordenstein and an anonymous reviewer, to whom I am grateful.

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A metafísica da evolução

The metaphysics of evolution

John Dupré

Published 18 August 2017.DOI: 10.1098/rsfs.2016.0148

Article Info & Metrics eLetters PDF

Abstract

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. It then explores the implications of process metaphysics for conceptualizing evolution. After explaining what it is for an organism to be a process, the paper takes up the Hull/Ghiselin thesis of species as individuals and explores the conditions under which a species or lineage could constitute an individual process. It is argued that only sexual species satisfy these conditions, and that within sexual species the degree of organization varies. This, in turn, has important implications for species' evolvability. One important moral is that evolution will work differently in different biological domains.

Competing interests

I declare I have no competing interests.

Funding

The research leading to this article has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 324186.

Acknowledgements

I am very grateful to Stephan Guttinger, Anne Sophie Meincke, and Dan Nicholson, and also members of the Egenis Biological Interest Group, for extensive discussion and comments on an earlier draft. I am also grateful for written comments to Carl Craver and two anonymous referees.

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O propósito (???) da adaptação evolucionária

The purpose of adaptation

Andy Gardner

Published 18 August 2017.DOI: 10.1098/rsfs.2017.0005

Source/Fonte

Abstract

A central feature of Darwin's theory of natural selection is that it explains the purpose of biological adaptation. Here, I: emphasize the scientific importance of understanding what adaptations are for, in terms of facilitating the derivation of empirically testable predictions; discuss the population genetical basis for Darwin's theory of the purpose of adaptation, with reference to Fisher's ‘fundamental theorem of natural selection'; and show that a deeper understanding of the purpose of adaptation is achieved in the context of social evolution, with reference to inclusive fitness and superorganisms.

Data accessibility

This article has no additional data.

Competing interests

I declare I have no competing interests.

Funding

I am supported by an Independent Research Fellowship awarded by the Natural Environment Research Council (NE/K009524/1).

Acknowledgement

I thank Steven Frank and two anonymous reviewers for helpful comments and discussion.

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Adaptação evolucionária revelada pela análise comparativa de genoma de mamutes lanosos e elefantes

Evolutionary adaptation revealed by comparative genome analysis of woolly mammoths and elephants 

Sean D. Smith Joseph K. Kawash Spyros Karaiskos Ian Biluck Andrey Grigoriev

DNA Research, Volume 24, Issue 4, 1 August 2017, Pages 359–369, https://doi.org/10.1093/dnares/dsx007

Published: 22 March 2017 Article history

Received: 21 October 2016 Accepted: 15 March 2017

Source/Fonte: Internet

Abstract

Comparative genomics studies typically limit their focus to single nucleotide variants (SNVs) and that was the case for previous comparisons of woolly mammoth genomes. We extended the analysis to systematically identify not only SNVs but also larger structural variants (SVs) and indels and found multiple mammoth-specific deletions and duplications affecting exons or even complete genes. The most prominent SV found was an amplification of RNase L (with different copy numbers in different mammoth genomes, up to 9-fold), involved in antiviral defense and inflammasome function. This amplification was accompanied by mutations affecting several domains of the protein including the active site and produced different sets of RNase L paralogs in four mammoth genomes likely contributing to adaptations to environmental threats. In addition to immunity and defense, we found many other unique genetic changes in woolly mammoths that suggest adaptations to life in harsh Arctic conditions, including variants involving lipid metabolism, circadian rhythms, and skeletal and body features. Together, these variants paint a complex picture of evolution of the mammoth species and may be relevant in the studies of their population history and extinction.

woolly mammoth, elephant, comparative genomics, evolution, viral defense

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Novo modelo computacional de blocos químicos construtores podem ajudar explicar as origens da vida

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

Elizaveta Guseva a,b,c, Ronald N. Zuckermann d, and Ken A. Dill a,b,c,1 ReadCube 

Author Affiliations

aLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794;

bDepartment of Chemistry, Stony Brook University, Stony Brook, NY 11794;

cDepartment of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794;

dMolecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Contributed by Ken A. Dill, July 10, 2017 (sent for review December 8, 2016; reviewed by Hue Sun Chan and Steve Harvey)

Source/Fonte: PhysOrg

Abstract

Significance

Today’s lifeforms are based on informational polymers, namely proteins and nucleic acids. It is thought that simple chemical processes on the early earth could have polymerized monomer units into short random sequences. It is not clear, however, what physical process could have led to the next level—to longer chains having particular sequences that could increase their own concentrations. We study polymers of hydrophobic and polar monomers, such as today’s proteins. We find that even some random sequence short chains can collapse into compact structures in water, with hydrophobic surfaces that can act as primitive catalysts, and that these could elongate other chains. This mechanism explains how random chemical polymerizations could have given rise to longer sequence-dependent protein-like catalytic polymers.

Abstract

It is not known how life originated. It is thought that prebiotic processes were able to synthesize short random polymers. However, then, how do short-chain molecules spontaneously grow longer? Also, how would random chains grow more informational and become autocatalytic (i.e., increasing their own concentrations)? We study the folding and binding of random sequences of hydrophobic (HH) and polar (PP) monomers in a computational model. We find that even short hydrophobic polar (HP) chains can collapse into relatively compact structures, exposing hydrophobic surfaces. In this way, they act as primitive versions of today’s protein catalysts, elongating other such HP polymers as ribosomes would now do. Such foldamer catalysts are shown to form an autocatalytic set, through which short chains grow into longer chains that have particular sequences. An attractive feature of this model is that it does not overconverge to a single solution; it gives ensembles that could further evolve under selection. This mechanism describes how specific sequences and conformations could contribute to the chemistry-to-biology (CTB) transition.

origin of life HP model biopolymers autocatalytic sets

Footnotes

1To whom correspondence should be addressed. Email: dill@laufercenter.org.

Author contributions: R.N.Z. and K.A.D. designed research; E.G. performed research; E.G. and R.N.Z. analyzed data; and E.G. and K.A.D. wrote the paper.

Reviewers: H.S.C., University of Toronto; and S.H., University of Pennsylvania.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1620179114/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Variação epigenética entre as populações urbana e rural dos tentilhões de Darwin

Epigenetic variation between urban and rural populations of Darwin’s finches

Sabrina M. McNew, Daniel Beck, Ingrid Sadler-Riggleman, Sarah A. Knutie, Jennifer A. H. Koop, Dale H. Clayton and Michael K. SkinnerEmail author

BMC Evolutionary Biology BMC series – open, inclusive and trusted 201717:183

https://doi.org/10.1186/s12862-017-1025-9 © The Author(s). 2017 

Received: 26 January 2017Accepted: 26 July 2017Published: 24 August 2017

Abstract

Background

The molecular basis of evolutionary change is assumed to be genetic variation. However, growing evidence suggests that epigenetic mechanisms, such as DNA methylation, may also be involved in rapid adaptation to new environments. An important first step in evaluating this hypothesis is to test for the presence of epigenetic variation between natural populations living under different environmental conditions.

Results

In the current study we explored variation between populations of Darwin’s finches, which comprise one of the best-studied examples of adaptive radiation. We tested for morphological, genetic, and epigenetic differences between adjacent “urban” and “rural” populations of each of two species of ground finches, Geospiza fortis and G. fuliginosa, on Santa Cruz Island in the Galápagos. Using data collected from more than 1000 birds, we found significant morphological differences between populations of G. fortis, but not G. fuliginosa. We did not find large size copy number variation (CNV) genetic differences between populations of either species. However, other genetic variants were not investigated. In contrast, we did find dramatic epigenetic differences between the urban and rural populations of both species, based on DNA methylation analysis. We explored genomic features and gene associations of the differentially DNA methylated regions (DMR), as well as their possible functional significance.

Conclusions

In summary, our study documents local population epigenetic variation within each of two species of Darwin’s finches.

Keywords

Epigenetics Geospiza Copy number variation Galápagos Islands DNA methylation

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Mudança de postura sobre o fato, Fato, FATO da evolução: NÓS NÃO SABEMOS COMO OCORREU!

A leitura desapaixonada, mas cientificamente objetiva revela que na literatura especializada evolucionária há uma mudança radical de postura no modo como muitos cientistas estão abordando a questão do fato, Fato, FATO da evolução:

ANTES: "TUDO JÁ ESTÁ EXPLICADO!"

AGORA: "NÓS NÃO SABEMOS COMO OCORREU!"

"

Fonte

A nova teoria geral da evolução - a Síntese Evolutiva Ampliada/Estendida, lançada em agosto de 2015, mas pouco debatida publicamente, ainda não explica como surgiram, evoluíram os novos planos corporais e sistemas biológicos funcionais sem a intervenção de uma causa inteligente. 

Pior a emenda do que o soneto - a nova teoria ainda se apoia na necessidade de se EXTRAPOLAR de pequenas variações baseadas na reorganização de recursos informacionais existentes nos organisms à macroevolução, isto é, o surgimento de características, sistemas e formas biológicas totalmente novas. No contexto de justificação teórica ainda não evidência empírica para essa extrapolação.

Melhor a emenda do que o soneto - muitos cientistas estão mais humildes em suas afirmações retóricas e, contrariando o CONSENSO do paradigma vigente, estão seguindo as evidências aonde elas forem dar!

A nova teoria geral da evolução - a Síntese Evolutiva Ampliada/Estendida, por não considerar a origem da informação genética, é uma teoria científica natimorta!

Que venha logo o upgrade Darwin 4.0!!!

O fato, Fato, FATO da evolução precisa de nova teoria geral: Síntese Evolucionária Ampliada/Estendida

Why an extended evolutionary synthesis is necessary

Gerd B. Müller1,2

1 Department of Theoretical Biology, University of Vienna, Vienna, Austria

2 Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria

GBM, 0000-0001-5011-0193

Source/Fonte

Abstract

Since the last major theoretical integration in evolutionary biology—the modern synthesis (MS) of the 1940s—the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the ‘-omics’ revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Some of these results are in agreement with the standard theory and others reveal different properties of the evolutionary process. A renewed and extended theoretical synthesis, advocated by several authors in this issue, aims to unite pertinent concepts that emerge from the novel fields with elements of the standard theory. The resulting theoretical framework differs from the latter in its core logic and predictive capacities. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. 

Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. All these features stimulate research into new areas of evolutionary biology.

Subject Areas: systems biology

Keywords: evolutionary biology, modern synthesis, extended synthesis, evolutionary developmental biology, niche construction, systems biology

Author for correspondence:

Gerd B. Müller

e-mail: gerhard.mueller@univie.ac.at

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INTERESTING EXCERPTS/EXCERTOS INTERESSANTES:

"As can be noted from the listed principles, current evolutionary theory is predominantly oriented towards a genetic explanation of variation, and, except for some minor semantic modifications, this has not changed over the past seven or eight decades. Whatever lip service is paid to taking into account other factors than those traditionally accepted, we find that the theory, as presented in extant writings, concentrates on a limited set of evolutionary explananda, excluding the majority of those mentioned among the explanatory goals above. The theory performs well with regard to the issues it concentrates on, providing testable and abundantly confirmed predictions on the dynamics of genetic variation in evolving populations, on the gradual variation and adaptation of phenotypic traits, and on certain genetic features of speciation. If the explanation would stop here, no controversy would exist. But it has become habitual in evolutionary biology to take population genetics as the privileged type of explanation of all evolutionary phenomena, thereby negating the fact that, on the one hand, not all of its predictions can be confirmed under all circumstances, and, on the other hand, a wealth of evolutionary phenomena remains excluded. For instance, the theory largely avoids the question of how the complex organizations of organismal structure, physiology, development or behaviour—whose variation it describes—actually arise in evolution, and it also provides no adequate means for including factors that are not part of the population genetic framework, such as developmental, systems theoretical, ecological or cultural influences."

“A rising number of publications argue for a major revision or even a replacement of the standard theory of evolution [2–14], indicating that this cannot be dismissed as a minority view but rather is a widespread feeling among scientists and philosophers alike.”

“Indeed, a growing number of challenges to the classical model of evolution have emerged over the past few years, such as from evolutionary developmental biology [16], epigenetics [17], physiology [18], genomics [19], ecology [20], plasticity research [21], population genetics [22], regulatory evolution [23], network approaches [14], novelty research [24], behavioural biology [12], microbiology [7] and systems biology [25], further supported by arguments from the cultural [26] and social sciences [27], as well as by philosophical treatments [28–31]. None of these contentions are unscientific, all rest firmly on evolutionary principles and all are backed by substantial empirical evidence.”

“Sometimes these challenges are met with dogmatic hostility, decrying any criticism of the traditional theoretical edifice as fatuous [32], but more often the defenders of the traditional conception argue that ‘all is well’ with current evolutionary theory, which they see as having ‘co-evolved’ together with the methodological and empirical advances that already receive their due in current evolutionary biology [33]. But the repeatedly emphasized fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them.”

"A subtler version of the this-has-been-said-before argument used to deflect any challenges to the received view is to pull the issue into the never ending micro-versus-macroevolution debate. Whereas ‘microevolution’ is regarded as the continuous change of allele frequencies within a species or population [109], the ill-defined macroevolution concept [36], amalgamates the issue of speciation and the origin of ‘higher taxa’ with so-called ‘major phenotypic change’ or new constructional types. Usually, a cursory acknowledgement of the problem of the origin of phenotypic characters quickly becomes a discussion of population genetic arguments about speciation, often linked to the maligned punctuated equilibria concept [9], in order to finally dismiss any necessity for theory change. The problem of phenotypic complexity thus becomes (in)elegantly bypassed. Inevitably, the conclusion is reached that microevolutionary mechanisms are consistent with macroevolutionary phenomena [36], even though this has very little to do with the structure and predictions of the EES. The real issue is that genetic evolution alone has been found insufficient for an adequate causal explanation of all forms of phenotypic complexity, not only of something vaguely termed ‘macroevolution’. Hence, the micro–macro distinction only serves to obscure the important issues that emerge from the current challenges to the standard theory. It should not be used in discussion of the EES, which rarely makes any allusions to macroevolution, although it is sometimes forced to do so. (emphasis added).

E a Nomenklatura científica e a Galera dos meninos e meninas de Darwin diziam que tudo ia bem com a Síntese Evolutiva Moderna, que não havia nenhuma necessidade de mudança, que a teoria da evolução de Darwin através da seleção natural é uma teoria científica tão comprovada quanto a lei da gravidade, y otras cositas mais, e o que encontramos intramuros na literatura especializada, é que o fato, Fato, FATO da evolução não é assim uma Brastemp no contexto de justificação teórica!

Fui, nem sei porque com o sorriso maroto do gato de Cheshire...

Darwin kaput! Viva Darwin!!!

Novo fóssil de mosca lança luz sobre a radiação explosiva de moscas durante a Era Cenozóica

First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences

Pierfilippo Cerretti , John O. Stireman III, Thomas Pape, James E. O’Hara, Marco A. T. Marinho, Knut Rognes, David A. Grimaldi

Published: August 23, 2017 https://doi.org/10.1371/journal.pone.0182101

Abstract

Calyptrate flies include about 22,000 extant species currently classified into Hippoboscoidea (tsetse, louse, and bat flies), the muscoid grade (house flies and relatives) and the Oestroidea (blow flies, bot flies, flesh flies, and relatives). Calyptrates are abundant in nearly all terrestrial ecosystems, often playing key roles as decomposers, parasites, parasitoids, vectors of pathogens, and pollinators. For oestroids, the most diverse group within calyptrates, definitive fossils have been lacking. The first unambiguous fossil of Oestroidea is described based on a specimen discovered in amber from the Dominican Republic. The specimen was identified through digital dissection by CT scans, which provided morphological data for a cladistic analysis of its phylogenetic position among extant oestroids. The few known calyptrate fossils were used as calibration points for a molecular phylogeny (16S, 28S, CAD) to estimate the timing of major diversification events among the Oestroidea. Results indicate that: (a) the fossil belongs to the family Mesembrinellidae, and it is identified and described as Mesembrinella caenozoica sp. nov.; (b) the mesembrinellids form a sister clade to the Australian endemic Ulurumyia macalpinei (Ulurumyiidae) (McAlpine’s fly), which in turn is sister to all remaining oestroids; (c) the most recent common ancestor of extant Calyptratae lived just before the K–Pg boundary (ca. 70 mya); and (d) the radiation of oestroids began in the Eocene (ca. 50 mya), with the origin of the family Mesembrinellidae dated at ca. 40 mya. These results provide new insight into the timing and rate of oestroid diversification and highlight the rapid radiation of some of the most diverse and ecologically important families of flies. ZooBank accession number–urn:lsid:zoobank.org:pub:0DC5170B-1D16-407A-889E-56EED3FE3627.

Citation: Cerretti P, Stireman JO III, Pape T, O’Hara JE, Marinho MAT, Rognes K, et al. (2017) First fossil of an oestroid fly (Diptera: Calyptratae: Oestroidea) and the dating of oestroid divergences. PLoS ONE 12(8): e0182101. https://doi.org/10.1371/journal.pone.0182101

Editor: Matt Friedman, University of Michigan, UNITED STATES

Received: April 3, 2017; Accepted: July 12, 2017; Published: August 23, 2017

Copyright: © 2017 Cerretti 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 acknowledge funding by U.S. National Science Foundation OPUS grant DEB 1556502 (DAG) (https://www.nsf.gov/awardsearch/showAward?AWD_ID=1556502&HistoricalAwards=false); U.S. National Science Foundation grant DEB 1146269 (JOS, JEOH, PC) (https://www.nsf.gov/awardsearch/showAward?AWD_ID=1146269); U.S. National Science Foundation grant DEB 1442134 (JOS); and FAPESP (2012/23200-2) and CNPq (150441/2016-2) (MATTM). The funders 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.

FREE PDF GRATIS: PLoS One

Status científico atual (2017) da evolução humana

Source/Fonte: New Scientist

Source/Fonte: New Scientist

Who are you? How the story of human origins is being rewritten.

The past 15 years have called into question every assumption about who we are and where we came from. Turns out our evolution is more baffling than we thought.

2017 Aug. 23, New Scientist

Quem sabe, entende e faz ciência polariza mais sobre tópicos científicos controversos!!!

Individuals with greater science literacy and education have more polarized beliefs on controversial science topics

Caitlin Drummond a,1 and Baruch Fischhoff b,c  

Author Affiliations

aDepartment of Social and Decision Sciences, Carnegie Mellon University, Pittsburgh, PA 15213;

bDepartment of Engineering and Public Policy, Carnegie Mellon University, Pittsburgh, PA 15213;

cInstitute for Politics and Strategy, Carnegie Mellon University, Pittsburgh, PA 15213

Edited by Roger E. Kasperson, Clark University, Worcester, MA, and approved July 19, 2017 (received for review March 23, 2017)

Edited by Roger E. Kasperson, Clark University, Worcester, MA, and approved July 19, 2017 (received for review March 23, 2017)

Source/Fonte: University of California - Berkeley

Significance

Public opinion toward some science and technology issues is polarized along religious and political lines. We investigate whether people with more education and greater science knowledge tend to express beliefs that are more (or less) polarized. Using data from the nationally representative General Social Survey, we find that more knowledgeable individuals are more likely to express beliefs consistent with their religious or political identities for issues that have become polarized along those lines (e.g., stem cell research, human evolution), but not for issues that are controversial on other grounds (e.g., genetically modified foods). These patterns suggest that scientific knowledge may facilitate defending positions motivated by nonscientific concerns.

Abstract

Although Americans generally hold science in high regard and respect its findings, for some contested issues, such as the existence of anthropogenic climate change, public opinion is polarized along religious and political lines. We ask whether individuals with more general education and greater science knowledge, measured in terms of science education and science literacy, display more (or less) polarized beliefs on several such issues. We report secondary analyses of a nationally representative dataset (the General Social Survey), examining the predictors of beliefs regarding six potentially controversial issues. We find that beliefs are correlated with both political and religious identity for stem cell research, the Big Bang, and human evolution, and with political identity alone on climate change. Individuals with greater education, science education, and science literacy display more polarized beliefs on these issues. We find little evidence of political or religious polarization regarding nanotechnology and genetically modified foods. On all six topics, people who trust the scientific enterprise more are also more likely to accept its findings. We discuss the causal mechanisms that might underlie the correlation between education and identity-based polarization.

science literacy polarization science communication science education trust

Footnotes

1To whom correspondence should be addressed. Email: cdrummon@andrew.cmu.edu.

Author contributions: C.D. and B.F. designed research; C.D. performed research; C.D. analyzed data; and C.D. and B.F. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1704882114/-/DCSupplemental.

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Epigenômica de plantas - decifrando os mecanismos da herança epigenética e plasticidade em plantas

Plant epigenomics—deciphering the mechanisms of epigenetic inheritance and plasticity in plants

Claudia Köhler and Nathan Springer

Genome Biology 201718:132

https://doi.org/10.1186/s13059-017-1260-9 © The Author(s). 2017

Source/Fonte: The Scientist

EDITORIAL

Published: 6 July 2017

It is an exciting time to study plant epigenetics. Technological advances are providing unprecedented opportunities to monitor chromatin modifications, gene expression, and genome structure. Many classical epigenetic phenomena (transposable element inactivation, imprinting, paramutation, transgene silencing, and co-suppression) were first documented in plants. Combined with classical genetic studies, newly available sequencing technologies are facilitating the study of these and other epigenetic phenomena at a level of detail that was unthinkable only a few years ago. Studies of epigenetics in plants are of great importance. Plants are heavily dependent upon changes in gene expression in order to respond to environmental stimuli, and chromatin-based regulation of gene expression is likely crucial for these responses. Furthermore, the level of chromatin ‘resetting’ during sexual reproduction appears to be lower in plants in comparison with animal species [1, 2], potentially allowing inheritance of epimutations acquired during plant life. In addition, many plant species can propagate asexually and produce vegetative clones, providing opportunities for mitotic inheritance of epigenetic states leading to important traits. This issue of Genome Biology highlights exciting progress in many areas of plant epigenetics and epigenomics.

DNA methylation is a well-studied chromatin modification in animals and plants that can be stably inherited, both following cell divisions and, to some extent, across generations. DNA methylation can be monitored at high resolution by using sodium bisulfite treatment of DNA, followed by next-generation sequencing. Cytosines in different sequence contexts (CG, CHG, and CHH (where H is any base other than G)) and at different types of loci in plant genomes can be targeted by DNA methylation. This modification has likely evolved as a mechanism to silence transposons, which are ‘genomic parasites’ invading the genome of their hosts. The vast majority of transposons are highly methylated and are likely a primary target for epigenetic silencing. However, the repetitive nature of transposons and the fact that they generate large insertion/deletion polymorphisms among genotypes has led to difficulties in monitoring the link between transposon polymorphism and DNA methylation variation. Daron and Slotkin describe a new tool to study the interactions between transposon methylation and transposon insertions using whole-genome bisulfite sequencing datasets [3]. This type of analysis is expected to be very useful in documenting the role of genetic and epigenetic variation in DNA methylation among individuals of the same species.

The RNA-dependent DNA methylation (RdDM) pathway is crucial for maintenance of CHH methylation and requires the plant-specific RNA polymerases IV and V (Pol IV and V, respectively). Pol IV generates precursor transcripts of 24-nt small RNAs (sRNAs) that target scaffold transcripts from Pol V by sequence complementarity and recruit the domains rearranged methyltransferase 2 [4]. A rather unexpected link between RdDM and the chromatin remodeling factor PICKLE (PKL) is revealed by Zhang and colleagues, who report that PKL is required for the accumulation of transcripts generated by Pol V and for the positioning of Pol V-stabilized nucleosomes at a subset of RdDM target loci [5]. These findings link nucleosome positioning with the initiation of RdDM, consistent with the previously proposed role of SWI/SNF chromatin remodeling complexes in establishing positioned nucleosomes on specific loci primed for RdDM [6]. It is well established that PKL regulates plant development and, in particular, regulates the access of Polycomb-group proteins to its targets [7]. Likewise, SWI/SNF complexes have well-described roles in plant development [7], extended by the study of Benhamed and colleagues in this issue showing that the SWI/SNF complex core subunit BAF60 regulates access of the Phytochrome Interacting Factor 4 (PIF4) to nucleosome-free regions [8]. The dual functional role of chromatin-remodeling factors in regulating plant development and RdDM suggests that both processes are more closely connected than is widely appreciated.

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Hierarquias na organização do genoma eucariótico: insights da teoria de polímeros e simulações

Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations

Balaji VS Iyer, Martin Kenward and Gaurav AryaEmail author

BMC Biophysics20114:8

https://doi.org/10.1186/2046-1682-4-8 © Iyer et al; licensee BioMed Central Ltd. 2011 ReadCube 

Received: 7 January 2011Accepted: 15 April 2011Published: 15 April 2011

Source/Fonte: BuhrooZafar 

Abstract

Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus. Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function. Elegant microscopy and chromosome conformation capture techniques supported by analysis based on polymer models are important steps in this direction. Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.

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A organização tridimensional do genoma de Drosophila melanogaster através da integração de dados

The three-dimensional genome organization of Drosophila melanogaster through data integration

Qingjiao Li†, Harianto Tjong†, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo and Frank Alber

†Contributed equally

Genome Biology201718:145

https://doi.org/10.1186/s13059-017-1264-5 ©  The Author(s). 2017 ReadCube

Received: 26 December 2016Accepted: 26 June 2017Published: 31 July 2017

Source/Fonte

Abstract

Background

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome’s organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments.

Results

Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data.

Conclusions

Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

Keywords

3D genome structure Higher order genome organization Population-based modeling Data integration Hi-C Lamina-DamID Homologous pairing Drosophila melanogaster Heterochromatin

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Pesquisa revela que dormir pode ajudar a memória

Formation and suppression of acoustic memories during human sleep

Thomas Andrillon, Daniel Pressnitzer, Damien Léger & Sid Kouider

Nature Communications 8, Article number: 179 (2017)

doi:10.1038/s41467-017-00071-z 

Human behaviour Perception Sleep

Received: 13 April 2016

Accepted: 30 May 2017

Published online: 08 August 2017

Source/Fonte

Abstract

Sleep and memory are deeply related, but the nature of the neuroplastic processes induced by sleep remains unclear. Here, we report that memory traces can be both formed or suppressed during sleep, depending on sleep phase. We played samples of acoustic noise to sleeping human listeners. Repeated exposure to a novel noise during Rapid Eye Movements (REM) or light non-REM (NREM) sleep leads to improvements in behavioral performance upon awakening. Strikingly, the same exposure during deep NREM sleep leads to impaired performance upon awakening. Electroencephalographic markers of learning extracted during sleep confirm a dissociation between sleep facilitating memory formation (light NREM and REM sleep) and sleep suppressing learning (deep NREM sleep). We can trace these neural changes back to transient sleep events, such as spindles for memory facilitation and slow waves for suppression. Thus, highly selective memory processes are active during human sleep, with intertwined episodes of facilitative and suppressive plasticity.

Acknowledgements

This research was supported by ANR grants (ANR-10-LABX-0087 and ANR-10-IDEX-0001-02), by the European Research Council (ERC project METAWARE to S.K. and ERC project ADAM to D.P.), by the EU H2020 program (COCOHA #644732 to DP), and by the Ministère de la Recherche and the Société Française de Recherche et Médecine du Sommeil (T.A.). We thank V. Bayon, A. Dalbin, L. de Sanctis, M. Elbaz, S. Rio, and C. Varazzani for their help.

Author information

Affiliations

Brain and Consciousness Group (ENS, EHESS, CNRS), Département d’Études Cognitives, École Normale Supérieure-PSL Research University, Paris, 75005, France

Thomas Andrillon & Sid Kouider

École Doctorale Cerveau Cognition Comportement, Université Pierre et Marie Curie, Paris, 75005, France

Thomas Andrillon

Laboratoire des Systèmes Perceptifs, CNRS UMR 8248, Département d’Études Cognitives, École Normale Supérieure-PSL Research University, Paris, 75005, France

Daniel Pressnitzer

Université Paris Descartes, Sorbonne Paris Cité, APHP, Hôtel Dieu, Centre du Sommeil et de la Vigilance et EA 7330 VIFASOM, Paris, 75006, France

Damien Léger

Contributions

T.A., D.P., D.L., and S.K. designed the study. T.A. collected and analyzed the data. T.A., D.P., D.L., and S.K. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Thomas Andrillon or Sid Kouider.

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