O passado, o presente e o futuro da genômica mitocondrial: já sequenciamos bastante mtDNAs?

segunda-feira, junho 29, 2015

The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

David Roy Smith

David Roy Smith is an assistant professor of biology at the University of Western Ontario, where he studies genome evolution of eukaryotic microbes. He can be found online at www.arrogantgenome.com and @arrogantgenome.

Corresponding author. David Roy Smith, Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada. Tel.: (519) 661 2111, ext. 86482; E-mail: dsmit242@uwo.ca

Source/Fonte: Science Magazine


The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission.

Key words

genome sequencing microbial diversity mitochondrial genome mitochondrial transcriptome Marine Microbial Eukaryotic Transcriptome Sequencing Project

Dinâmicas de equilíbrio e não equilíbrio operam simultaneamente nas ilhas Galápagos: chegaram ao limite evolucionário???

terça-feira, junho 23, 2015

Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands

Luis M. Valente 1,*, Albert B. Phillimore 2 and Rampal S. Etienne 3

Article first published online: 23 JUN 2015

DOI: 10.1111/ele.12461

© 2015 The Authors Ecology Letters published by John Wiley & Sons Ltd and CNRS.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.


Community assembly; diversification; dynamic equilibrium; island biogeography; phylogeny


Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent-like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non-equilibrium and equilibrium ecological paradigms.

FREE PDF GRATIS: Ecology Letters

A falácia da teoria evolucionária da deriva genética

segunda-feira, junho 22, 2015

The "Random Genetic Drift" Fallacy Paperback – September 10, 2014

by Prof William B. Provine (Author)

Much of my life has been devoted to the history of population genetics. My early book was my Ph.D. thesis still in print: The Origins of Theoretical Populations Genetics (1971, 2nd edition, 1991). I stated in the 2nd edition in the Afterword that “random genetic drift” was giving me pause, as does the evolutionary synthesis. My later book was Sewall Wright and Evolutionary Biology (1986) and is also still in print. Now I am writing this book against “random genetic drift,” invented by R. A. Fisher and followed by Sewall Wright and J. B. S. Haldane. “Random genetic drift” is the core of population genetics. Any person who believes in “random genetic drift” should read this book.

Source: Amazon Books


Dr. William B. Provine é professor da cátedra Charles A. Alexander, de Ciências Biológicas e de História da Ciência na Cornell University.



E os darwinistas ortodoxos fundamentalistas xiitas pós-modernos, chiques e perfumados a la Dawkins, têm a cara de pau de dizer que a teoria da evolução de Darwin através da seleção natural (e n mecanismos de A a Z - vai que um falhe...) não passa por uma profunda crise epistemológica no contexto de justificação teórica? E não querem que os alunos saibam e discutam isso em salas de aulas de ciência???

Entrando na sexta extinção em massa - antropogenicamente provocada???

domingo, junho 21, 2015

Accelerated modern human–induced species losses: Entering the sixth mass extinction

Gerardo Ceballos1,*, Paul R. Ehrlich2, Anthony D. Barnosky3, Andrés García4, Robert M. Pringle5 and Todd M. Palmer6

- Author Affiliations

1Instituto de Ecología, Universidad Nacional Autónoma de México, México D.F. 04510, México.

2Department of Biology, Stanford University, Stanford, CA 94304, USA.

3Department of Integrative Biology and Museums of Paleontology and Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720–3140, USA.

4Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Jalisco 48980, México.

5Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.

6Department of Biology, University of Florida, Gainesville, FL 32611–8525, USA.

↵*Corresponding author. E-mail: gceballo@ecologia.unam.mx

Science Advances 19 Jun 2015:

Vol. 1, no. 5, e1400253

DOI: 10.1126/sciadv.1400253

Source/Fonte: The New York Times


The oft-repeated claim that Earth’s biota is entering a sixth “mass extinction” depends on clearly demonstrating that current extinction rates are far above the “background” rates prevailing in the five previous mass extinctions. Earlier estimates of extinction rates have been criticized for using assumptions that might overestimate the severity of the extinction crisis. We assess, using extremely conservative assumptions, whether human activities are causing a mass extinction. First, we use a recent estimate of a background rate of 2 mammal extinctions per 10,000 species per 100 years (that is, 2 E/MSY), which is twice as high as widely used previous estimates. We then compare this rate with the current rate of mammal and vertebrate extinctions. The latter is conservatively low because listing a species as extinct requires meeting stringent criteria. Even under our assumptions, which would tend to minimize evidence of an incipient mass extinction, the average rate of vertebrate species loss over the last century is up to 114 times higher than the background rate. Under the 2 E/MSY background rate, the number of species that have gone extinct in the last century would have taken, depending on the vertebrate taxon, between 800 and 10,000 years to disappear. These estimates reveal an exceptionally rapid loss of biodiversity over the last few centuries, indicating that a sixth mass extinction is already under way. Averting a dramatic decay of biodiversity and the subsequent loss of ecosystem services is still possible through intensified conservation efforts, but that window of opportunity is rapidly closing.

Key words Sixth mass extinction vertebrate extinctions rates of extinction background extinction modern vertebrate losses


Repositório de genoma antigo online

quinta-feira, junho 18, 2015

Vale a pena pesquisar utilizando esses dados online do Online Ancient Genome Repository

Dr. Michael Lynch palestra sobre mutação, deriva, e a origem das características subcelulares


Prestem bem atenção no que o Dr. Michael Lynch tem a dizer sobre a seleção natural.

Pesquisadores descobrem o primeiro sensor do campo magnético da Terra em um animal

quarta-feira, junho 17, 2015


Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans

Andrés Vidal-Gadea, Kristi Ward, Celia Beron, Navid Ghorashian, Sertan Gokce, Joshua Russell, Nicholas Truong, Adhishri Parikh, Otilia Gadea, Adela Ben-Yakar, Jonathan Pierce-ShimomuraCorresponding Author

DOI: http://dx.doi.org/10.7554/eLife.07493

Published June 17, 2015

Cite as eLife 2015;10.7554/eLife.07493

Inside the head of the worm C. elegans, the TV antenna-like structure at the tip of the AFD neuron (green) is the first identified sensor for Earth's magnetic field. Credit: Andres Vidal-Gadea.


Many organisms spanning from bacteria to mammals orient to the earth's magnetic field. For a few animals, central neurons responsive to earth-strength magnetic fields have been identified; however, magnetosensory neurons have yet to be identified in any animal. We show that the nematode Caenorhabditis elegans orients to the earth's magnetic field during vertical burrowing migrations. Well-fed worms migrated up, while starved worms migrated down. Populations isolated from around the world, migrated at angles to the magnetic vector that would optimize vertical translation in their native soil, with northern- and southern-hemisphere worms displaying opposite migratory preferences. Magnetic orientation and vertical migrations required the TAX-4 cyclic nucleotide-gated ion channel in the AFD sensory neuron pair. Calcium imaging showed that these neurons respond to magnetic fields even without synaptic input. C. elegans may have adapted magnetic orientation to simplify their vertical burrowing migration by reducing the orientation task from three dimensions to one. 


Calibrando a taxa de mutação humana via densidade de recombinação ancestral em genomas diploides

terça-feira, junho 16, 2015

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

Mark Lipson, Po-Ru Loh, Sriram Sankararaman, Nick Patterson, Bonnie Berger, David Reich


The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Classical methods based on sequence divergence have yielded significantly larger values than more recent approaches based on counting de novo mutations in family pedigrees. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.65 +/- 0.10 x 10^(-8) mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.


The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.


Mais uma hipótese sobre a origem da vida: a físico-química muda o paradigma. Será???

Emergence of life: Physical chemistry changes the paradigm

Jan Spitzer 1, Gary J. Pielak 2 and Bert Poolman 3

Corresponding authors: Jan Spitzer jspitz@mcpolymers.com - Gary J Pielak gary_pielak@unc.edu - Bert Poolman b.poolman@rug.nl

Author Affiliations

1 R&D Department, Mallard Creek Polymers, Inc., 2800 Morehead Rd, Charlotte 28262, NC, USA

2 Department of Chemistry, Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill 27599, NC, USA

3 Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, 9747, AG, The Netherlands

Biology Direct 2015, 10:33 doi:10.1186/s13062-015-0060-y

Received: 9 February 2015

Accepted: 14 May 2015

Published: 10 June 2015

© 2015 Spitzer et al. 

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.


Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of ‘what is life?’. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life’s emergence:

(1) Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity.

(2) Earth’s chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents.

(3) Earth’s overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states.

(4) Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization.

We discuss these premises in relation to current ‘constructive’ (non-evolutionary) paradigm of origins research – the process of complexification of chemical matter ‘from the simple to the complex’. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.

Keywords: Chemical evolution; Darwinian evolution; Origin of life; Diurnal gradients; Chemical complexity; Biomacromolecular crowding; Non-covalent intermolecular forces; Molecular recognition; Cellular organization

FREE PDF GRATIS: Biology Direct

Luiz Felipe Pondé: Não existe liberdade de pensamento na universidade brasileira. Especialmente quando a questão é Darwin...

segunda-feira, junho 15, 2015


Da missa a metade

A universidade está longe de ser uma instituição livre, por causas internas à própria máquina acadêmica

Tenho acompanhando a polêmica da PUC e a proibição da cátedra Foucault. Mas, se formos falar da liberdade de pensamento que a universidade supostamente defende (e que foi apontada pelos colegas que criticaram a PUC duramente), não me parece que o assunto seja tão simples. E não me refiro apenas a universidades ligadas a instituições religiosas. As públicas também caçam suas bruxas.

Numa frase: não existe liberdade de pensamento na universidade. Isso é uma falácia. A universidade corre o risco de virar um celeiro de crenças ideológicas, vendidas aos alunos como "saber".

Esta suposta liberdade de pensamento, que oporia aqui a Igreja Católica a uma universidade livre, é matéria de dúvida para qualquer um que conheça a realidade universitária. Não existe liberdade de pensamento na universidade e a igreja está longe de ser o maior ator em termos de "censura".

Voltemos ao contexto: a Igreja Católica proibiu a instalação de uma cátedra Foucault na PUC. Cátedras são instrumentos de poder na universidade. Uma cátedra significa a difusão de uma visão de mundo. E de verbas, claro.

Levantemos alguns cenários sobre o tema da liberdade na universidade. A afirmação de que existe uma universidade livre, sendo "oprimida" por instâncias religiosas (no caso específico da PUC), "não é da missa a metade" quando falamos de "censura" à liberdade de ação na academia em geral. Sim, limites teológicos para o conhecimento são ruins mesmo, concordo. Mas, a universidade está longe de ser uma instituição livre, por causas internas à própria máquina acadêmica.

Leia mais aqui: Folha de São Paulo (Assinantes)



Não existe liberdade de pensamento na universidade brasileira, disse Pondé em 2015. Este blogger vem denunciando essa falta de liberdade de pensamento nas universidades brasileiras desde 1998. Especialmente quando paradigmas científicos aceitos são questionados. Mesmo a comunidade científica sabendo, e como sabe, que esses paradigmas já entraram em colapso epistemológico há muitos anos.

Por que é assim? Kuhn disse que quando os paradigmas não respondem a anomalias encontradas nas pesquisas, os que praticam ciência normal varrem essas dificuldades para debaixo do tapete, a vida científica continua, e os novos cientistas que levantam a lebre, são hostilizados e perseguidos como hereges. Esses ares de mudança na ciência somente se dão quando ocorre a "solução biológica" dos que praticam ciência normal, e os novos cientistas assumem as pesquisas e as ideias heréticas são consideradas livremente.

O artigo do Pondé sobre a recusa de uma cátedra Foucault na PUC-SP bem que poderia ser lida ao avesso - a situação daqueles que ousam criticar os paradigmas da origem e evolução do universo e da vida nas universidades tupiniquins - são considerados heréticos, são impedidos de falar sobre isso, têm suas palestras impedidas de serem realizadas no espaço onde deveria ocorrer o debate científico - nas universidades.

Por que essa resistência? É porque os paradigmas colapsaram, e a comunidade científica que defendia esses paradigmas dogmaticamente, foi encontrada em falta. Daí o silêncio pétreo sobre essas questões científicas maiores que demandam um ceticismo maior de suas afirmações.

Pondé, você cravou uma estaca no peito desses mandarins do poder acadêmico tupiniquim!!! 

Simpósio sobre a teoria do Design Inteligente em Anápolis - GO 18 e 19 de setembro de 2015

sábado, junho 13, 2015

Maiores informações

Fibras e estruturas celulares preservadas em espécimes de dinossauro de 75 milhões de anos

terça-feira, junho 09, 2015

Fibres and cellular structures preserved in 75-million–year-old dinosaur specimens

Sergio Bertazzo, Susannah C. R. Maidment, Charalambos Kallepitis, Sarah Fearn, Molly M. Stevens & Hai-nan Xie

Affiliations Contributions Corresponding authors

Nature Communications 6, Article number: 7352 doi:10.1038/ncomms8352

Received 25 January 2015 Accepted 30 April 2015 Published 09 June 2015


Abstract• References• Author information• Supplementary information

Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ~67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.

Subject terms: Biological sciences Palaeontology

FREE PDF GRATIS: Nature Communications

Epigenética, Darwin e Lamarck

sábado, junho 06, 2015

Epigenetics, Darwin and Lamarck

David Penny

- Author Affiliations

Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

*Author for Correspondence: David Penny, Massey University, Palmerston North, New Zealand, +64 6 350 5033, +64 6 355 7953, address for correspondence D.Penny@massey.ac.nz.

Received February 26, 2015.

Revision received April 20, 2015.

Accepted May 26, 2015.


It is not really helpful to consider modern environmental epigenetics as neo-Lamarckian; and there is no evidence that Lamarck considered the idea original to himself. We must all keep learning about inheritance, but attributing modern ideas to early researchers is not helpful, and can be misleading.

Key words: Darwinism epigenetics evolution genetics Lamarck

© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.


FREE PDF GRATIS: Genome Biol Evol

Reprogramação do epigenoma em células germinais humanas observada pela primeira vez

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

Walfred W.C. Tang5, Sabine Dietmann5, Naoko Irie, Harry G. Leitch, Vasileios I. Floros, Charles R. Bradshaw, Jamie A. Hackett, Patrick F. Chinnery, M. Azim Surani correspondence email

5Co-first author

Open Access

DOI: http://dx.doi.org/10.1016/j.cell.2015.04.053

Open access funded by Wellcome Trust

Article Info

Publication History

Accepted: April 14, 2015

Received in revised form: March 27, 2015

Received: January 28, 2015


• SOX17-BLIMP1 with TFCP2L1 and KLF4 constitute a unique hPGC transcriptome

• hPGC transcriptome drives extensive DNA demethylation and chromatin reorganization

• Evolutionarily young and hazardous retrotransposons remain partially methylated

• Some demethylation resistant loci are candidates for epigenetic inheritance


Resetting of the epigenome in human primordial germ cells (hPGCs) is critical for development. We show that the transcriptional program of hPGCs is distinct from that in mice, with co-expression of somatic specifiers and naive pluripotency genes TFCP2L1 and KLF4. This unique gene regulatory network, established by SOX17 and BLIMP1, drives comprehensive germline DNA demethylation by repressing DNA methylation pathways and activating TET-mediated hydroxymethylation. Base-resolution methylome analysis reveals progressive DNA demethylation to basal levels in week 5–7 in vivo hPGCs. Concurrently, hPGCs undergo chromatin reorganization, X reactivation, and imprint erasure. Despite global hypomethylation, evolutionarily young and potentially hazardous retroelements, like SVA, remain methylated. Remarkably, some loci associated with metabolic and neurological disorders are also resistant to DNA demethylation, revealing potential for transgenerational epigenetic inheritance that may have phenotypic consequences. We provide comprehensive insight on early human germline transcriptional network and epigenetic reprogramming that subsequently impacts human development and disease.

This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Received: January 28, 2015; Received in revised form: March 27, 2015; Accepted: April 14, 2015;

© 2015 The Authors. Published by Elsevier Inc.


O decaimento do RNA conta outra história sobre informação biológica: mero acaso, fortuita necessidade ou design inteligente?

sexta-feira, junho 05, 2015

Assim que o RNA mensageiro (mRNA) executa sua tarefa – transmitindo a informação para produzir as proteínas necessárias para o funcionamento de uma célula – ele não é necessário e se degrada. Os cientistas há muito tempo pensaram que o decaimento começava após o término da tradução e que as moléculas de RNA decaídas forneciam pouca informação biológica.

Agora uma equipe de pesquisadores da EMBL Heidelberg e da Universidade Stanford, dirigida por Lars Steinmetz muda nosso conhecimento em um artigo publicado na revista Cell. Os pesquisadores demonstraram que uma extremidade do mRNA começa a decair enquanto que a outra ainda está servindo de molde para a produção de proteína. A pesquisa revela que o decaimento do mRNA fornece uma pista de como as proteínas são produzidas.

Mero acaso? Fortuita necessidade? Ou design inteligente?

Widespread Co-translational RNA Decay Reveals Ribosome Dynamics

Vicent Pelechano4, Wu Wei4, Lars M. Steinmetzcorrespondenceemail
4Co-first author

DOI: http://dx.doi.org/10.1016/j.cell.2015.05.008


•Co-translational RNA degradation produces an in vivo ribosomal footprint

•Profiling mRNA degradation provides a measurement of ribosome dynamics

•Oxidative stress causes tRNA-specific translation pausing sites dependent on RNY1


It is generally assumed that mRNAs undergoing translation are protected from decay. Here, we show that mRNAs are, in fact, co-translationally degraded. This is a widespread and conserved process affecting most genes, where 5′–3′ transcript degradation follows the last translating ribosome, producing an in vivo ribosomal footprint. By sequencing the ends of 5′ phosphorylated mRNA degradation intermediates, we obtain a genome-wide drug-free measurement of ribosome dynamics. We identify general translation termination pauses in both normal and stress conditions. In addition, we describe novel codon-specific ribosomal pausing sites in response to oxidative stress that are dependent on the RNase Rny1. Our approach is simple and straightforward and does not require the use of translational inhibitors or in vitro RNA footprinting that can alter ribosome protection patterns.


Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site CAPES/Periódicos podem ler gratuitamente este artigo da Cell e de mais 37.000 publicações científicas.

Uma nova datação para a evolução eucariótica???

terça-feira, junho 02, 2015

Reappraisal of hydrocarbon biomarkers in Archean rocks

Katherine L. Frencha,1,2, Christian Hallmannb,c, Janet M. Hoped, Petra L. Schoone, J. Alex Zumbergee, Yosuke Hoshinof, Carl A. Petersf, Simon C. Georgef, Gordon D. Lovee, Jochen J. Brocksd, Roger Buickg, and Roger E. Summonsh

aJoint Program in Chemical Oceanography, Massachusetts Institute of Technology and Woods Hole Oceanographic Institution, Cambridge, MA 02139;

bMax Planck Institute for Biogeochemistry, 07745 Jena, Germany;

cCenter for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany;

dResearch School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia;

eDepartment of Earth Sciences, University of California, Riverside, CA 92521;

fDepartment of Earth and Planetary Sciences, Macquarie University, Sydney, NSW 2109, Australia;

gDepartment of Earth & Space Sciences and Astrobiology Program, University of Washington, Seattle, WA 98195-1310; and

hDepartment of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139

Edited by Andrew H. Knoll, Harvard University, Cambridge, MA, and approved March 16, 2015 (received for review October 21, 2014)


The advent of oxygenic photosynthesis set the stage for the evolution of complex life on an oxygenated planet, but it is unknown when this transformative biochemistry emerged. The existing hydrocarbon biomarker record requires that oxygenic photosynthesis and eukaryotes emerged more than 300 million years before the Great Oxidation Event [∼2.4 billion years ago (Ga)]. We report that hopane and sterane concentrations measured in new ultraclean Archean drill cores from Australia are comparable to blank concentrations, yet their concentrations in the exteriors of conventionally collected cores of stratigraphic equivalence exceed blank concentrations by more than an order of magnitude due to surficial contamination. Consequently, previous hydrocarbon biomarker reports no longer provide valid evidence for the advent of oxygenic photosynthesis and eukaryotes by ∼2.7 Ga.


Hopanes and steranes found in Archean rocks have been presented as key evidence supporting the early rise of oxygenic photosynthesis and eukaryotes, but the syngeneity of these hydrocarbon biomarkers is controversial. To resolve this debate, we performed a multilaboratory study of new cores from the Pilbara Craton, Australia, that were drilled and sampled using unprecedented hydrocarbon-clean protocols. Hopanes and steranes in rock extracts and hydropyrolysates from these new cores were typically at or below our femtogram detection limit, but when they were detectable, they had total hopane < 37.9 pg per gram of rock > and total sterane < 32.9 pg per gram of rock > concentrations comparable to those measured in blanks and negative control samples. In contrast, hopanes and steranes measured in the exteriors of conventionally drilled and curated rocks of stratigraphic equivalence reach concentrations of 389.5 pg per gram of rock and 1,039 pg per gram of rock, respectively. Polycyclic aromatic hydrocarbons and diamondoids, which exceed blank concentrations, exhibit individual concentrations up to 80 ng per gram of rock in rock extracts and up to 1,000 ng per gram of rock in hydropyrolysates from the ultraclean cores.These results demonstrate that previously studied Archean samples host mixtures of biomarker contaminants and indigenous overmature hydrocarbons.

Therefore, existing lipid biomarker evidence cannot be invoked to support the emergence of oxygenic photosynthesis and eukaryotes by ∼2.7 billion years ago. Although suitable Proterozoic rocks exist, no currently known Archean strata lie within the appropriate thermal maturity window for syngenetic hydrocarbon biomarker preservation, so future exploration for Archean biomarkers should screen for rocks with milder thermal histories.

oxygenic photosynthesis eukaryotes cyanobacteria Great Oxidation Event Pilbara


1Present address: Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543.

2To whom correspondence should be addressed. Email: kfrench{at}whoi.edu.

Author contributions: K.L.F., C.H., S.C.G., G.D.L., J.J.B., R.B., and R.E.S. designed research; K.L.F., C.H., J.M.H., P.L.S., J.A.Z., Y.H., C.A.P., and R.B. performed research; K.L.F., C.H., Y.H., S.C.G., G.D.L., J.J.B., and R.E.S. analyzed data; and K.L.F., C.H., Y.H., S.C.G., G.D.L., J.J.B., R.B., and R.E.S. 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.1419563112/-/DCSupplemental.


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O dogma central em biologia nem errado era!

segunda-feira, junho 01, 2015

The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing

Shahar Alon, Sandra C Garrett, Erez Y Levanon, Sara Olson, Brenton R Graveley, Joshua J C Rosenthal, Eli Eisenberg Corresponding Author
Tel Aviv University, Israel; University of Connecticut Health Center, United States; Bar-Ilan University, Israel; University of Puerto Rico Medical Sciences Campus, Puerto Rico 

DOI: http://dx.doi.org/10.7554/eLife.05198
Published January 8, 2015
Cite as eLife 2015;4:e05198


RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

DOI: http://dx.doi.org/10.7554/eLife.05198.001



The central dogma of biology maintains that genetic information passes faithfully from DNA to RNA to proteins; however, with the help of tools such as alternative splicing, organisms use RNA as a canvas to modify and enrich this flow of information. RNA editing by deamination of adenosine to inosine (A-to-I) is another process used to alter genetic information (Nishikura, 2010). Unlike alternative splicing, which shuffles relatively large regions of RNA, editing targets single bases in order to fine-tune protein function. Because inosine is interpreted as guanosine by the cellular machinery, this process can recode codons (Basilio et al., 1962). A-to-I RNA editing is catalyzed by the ADAR (adenosine deaminase that acts on RNA) family of enzymes. All eumetazoans, from cnidarians to mammals, express ADARs but the extent to which they use them to recode has been explored in few representatives (Nishikura, 2010).
Recent advances in DNA sequencing and the supporting computational analyses have permitted transcriptome-wide screens for RNA editing events. So far, such studies have been limited to organisms with a sequenced genome (Ramaswami et al., 20122013). In general, these screens have looked for variation in RNA at positions that are invariant in the genome. In humans, inosine is abundant in RNA (Paul and Bass, 1998Bazak et al., 2014), but almost all of it lies within transcribed repetitive elements in untranslated regions or introns (Nishikura, 2010). A compilation of recoding sites in human transcriptomes revealed 1183 events (Xu and Zhang, 2014), but most were observed in only a single sample. Individual searches (Danecek et al., 2012Ramaswami et al., 2013) uncovered only 115 (non-repetitive) recoding events, and 53 in mice; 34 recoding sites are conserved across mammals (Pinto et al., 2014). In Drosophila, an order of magnitude more recoding sites have been identified, residing in about 3% of all messages (St Laurent et al., 2013). Although individual editing sites are clearly essential (Brusa et al., 1995), these data suggest that RNA editing is not a broadly used mechanism for proteome diversification.
However, anecdotal data suggest this assumption might not apply across the animal kingdom. For example, using traditional cloning methods, scores of recoding sites have been uncovered in a small number of squid and octopus transcripts encoding potassium channels, ADARs, and ion pumps (Garrett and Rosenthal, 2012a). As for most organisms, there are no genomes available for cephalopods. Here we apply a novel approach for editing site detection in the absence of a sequenced genome. We use it to comprehensively identify editing sites in the squid giant axon system and other areas of the nervous system. Surprisingly, almost 60% of all mRNAs studied harbor recoding events, and most at multiple sites. These data show orders of magnitude more recoding in the squid proteome than in any other species studied to date. In squid, editing is so pervasive that the central dogma should be modified to include this process. Our results open the possibility that extensive recoding is common in many organisms, rivaling alternative splicing as a means of creating functional diversity.

Results and discussion

To detect RNA editing sites in the squid nervous system, we generated millions of RNA and genomic DNA reads from an individual squid. Our method differed from previous approaches by using a de novo transcriptome as the point of reference instead of a genome (Figure 1A). The transcriptome was assembled from RNA-seq reads, and each nucleotide within it represents the consensus of many reads. If the majority of RNA reads were edited (‘strong’ editing sites), the transcriptome would differ from the genomic DNA and read ‘G’ where gDNA reads would show ‘A’ (the sequencing process identifies inosines as guanosines). We detected such sites by aligning DNA-seq reads to the transcriptome (Figure 1B). At positions where editing occurred in the minority of RNA-seq reads (‘weak’ editing sites), however, the transcriptome and the genomic DNA would be identical. These sites were detected by identifying variability in RNA-seq, but not DNA-seq, reads (Figure 1B). This general approach is applicable to all organisms that lack a sequenced genome.


Dogma central em biologia evolucionária: DNA >>> RNA >>> Proteínas + mutações serviriam de material para a seleção natural "criar" novas espécies. E agora Darwin? O dogma central em biologia evolucionária foi para a lata do lixo da história da ciência. E o que restou, guru de Down? Ficou simplesmente o dogma que ainda vai continuar sendo "rezado" em muitos livros didáticos de biologia do ensino médio recomendados pelo MEC/SEMTEC/PNLEM, e em muitas universidades onde dizer que Darwin está nu é considerado pecado mortal acadêmico.
Darwin morreu! Viva Darwin!!!