Mitocôndria - um mapa da casa de força da célula: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, agosto 31, 2017

Landscape of submitochondrial protein distribution

F.-Nora Vögtle, Julia M. Burkhart, Humberto Gonczarowska-Jorge, Cansu Kücükköse, Asli Aras Taskin, Dominik Kopczynski, Robert Ahrends, Dirk Mossmann, Albert Sickmann, René P. Zahedi & Chris Meisinger

Nature Communications 8, Article number: 290 (2017)

Mitochondria Proteomics

Received: 02 February 2017 Accepted: 15 June 2017

Published online: 18 August 2017

Source/Fonte: Chris Meisinger


The mitochondrial proteome comprises ~1000 (yeast)–1500 (human) different proteins, which are distributed into four different subcompartments. The sublocalization of these proteins within the organelle in most cases remains poorly defined. Here we describe an integrated approach combining stable isotope labeling, various protein enrichment and extraction strategies and quantitative mass spectrometry to produce a quantitative map of submitochondrial protein distribution in S. cerevisiae. This quantitative landscape enables a proteome-wide classification of 986 proteins into soluble, peripheral, and integral mitochondrial membrane proteins, and the assignment of 818 proteins into the four subcompartments: outer membrane, inner membrane, intermembrane space, or matrix. We also identified 206 proteins that were not previously annotated as localized to mitochondria. Furthermore, the protease Prd1, misannotated as intermembrane space protein, could be re-assigned and characterized as a presequence peptide degrading enzyme in the matrix.


We thank B. Schönfisch, C. Prinz and L. Myketin for expert technical assistance. We thank Dr. J.C. Martinou for the Bax protein. Work included in this study has also been performed in partial fulfillment of the requirements for the doctoral thesis of C.K. This work was supported by the Deutsche Forschungsgemeinschaft, Excellence Initiative of the German Federal & State Governments (EXC 294 BIOSS), the RTG GRK2202 (to C.M.), the Ministerium für Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen (to R.P.Z., J.M.B., and H.G.J.), the Emmy-Noether Programm of the Deutsche Forschungsgemeinschaft to F.N.V. and the CAPES Foundation to H.G.J.

Author information

Author notes

F.-Nora Vögtle and Julia M. Burkhart contributed equally to this work.


Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, 79104, Germany

F.-Nora Vögtle, Cansu Kücükköse, Asli Aras Taskin, Dirk Mossmann & Chris Meisinger

Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany

Julia M. Burkhart, Humberto Gonczarowska-Jorge, Dominik Kopczynski, Robert Ahrends, Albert Sickmann & René P. Zahedi

Faculty of Biology, University of Freiburg, Freiburg im Breisgau, 79104, Germany

Cansu Kücükköse

Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB24 3FX, UK

Albert Sickmann

Medizinisches Proteom Center, Ruhr Universität Bochum, Bochum, 44801, Germany

Albert Sickmann

BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, 79104, Germany

Chris Meisinger


F.-N.V., J.M.B., H.G.-J., C.K., A.A.T., and D.M. performed the experiments. D.K. and R.A. performed statistical analysis. F.-N.V., J.M.B., R.P.Z., and C.M. designed experiments, analyzed, and interpreted the data. C.M., F.-N.V., J.M.B., and R.P.Z. developed the project and wrote the manuscript. H.G.-J. and A.S. reviewed and edited the manuscript. C.M. and R.P.Z. coordinated and directed the project. All authors approved the final version of the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to René P. Zahedi or Chris Meisinger.

FREE PDF GRATIS: Nature Communications Sup. Info. Peer Review File Sup. 

Data 1, 2, 3, 4, 5.

Histona 1, o guardião da estabilidade genômica: mero acaso, fortuita necessidade ou design inteligente?

Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin

Aleix Bayona-Feliu, Anna Casas-Lamesa, Oscar Reina, Jordi Bernués & Fernando Azorín

Nature Communications 8, Article number: 283 (2017)

Chromatin DNA damage and repair

Received: 29 January 2016 Accepted: 22 June 2017

Published online: 18 August 2017


Linker histone H1 is an important structural component of chromatin that stabilizes the nucleosome and compacts the nucleofilament into higher-order structures. The biology of histone H1 remains, however, poorly understood. Here we show that Drosophila histone H1 (dH1) prevents genome instability as indicated by the increased γH2Av (H2AvS137P) content and the high incidence of DNA breaks and sister-chromatid exchanges observed in dH1-depleted cells. Increased γH2Av occurs preferentially at heterochromatic elements, which are upregulated upon dH1 depletion, and is due to the abnormal accumulation of DNA:RNA hybrids (R-loops). R-loops accumulation is readily detectable in G1-phase, whereas γH2Av increases mainly during DNA replication. These defects induce JNK-mediated apoptosis and are specific of dH1 depletion since they are not observed when heterochromatin silencing is relieved by HP1a depletion. Altogether, our results suggest that histone H1 prevents R-loops-induced DNA damage in heterochromatin and unveil its essential contribution to maintenance of genome stability.


We are thankful to Drs A. Casali, J. Casanova, O. Fernández-Capetillo, G. Fernández-Miranda, J.T. Kadonaga, R. Méndez, G. Roncador, T. Stracker and A. Vaquero for materials and advise. This work was supported by grants from MICINN (BFU2012-30724 and BFU2015-65082-P), the Generalitat de Catalunya (SGR2014-204) and by the European Community FEDER program. A.B.-F. and A.C.-L. acknowledge receipt of FPU (MED) and FPI (MINECO) fellowships, respectively.

Author information

Author notes

Aleix Bayona-Feliu

Present address: Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain

Aleix Bayona-Feliu and Anna Casas-Lamesa contributed equally to this work.


Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain

Aleix Bayona-Feliu, Anna Casas-Lamesa, Jordi Bernués & Fernando Azorín

Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain

Aleix Bayona-Feliu, Anna Casas-Lamesa, Oscar Reina, Jordi Bernués & Fernando Azorín


A.B.-F., A.C.-L. and J.B. performed the experiments. O.R. performed the Bioinformatics analyses. J.B. and F.A. designed the experiments and wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Jordi Bernués or Fernando Azorín.

"Furadeiras" moleculares abrem membranas celulares: mero acaso, fortuita necessidade ou design inteligente?

Molecular machines open cell membranes

Víctor García-López, Fang Chen, Lizanne G. Nilewski, Guillaume Duret, Amir Aliyan, Anatoly B. Kolomeisky, Jacob T. Robinson, Gufeng Wang, Robert Pal & James M. Tour

Affiliations Contributions Corresponding authors

Nature 548, 567–572 (31 August 2017) doi:10.1038/nature23657   

Received 07 September 2016 Accepted 05 July 2017 

Published online 30 August 2017


Beyond the more common chemical delivery strategies, several physical techniques are used to open the lipid bilayers of cellular membranes1. These include using electric2 and magnetic3 fields, temperature4, ultrasound5 or light6 to introduce compounds into cells, to release molecular species from cells or to selectively induce programmed cell death (apoptosis) or uncontrolled cell death (necrosis). More recently, molecular motors and switches that can change their conformation in a controlled manner in response to external stimuli have been used to produce mechanical actions on tissue for biomedical applications789. Here we show that molecular machines can drill through cellular bilayers using their molecular-scale actuation, specifically nanomechanical action. Upon physical adsorption of the molecular motors onto lipid bilayers and subsequent activation of the motors using ultraviolet light, holes are drilled in the cell membranes. We designed molecular motors and complementary experimental protocols that use nanomechanical action to induce the diffusion of chemical species out of synthetic vesicles, to enhance the diffusion of traceable molecular machines into and within live cells, to induce necrosis and to introduce chemical species into live cells. We also show that, by using molecular machines that bear short peptide addends, nanomechanical action can selectively target specific cell-surface recognition sites. Beyond the in vitro applications demonstrated here, we expect that molecular machines could also be used in vivo, especially as their design progresses to allow two-photon, near-infrared and radio-frequency activation10.

Como o genoma estabelece sua microarquitetura funcional: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, agosto 30, 2017

Large scale genomic reorganization of topological domains at the HoxD locus

Pierre J. Fabre, Marion Leleu, Benjamin H. Mormann, Lucille Lopez-Delisle, Daan Noordermeer, Leonardo Beccari and Denis Duboule

Genome Biology201718:149

Received: 13 March 2017Accepted: 14 July 2017Published: 7 August 2017



The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts.


To assess the structure–function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. We assessed the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel long-range contacts. We report multi-partite associations between HoxD genes and up to three enhancers. We find that the loss of native chromatin topology leads to the remodeling of TAD structure following distinct parameters.


Our results reveal that the recomposition of TAD architectures after large genomic re-arrangements is dependent on a boundary-selection mechanism in which CTCF mediates the gating of long-range contacts in combination with genomic distance and sequence specificity. Accordingly, the building of a recomposed TAD at this locus depends on distinct functional and constitutive parameters.


Regulatory landscape Chromatin organization Gene regulation Topologically associating domains TAD Enhancer Hox CTCF Limb development

FREE PDF GRATIS: Genome Biology

Gerd B. Müller, teórico evolucionista expoente admite: a evolução “evita amplamente” as maiores questões das origens biológicas

Evolution News | @DiscoveryCSC

28 de agosto de 2017, 12:55 PM

Neste último encontro de novembro de 2016 da Royal Society, “New Trends in Evolutionary Biology” [Novas tendências em biologia evolucionária] o renomado teórico evolucionista austríaco Gerd B. Müller [foto ao lado] deu a primeira apresentação. Como nós destacamos antes, foi uma apresentação devastadora para alguém que quer pensar que, sobre as grandes questões de origens biológicas, a teoria evolucionária ortodoxa já explicou tudo. Em vez disso, Müller apontou para as lacunas de “déficits explanatórios” na teoria. Agora a publicação científica da Royal Society, o Interface Focus, oferece uma edição especial reunindo artigos baseados nas palestras da conferência.

Vejamos o que o Dr. Müller tem a dizer no artigo intitulado, “Why an extended evolutionary synthesis is necessary” [Porque é necessária uma síntese evolutiva ampliada/estendida] Um amigo destacou o seguinte parágrafo, com suas ênfases adicionadas.

Como pode ser notado dos princípios relacionados, a atual teoria evolucionária é predominantemente orientada para uma explicação genética de variação e, exceto por algumas modificações semânticas mínimas, isso não tem mudado ao longo das últimas sete ou oito décadas. Qualquer que seja o apoio da boca para fora pago para leva rem consideração outros fatores do que aqueles aceitos tradicionalmente, nós descobrimos que a teoria, conforme apresentada em artigos existentes, concentra-se em uma limitada série de explananda evolutiva, excluindo a maioria daqueles mencionados entre os objetivos explanatórios acima. A teoria cumpre bem seu papel no que diz respeito às questões em que se concentra, fornecendo predições testáveis e abundantemente confirmadas na dinâmica da variação genética em populações evoluindo, na variação gradual e adaptação de características fenotípicas, e sobre certas características genéticas de especiação. Se a explanação parasse aqui, não existiria controvérsia. Mas, tem se tornado habitual em biologia evolucionária se tomar a genética de população como o tipo de explicação privilegiado de todos os fenômenos evolutivos, negando assim o fato de que, por um lado, nem todas as suas predições podem ser confirmadas sob todas as circunstâncias e, por outro lado, um grande número de fenômenos evolucionários permanece excluído. Por exemplo, a teoria evita largamente a questão de como as organizações complexas de estrutura organismal, a fisiologia, o desenvolvimento ou comportamento — cuja variação ela descreve — surgem realmente na evolução, e também não fornece meios adequados para incluir fatores que não fazem parte da estrutura da genética populacional tais como as influências de desenvolvimento, sistemas teóricos, ecológicos ou culturais.

Uh, uau. Ou como o nosso amigo disse, “BOOM.” Leia isso de novo. Müller diz que “a atual teoria evolucionária… amplamente evita a questão de como as organizações complexas de estrutura organismal, fisiologia, desenvolvimento ou comportamento… surgem de verdade na evolução”. Mas como a coisa biológica “surge de verdade” é exatamente o que a maioria das pessoas pensa quando elas pensam da “evolução”.

Diz o nosso amigo, vide Michael Behe no seu livro The Edge of Evolution, onde o Dr. Behe pergunta, “A grande questão, contudo, não é ‘Quem sobreviverá, o mais apto ou o menos apto?’. A grande questão é ‘Como os organismos se tornam mais aptos? ’” Müller concede que o pensamento evolucionário convencional “amplamente evita” essa “grande questão”. Embora expressada em termos anódinos, isso é uma acusação gravíssima.

Eis aqui outras pérolas do artigo (as ênfases foram adicionadas):

Um número crescente de publicações defende uma profunda revisão ou até mesmo a substituição da teoria da evolução padrão [2–14], indicando que isso não pode ser desconsiderado como uma opinião minoritária, mas antes, é um amplo sentimento idêntico entre cientistas e filósofos.

Essa afirmação poderia ter aparecido em um trabalho de proponente de design inteligente. Mas espere, isso ainda fica melhor:

Na verdade, um número crescente de desafios ao modelo clássico de evolução tem surgido ao longo dos últimos anos, tais como da biologia de desenvolvimento evolucionário [16], epigenética [17], fisiologia [18], genômica [19], ecologia [20], pesquisa de plasticidade [21], genética populacional [22], evolução regulatória [23], abordagens de redes [14], pesquisa de novidade biológica [24], biologia comportamental [12], microbiologia [7] e biologia de sistemas [25], ainda mais apoiado pelos argumentos das ciências culturais [26] e sociais [27], bem como por tratamentos filosóficos [28–31]. Nenhuma dessas contenções é acientífica, todas repousam firmemente em princípios evolucionários e todas são apoiadas por evidência empírica substancial.

“Desafios ao modelo clássico” são “amplas” e “nenhuma … é acientífica”. Uau — arquive isso para future referência.


Algumas vezes esses desafios são tratados com hostilidade dogmática, denunciando qualquer crítica do edifício teórico tradicional como estúpida [32], mas mais frequentemente os defensores da concepção tradicional argumentam que ‘tudo vai bem’ com a atual teoria evolucionária, que eles veem como tendo ‘coevoluído’ junto com os avanços metodológico e empírico que já recebem o que lhes é devido na atual biologia evolucionária [33]. Mas o fato repetidamente enfatizado de que os mecanismos evolucionários inovadores têm sido mencionados em certos artigos mais antigos ou mais recentes não quer dizer que a estrutura formal da teoria evolutiva tenha se ajustado a eles.

Os darwinistas ortodoxos da escola “Tudo Vai Bem” enfrentam os desafios com “hostilidade dogmática”? Sim. Nós estávamos cientes.

Aqui ele destrói a noção, uma verdadeira extrapolação vazia, que as mudanças microevolutivas podem explicar as tendências macroevolutivas:

Uma versão mais sútil do argumento isso-já-foi-dito-antes usado para desviar quaisquer desafios à visão recebida é levar a questão para o interminável debate da micro-versus-macroevolução. Enquanto que a ‘microevolução’ é considerada como a mudança contínua das frequências de alelos dentro de uma espécie ou população [109], o conceito mal definido de macroevolução [36], amalgama a questão de especiação e a origem dos ‘táxons superiores’ com a tão chamada ‘principal mudança fenotípica’ ou novo tipos construcionais. Geralmente, um reconhecimento superficial do problema da origem dos caracteres fenotípicos rapidamente se torna uma discussão de argumentos de genética de população sobre a especiação, muitas vezes ligada ao conceito difamado de equilíbrio pontuado [9], a fim de finalmente desconsiderar qualquer necessidade da mudança de teoria. Assim, o problema da complexidade fenotípica se torna (des)elegantemente ignorado. Inevitavelmente, a conclusão é alcançada de que os mecanismos microevolucionários são consistentes com os fenômenos macroevolucionários [36], muito embora isso tem muito pouco a ver com a estrutura e predições da Síntese Evolutiva Ampliada/Estendida. A verdadeira questão é que a evolução genética sozinha tem sido encontrada insuficiente para uma explicação causal adequada de todas as formas de complexidade fenotípica, não somente de algo vagamente denominado ‘macroevolução’. Consequentemente, a distinção micro–macro serve somente para obscurecer as questões importantes que surgem dos atuais desafios à teoria padrão. Isso não deveria ser usado na discussão da Síntese Evolutiva Ampliada/Estendida, que raramente faz quaisquer alusões à macroevolução, embora algumas vezes seja forçada a fazer.

Isso é uma concessão maior da parte de uma figura principal no mundo da teoria da evolução. É um grande olho preto à turma do “Tudo Vai Bem”. Quem irá dizer para a mídia? Quem irá dizer aos leões de chácara de Darwin? Quem irá dizer aos estudantes de biologia no ensino médio ou na faculdade, mantidos nas trevas pela rígida pedagogia darwinista?

A evolução tem somente “pontos fortes” e nenhum “ponto fraco”, você diz? A teoria darwinista estão tão firmemente estabelecida como “a gravidade, o heliocentrismo, e a forma redonda da Terra“? Realmente? Como alguém pode manter possivelmente manter esse tanto considerando-se essa afirmação cristalina, não de nenhum defensor do DI ou cético de Darwin, não de um tão-chamado “criacionista”, mas de uma figura central em pesquisa evolucionária, escrevendo em um journal publicado pela augusta sociedade científica uma vez presidida por Isaac Newton, por ter gritado tão alto?

Manter este ponto de que “Tudo Vai Bem” com a evolução, você deve estar em um estado sério de negacionismo.

Scholars e professores das universidades de Princeton, Harvard e Yale aconselham alunos a pensar criticamente e questionar tudo!

Alguns pensamentos e conselho para nossos estudantes e todos os estudantes

29 de agosto de 2017

Nós somos scholars e professores nas universidades de Princeton, Harvard, e Yale que temos alguns pensamentos a compartilhar e conselho para oferecer aos estudantes que estão indo para faculdades por todo o país. Nosso conselho pode reduzido a três palavras:

Pense por si [mesmo].

Bem, isso pode parecer fácil. Mas você descobrirá —como você já ter descoberto no ensino médio— que pensar por si mesmo pode ser um desafio. Isso sempre demanda autodisciplina e nesses dias pode exigir coragem.

No clima [cultural] de hoje, é tudo muito fácil permitir que suas opiniões e postura podem ser modeladas pela opinião dominante em seu campus ou na cultura acadêmica mais ampla. O perigo que qualquer estudante —ou membro de faculdade— enfrenta hoje está caindo no vício do conformismo, resultando em pensamento de grupo.

Nas muitas faculdades e universidades, aquilo que John Stuart Mill chamou de “a tirania da opinião pública” faz mais do que meramente desencorajar os estudantes em dissentir de opiniões morais, políticas prevalecentes, e outros tipos de questões. Isso os leva supor que as opiniões dominantes são tão obviamente corretas que somente um intolerante ou um maluco poderia questioná-las.

Desde que ninguém ser, ou ser tido como um intolerante ou um maluco, o jeito fácil e preguiçoso de proceder é simplesmente se ajustar com as ortodoxias do campus.

Não faça isso. Pense por si mesmo.

Pensar por si mesmo significa questionar as ideias dominantes mesmo quando outras pessoas insistirem que elas sejam tratadas como inquestionáveis. Isso significa decidir o que alguém crê não se conformando com as opiniões da época, mas em ter o trabalho de aprender e considerar honestamente os argumentos mais fortes para serem avançados pelos dois lados das questões —inclusive argumentos para posições que outros ultrajam e querem estigmatizar e contra posições que outras pessoas procuram imunizar do escrutínio crítico.

O amor da verdade e o desejo de alcança-la deveria lhe motivar a pensar por si mesmo. O ponto central de uma educação universitária é buscar a verdade, aprender as capacidades e obter as virtudes necessárias para ser um buscador da verdade a vida toda. Mente aberta, pensamento crítico, e o debate são essenciais para descobrir a verdade. Além disso, elas são os melhores antídotos contra a intolerância. 

A primeira definição do dicionário Merriam-Webster para a palavra “bigot” é uma pessoa “que é obstinadamente ou intolerantemente devotada para suas próprias opiniões e preconceitos”. As únicas pessoas que precisam temer a pesquisa de mente aberta e debate robusto são os verdadeiros intolerantes, incluindo aqueles nos campi ou no espectro maior da sociedade que buscam proteger a hegemonia de suas opiniões ao afirmarem que questionar essas opiniões é intolerância em si mesma.

Desse modo, não seja oprimido pela opinião pública. Não fique preso numa câmara de eco. Mesmo que no fim você rejeite ou defenda uma opinião, certifique-se que você decide onde que você vai ficar por ponderar criticamente os argumentos das posições competidoras.

Pense por si [mesmo].

Boa sorte para você na faculdade!

Paul Bloom
Brooks and Suzanne Ragen Professor of Psychology
Yale University

Nicholas Christakis
Sol Goldman Family Professor of Social and Natural Science
Yale University

Carlos Eire
T. Lawrason Riggs Professor of History and Religious Studies
Yale University

Maria E. Garlock
Professor of Civil and Environmental Engineering and Co-Director of the Program in Architecture and Engineering
Princeton University

Robert P. George
McCormick Professor of Jurisprudence and Director of the James Madison Program in American Ideals and Institutions

Princeton University

Mary Ann Glendon
Learned Hand Professor of Law
Harvard University

Joshua Katz
Cotsen Professor in the Humanities and Professor of Classics
Princeton University

Thomas P. Kelly
Professor of Philosophy
Princeton University

Jon Levenson
Albert A. List Professor of Jewish Studies
Harvard University

John B. Londregan
Professor of Politics and International Affairs
Princeton University

Michael A. Reynolds
Associate Professor of Near Eastern Studies
Princeton University

Jacqueline C. Rivers
Lecturer in Sociology and African and African-American Studies
Harvard University

Noël Valis
Professor of Spanish
Yale University

Tyler Vander Weele
Professor of Epidemiology and Biostatistics and Director of the Program on Integrative Knowledge and Human Flourishing
Harvard University

Adrian Vermeule
Ralph S. Tyler, Jr. Professor of Constitutional Law
Harvard University


Armazenagem de informações biológicas nas nuves - Literalmente!!!

segunda-feira, agosto 28, 2017

Active microorganisms thrive among extremely diverse communities in cloud water

Pierre Amato , Muriel Joly, Ludovic Besaury, Anne Oudart, Najwa Taib, Anne I. Moné, Laurent Deguillaume, Anne-Marie Delort, Didier Debroas


Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active in situ remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~103−104 bacteria and archaea mL-1 and ~102−103 eukaryote cells mL-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.


We warmly thank the numerous people who helped us concretizing this study: J. Colombet, L. Nauton, J.M. Pichon, I. Mary, F. Enault, J.C. Charvy, A. Mahul and the Mesocentre Calcul Center, and G. Lefebvre for language corrections in the manuscript.


Será que vão derrubar essa estátua de Darwin???

sábado, agosto 26, 2017

"Em algum período futuro, não muito distante sendo medido pelos séculos, as raças civilizadas do homem certamente irão exterminar, e substituir as raças selvagens por todo o mundo. Ao mesmo tempo os macacos antropomorfos, como destacou o Professor Schaaffhausen, sem dúvida, serão exterminados. A distinção entre o homem e os seus aliados mais próximos será então muito mais ampla, pois intervirá entre o homem em um estado mais civilizado, como nós esperamos, até mesmo do Caucasiano, e alguns macacos tão inferiores como o babuíno, em vez de como é agora entre o negro, ou o indígena australiano e o gorila."

"At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate and replace throughout the world the savage races. At the same time the anthropomorphous apes, as Professor Schaaffhausen has remarked, will no doubt be exterminated. The break will then be rendered wider, for it will intervene between man in a more civilised state as we may hope, than the Caucasian and some ape as low as a baboon, instead of as at present between the negro or Australian and the gorilla." 

― Charles Darwin, 1871. The descent of man, and selection in relation to sex. London: John Murray. Volume 1, p. 105.

EXTRA! EXTRA! EXTRA! Como os biólogos darwinistas falharam em compreender a evolução através da Síntese Evolutiva Moderna!!!

Source/Fonte: LinkedIn

Special Issue "Beyond the Modern Evolutionary Synthesis- what have we missed?"
1. Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development via Differentiation Trees of Embryos
by Bradly Alicea and Richard Gordon

Biology 2016, 5(3), 33; doi:10.3390/biology5030033
Received: 3 April 2016 / Revised: 4 July 2016 / Accepted: 9 August 2016 / Published: 18 August 2016

Abstract Embryonic development proceeds through a series of differentiation events. The mosaic version of this process (binary cell divisions) can be analyzed by comparing early development of Ciona intestinalis and Caenorhabditis elegans. To do this, we reorganize lineage trees into differentiation trees using the graph theory ordering of relative cell volume. Lineage and differentiation trees provide us with means to classify each cell using binary codes. Extracting data characterizing lineage tree position, cell volume, and nucleus position for each cell during early embryogenesis, we conduct several statistical analyses, both within and between taxa. We compare both cell volume distributions and cell volume across developmental time within and between single species and assess differences between lineage tree and differentiation tree orderings. This enhances our understanding of the differentiation events in a model of pure mosaic embryogenesis and its relationship to evolutionary conservation. We also contribute several new techniques for assessing both differences between lineage trees and differentiation trees, and differences between differentiation trees of different species. The results suggest that at the level of differentiation trees, there are broad similarities between distantly related mosaic embryos that might be essential to understanding evolutionary change and phylogeny reconstruction. Differentiation trees may therefore provide a basis for an Evo-Devo Postmodern Synthesis.

2. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process
by James A. Shapiro

Biology 2016, 5(2), 27; doi:10.3390/biology5020027
Received: 12 February 2016 / Revised: 20 May 2016 / Accepted: 2 June 2016 / Published: 8 June 2016

Abstract The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

3. An Evolutionary Framework for Understanding the Origin of Eukaryotes
by Neil W. Blackstone

Biology 2016, 5(2), 18; doi:10.3390/biology5020018
Received: 28 February 2016 / Revised: 15 April 2016 / Accepted: 25 April 2016 / Published: 27 April 2016

Abstract Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. 

4. Phenotype as Agent for Epigenetic Inheritance
by John S. Torday and William B. Miller

Biology 2016, 5(3), 30; doi:10.3390/biology5030030
Received: 8 April 2016 / Revised: 24 May 2016 / Accepted: 5 July 2016 / Published: 8 July 2016

Abstract The conventional understanding of phenotype is as a derivative of descent with modification through Darwinian random mutation and natural selection. Recent research has revealed Lamarckian inheritance as a major transgenerational mechanism for environmental action on genomes whose extent is determined, in significant part, by germ line cells during meiosis and subsequent stages of embryological development. In consequence, the role of phenotype can productively be reconsidered. The possibility that phenotype is directed towards the effective acquisition of epigenetic marks in consistent reciprocation with the environment during the life cycle of an organism is explored. It is proposed that phenotype is an active agent in niche construction for the active acquisition of epigenetic marks as a dominant evolutionary mechanism rather than a consequence of Darwinian selection towards reproductive success. The reproductive phase of the life cycle can then be appraised as a robust framework in which epigenetic inheritance is entrained to affect growth and development in continued reciprocal responsiveness to environmental stresses. Furthermore, as first principles of physiology determine the limits of epigenetic inheritance, a coherent justification can thereby be provided for the obligate return of all multicellular eukaryotes to the unicellular state. 

5. Evolution of Microbial Quorum Sensing to Human Global Quorum Sensing: An Insight into How Gap Junctional Intercellular Communication Might Be Linked to the Global Metabolic Disease Crisis
by James E. Trosko

Biology 2016, 5(2), 29; doi:10.3390/biology5020029
Received: 7 March 2016 / Revised: 25 May 2016 / Accepted: 3 June 2016 / Published: 15 June 2016

Abstract The first anaerobic organism extracted energy for survival and reproduction from its source of nutrients, with the genetic means to ensure protection of its individual genome but also its species survival. While it had a means to communicate with its community via simple secreted molecules (“quorum sensing”), the eventual shift to an aerobic environment led to multi-cellular metazoan organisms, with evolutionary-selected genes to form extracellular matrices, stem cells, stem cell niches, and a family of gap junction or “connexin” genes. These germinal and somatic stem cells responded to extracellular signals that triggered intra-cellular signaling to regulate specific genes out of the total genome. These extra-cellular induced intra-cellular signals also modulated gap junctional intercellular communication (GJIC) in order to regulate the new cellular functions of symmetrical and asymmetrical cell division, cell differentiation, modes of cell death, and senescence. Within the hierarchical and cybernetic concepts, differentiated by neurons organized in the brain of the Homo sapiens, the conscious mind led to language, abstract ideas, technology, myth-making, scientific reasoning, and moral decision–making, i.e., the creation of culture. Over thousands of years, this has created the current collision between biological and cultural evolution, leading to the global “metabolic disease” crisis.

6. Cryptic Genetic Variation in Evolutionary Developmental Genetics
by Annalise B. Paaby and Greg Gibson

Biology 2016, 5(2), 28; doi:10.3390/biology5020028

Received: 11 April 2016 / Revised: 1 June 2016 / Accepted: 6 June 2016 / Published: 13 June 2016

Abstract Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

7. Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives
by Warren Burggren

Biology 2016, 5(2), 24; doi:10.3390/biology5020024

Received: 16 March 2016 / Revised: 26 April 2016 / Accepted: 11 May 2016 / Published: 25 May 2016

Abstract Epigenetics increasingly occupies a pivotal position in our understanding of inheritance, natural selection and, perhaps, even evolution. A survey of the PubMed database, however, reveals that the great majority (>93%) of epigenetic papers have an intra-, rather than an inter-generational focus, primarily on mechanisms and disease. Approximately ~1% of epigenetic papers even mention the nexus of epigenetics, natural selection and evolution. Yet, when environments are dynamic (e.g., climate change effects), there may be an “epigenetic advantage” to phenotypic switching by epigenetic inheritance, rather than by gene mutation. An epigenetically-inherited trait can arise simultaneously in many individuals, as opposed to a single individual with a gene mutation. Moreover, a transient epigenetically-modified phenotype can be quickly “sunsetted”, with individuals reverting to the original phenotype. Thus, epigenetic phenotype switching is dynamic and temporary and can help bridge periods of environmental stress. Epigenetic inheritance likely contributes to evolution both directly and indirectly. While there is as yet incomplete evidence of direct permanent incorporation of a complex epigenetic phenotype into the genome, doubtlessly, the presence of epigenetic markers and the phenotypes they create (which may sort quite separately from the genotype within a population) will influence natural selection and, so, drive the collective genotype of a population.

8. Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow
by William B. Miller

Biology 2016, 5(2), 21; doi:10.3390/biology5020021

Received: 18 February 2016 / Revised: 3 May 2016 / Accepted: 11 May 2016 / Published: 21 May 2016

Abstract As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses.

9. The Cell as the First Niche Construction
by John S. Torday

Biology 2016, 5(2), 19; doi:10.3390/biology5020019

Received: 17 February 2016 / Revised: 14 April 2016 / Accepted: 18 April 2016 / Published: 28 April 2016

Abstract Niche construction nominally describes how organisms can form their own environments, increasing their capacity to adapt to their surroundings. It is hypothesized that the formation of the first cell as ‘internal’ Niche Construction was the foundation for life, and that subsequent niche constructions were iterative exaptations of that event. The first instantation of niche construction has been faithfully adhered to by returning to the unicellular state, suggesting that the life cycle is zygote to zygote, not adult to adult as is commonly held. The consequent interactions between niche construction and epigenetic inheritance provide a highly robust, interactive, mechanistic way of thinking about evolution being determined by initial conditions rather than merely by chance mutation and selection. This novel perspective offers an opportunity to reappraise the processes involved in evolution mechanistically, allowing for scientifically testable hypotheses rather than relying on metaphors, dogma, teleology and tautology.

10. The Emergence of Physiology and Form: Natural Selection Revisited
by John S. Torday

Biology 2016, 5(2), 15; doi:10.3390/biology5020015
Received: 17 February 2016 / Revised: 23 March 2016 / Accepted: 25 March 2016 / Published: 1 April 2016

Abstract Natural Selection describes how species have evolved differentially, but it is descriptive, non-mechanistic. What mechanisms does Nature use to accomplish this feat? One known way in which ancient natural forces affect development, phylogeny and physiology is through gravitational effects that have evolved as mechanotransduction, seen in the lung, kidney and bone, linking as molecular homologies to skin and brain. Tracing the ontogenetic and phylogenetic changes that have facilitated mechanotransduction identifies specific homologous cell-types and functional molecular markers for lung homeostasis that reveal how and why complex physiologic traits have evolved from the unicellular to the multicellular state. Such data are reinforced by their reverse-evolutionary patterns in chronic degenerative diseases. The physiologic responses of model organisms like Dictyostelium and yeast to gravity provide deep comparative molecular phenotypic homologies, revealing mammalian Target of Rapamycin (mTOR) as the final common pathway for vertical integration of vertebrate physiologic evolution; mTOR integrates calcium/lipid epistatic balance as both the proximate and ultimate positive selection pressure for vertebrate physiologic evolution. The commonality of all vertebrate structure-function relationships can be reduced to calcium/lipid homeostatic regulation as the fractal unit of vertebrate physiology, demonstrating the primacy of the unicellular state as the fundament of physiologic evolution.