Cavidades orbitárias humanas fornecem visão mais ampla do que os demais símios

sábado, julho 04, 2015

Unique human orbital morphology compared with that of apes

Eric Denion, Martin Hitier, Vincent Guyader, Audrey-Emmanuelle Dugué & Frédéric Mouriaux

AffiliationsContributionsCorresponding author

Scientific Reports 5, Article number: 11528 doi:10.1038/srep11528

Received 19 January 2015 Accepted 20 May 2015 Published 25 June 2015

Source/Fonte: Natural History National Museum (Paris, France)

Abstract

Humans’ and apes’ convergent (front-facing) orbits allow a large overlap of monocular visual fields but are considered to limit the lateral visual field extent. However, humans can greatly expand their lateral visual fields using eye motion. This study aimed to assess whether the human orbital morphology was unique compared with that of apes in avoiding lateral visual field obstruction. The orbits of 100 human skulls and 120 ape skulls (30 gibbons; 30 orangutans; 30 gorillas; 30 chimpanzees and bonobos) were analyzed. The orbital width/height ratio was calculated. Two orbital angles representing orbital convergence and rearward position of the orbital margin respectively were recorded using a protractor and laser levels. Humans have the largest orbital width/height ratio (1.19; p < 0.001). Humans and gibbons have orbits which are significantly less convergent than those of chimpanzees / bonobos, gorillas and orangutans (p < 0.001). These elements suggest a morphology favoring lateral vision in humans. More specifically, the human orbit has a uniquely rearward temporal orbital margin (107.1°; p < 0.001), suitable for avoiding visual obstruction and promoting lateral visual field expansion through eye motion. Such an orbital morphology may have evolved mainly as an adaptation to open-country habitat and bipedal locomotion.

Subject terms: Biological anthropology Evolutionary theory

FREE PDF GRATIS: Nature Science Reports

Descoberto novo mecanismo de reparo do DNA: mais complexidade que Darwin não explica!

Structure of transcribed chromatin is a sensor of DNA damage

Nikolay A. Pestov1,*, Nadezhda S. Gerasimova2,*, Olga I. Kulaeva2,3 and Vasily M. Studitsky1,2,3,†

+ Author Affiliations

↵†Corresponding author. E-mail: vasily.studitsky@fccc.edu

↵* These authors contributed equally to this work.

Science Advances 03 Jul 2015:

Vol. 1, no. 6, e1500021

DOI: 10.1126/sciadv.1500021

Article



Abstract

Early detection and repair of damaged DNA is essential for cell functioning and survival. Although multiple cellular systems are involved in the repair of single-strand DNA breaks (SSBs), it remains unknown how SSBs present in the nontemplate strand (NT-SSBs) of DNA organized in chromatin are detected. The effect of NT-SSBs on transcription through chromatin by RNA polymerase II was studied. NT-SSBs localized in the promoter-proximal region of nucleosomal DNA and hidden in the nucleosome structure can induce a nearly quantitative arrest of RNA polymerase downstream of the break, whereas more promoter-distal SSBs moderately facilitate transcription. The location of the arrest sites on nucleosomal DNA suggests that formation of small intranucleosomal DNA loops causes the arrest. This mechanism likely involves relief of unconstrained DNA supercoiling accumulated during transcription through chromatin by NT-SSBs. These data suggest the existence of a novel chromatin-specific mechanism that allows the detection of NT-SSBs by the transcribing enzyme.

Keywords DNA damage chromatin structure transcription-coupled DNA repair single-strand DNA breaks DNA loop nucleosome

Copyright © 2015, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

FREE PDF GRATIS: Science Advances

Uma estrutura "invisível" de proteína explica o poder das enzimas

Structural basis for catalytically restrictive dynamics of a high-energy enzyme state

Michael Kovermann, Jörgen Ådén, Christin Grundström, A. Elisabeth Sauer-Eriksson, Uwe H. Sauer & Magnus Wolf-Watz

AffiliationsContributionsCorresponding author

Nature Communications 6, Article number: 7644 doi:10.1038/ncomms8644

Received 13 January 2015 Accepted 27 May 2015 Published 03 July 2015



Abstract

An emerging paradigm in enzymology is that transient high-energy structural states play crucial roles in enzymatic reaction cycles. Generally, these high-energy or ‘invisible’ states cannot be studied directly at atomic resolution using existing structural and spectroscopic techniques owing to their low populations or short residence times. Here we report the direct NMR-based detection of the molecular topology and conformational dynamics of a catalytically indispensable high-energy state of an adenylate kinase variant. On the basis of matching energy barriers for conformational dynamics and catalytic turnover, it was found that the enzyme’s catalytic activity is governed by its dynamic interconversion between the high-energy state and a ground state structure that was determined by X-ray crystallography. Our results show that it is possible to rationally tune enzymes’ conformational dynamics and hence their catalytic power—a key aspect in rational design of enzymes catalysing novel reactions.

Subject terms: Biological sciences Biophysics Biochemistry

FREE PDF GRATIS: Nature Communications

Genomas elefantídeos revelam as bases moleculares das adaptações do mamute peludo ao Ártico

sexta-feira, julho 03, 2015

Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic

Vincent J. Lynchcorrespondenceemail, Oscar C. Bedoya-Reina4, Aakrosh Ratan5, Michael Sulak, Daniela I. Drautz-Moses6, George H. Perry, Webb Millercorrespondenceemail, Stephan C. Schuster6

4Present address: MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK

5Present address: Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA

6Present address: Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore 637551, Singapore

Publication stage: In Press Corrected Proof



Highlights

•Complete genomes of three Asian elephants and two woolly mammoths were sequenced

•Mammoth-specific amino acid changes were found in 1,642 protein-coding genes

•Genes with mammoth-specific changes are associated with adaptation to extreme cold

•An amino acid change in TRPV3 may have altered temperature sensation in mammoths

Summary

Woolly mammoths and living elephants are characterized by major phenotypic differences that have allowed them to live in very different environments. To identify the genetic changes that underlie the suite of woolly mammoth adaptations to extreme cold, we sequenced the nuclear genome from three Asian elephants and two woolly mammoths, and we identified and functionally annotated genetic changes unique to woolly mammoths. We found that genes with mammoth-specific amino acid changes are enriched in functions related to circadian biology, skin and hair development and physiology, lipid metabolism, adipose development and physiology, and temperature sensation. Finally, we resurrected and functionally tested the mammoth and ancestral elephant TRPV3 gene, which encodes a temperature-sensitive transient receptor potential (thermoTRP) channel involved in thermal sensation and hair growth, and we show that a single mammoth-specific amino acid substitution in an otherwise highly conserved region of the TRPV3 channel strongly affects its temperature sensitivity.

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

Received: February 13, 2015; Received in revised form: May 18, 2015; Accepted: June 5, 2015; Published Online: July 02, 2015

© 2015 The Authors. Published by Elsevier Inc.

FREE PDF GRATIS: Cell Reports 

A galinha lamarckiana e o ovo darwiniano

quinta-feira, julho 02, 2015

The Lamarckian chicken and the Darwinian egg

Yitzhak Pilpel 1 and Oded Rechavi 2

Corresponding authors: Yitzhak Pilpel pilpel@weizmann.ac.il - Oded Rechavi odedrechavi@gmail.com

Author Affiliations

1 Department of Molecular genetics, Weizmann Institute of Science, Rehovot 76100, Israel

2 Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School, Tel Aviv University, Tel Aviv 69978, Israel

Biology Direct 2015, 10:34 doi:10.1186/s13062-015-0062-9

Received: 29 March 2015

Accepted: 22 June 2015

Published: 1 July 2015

© 2015 Pilpel and Rechavi. 



Abstract

“Which came first, the Chicken or the Egg?” We suggest this question is not a paradox. The Modern Synthesis envisions speciation through genetic changes in germ cells via random mutations, an “Egg first” scenario, but perhaps epigenetic inheritance mechanisms can transmit adaptive changes initiated in the soma (“Chicken first”).

Reviewers

The article was reviewed by Dr. Eugene Koonin, Dr. Itai Yanai, Dr. Laura Landweber.

Keywords: Evolution; Darwinian Evolution; Lamarckian Evolution; Modern Synthesis; Weismann Barrier; Epigenetic Inheritance; Transgenerational RNA Interference

Background

In this commentary paper we wish to use the well-known “Chicken and Egg” paradox as a gateway for discussing different processes of evolution. While in the biological sense this is not a paradox at all, the metaphor is still useful because it allows examining of the distinction between Lamarckian and Darwinian evolution, and specifically, since it enables us to raise an important and unsolved question: “Can the phenotype affect the genotype?” or in other words, “can epigenetics translate into genetics”?

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.

FREE PDF GRATIS: Biology Direct

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NOTA DESTE BLOGGER:

O flerte dos evolucionistas darwinistas com Lamarck é de priscas eras. Volta e meia é um olho voltado para Lamarck, sem tirar o outro em Darwin. Apesar de Pilpel e Rochav terem proposto mecanismos evolucionários para solucionar o problema "Primeiro a galinha ou primeiro o ovo", eles não apresentaram evidências para tais mecanismos.

Especulações deles à parte, uma pergunta causticante deste blogger: Por que esses pesquisadores estão "mijando" fora do caco de Darwin se, pelo menos nos livros didáticos do ensino médio, a teoria da evolução é apresentada com o status de cientificamente confirmada assim como a lei da gravidade, bem como a Terra é redonda e gira em torno do Sol, e não é o centro do universo?

E o que significa esse flerte incessante com Lamarck? Darwin kaput? Que venha a nova teoria geral da evolução - a SÍNTESE EVOLUTIVA AMPLIADA/ESTENDIDA - que não será selecionista e deverá incorporar alguns aspectos neolamarckistas - contrariando Darwin, mas 
será somente anunciada em 2020, se anunciarem...

Ajuste fino no cérebro de mamíferos: nós somos mamíferos!

Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity

Sadra Sadeh , Claudia Clopath , Stefan Rotter 

Published: June 19, 2015DOI: 10.1371/journal.pcbi.1004307

Abstract

In rodent visual cortex, synaptic connections between orientation-selective neurons are unspecific at the time of eye opening, and become to some degree functionally specific only later during development. An explanation for this two-stage process was proposed in terms of Hebbian plasticity based on visual experience that would eventually enhance connections between neurons with similar response features. For this to work, however, two conditions must be satisfied: First, orientation selective neuronal responses must exist before specific recurrent synaptic connections can be established. Second, Hebbian learning must be compatible with the recurrent network dynamics contributing to orientation selectivity, and the resulting specific connectivity must remain stable for unspecific background activity. Previous studies have mainly focused on very simple models, where the receptive fields of neurons were essentially determined by feedforward mechanisms, and where the recurrent network was small, lacking the complex recurrent dynamics of large-scale networks of excitatory and inhibitory neurons. Here we studied the emergence of functionally specific connectivity in large-scale recurrent networks with synaptic plasticity. Our results show that balanced random networks, which already exhibit highly selective responses at eye opening, can develop feature-specific connectivity if appropriate rules of synaptic plasticity are invoked within and between excitatory and inhibitory populations. If these conditions are met, the initial orientation selectivity guides the process of Hebbian learning and, as a result, functionally specific and a surplus of bidirectional connections emerge. Our results thus demonstrate the cooperation of synaptic plasticity and recurrent dynamics in large-scale functional networks with realistic receptive fields, highlight the role of inhibition as a critical element in this process, and paves the road for further computational studies of sensory processing in neocortical network models equipped with synaptic plasticity.

Author Summary

In primary visual cortex of mammals, neurons are selective to the orientation of contrast edges. In some species, as cats and monkeys, neurons preferring similar orientations are adjacent on the cortical surface, leading to smooth orientation maps. In rodents, in contrast, such spatial orientation maps do not exist, and neurons of different specificities are mixed in a salt-and-pepper fashion. During development, however, a “functional” map of orientation selectivity emerges, where connections between neurons of similar preferred orientations are selectively enhanced. Here we show how such feature-specific connectivity can arise in realistic neocortical networks of excitatory and inhibitory neurons. Our results demonstrate how recurrent dynamics can work in cooperation with synaptic plasticity to form networks where neurons preferring similar stimulus features connect more strongly together. Such networks, in turn, are known to enhance the specificity of neuronal responses to a stimulus. Our study thus reveals how self-organizing connectivity in neuronal networks enable them to achieve new or enhanced functions, and it underlines the essential role of recurrent inhibition and plasticity in this process.

Citation: Sadeh S, Clopath C, Rotter S (2015) Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity. PLoS Comput Biol 11(6): e1004307. doi:10.1371/journal.pcbi.1004307

Editor: Boris S. Gutkin, École Normale Supérieure, College de France, CNRS, FRANCE

Received: October 16, 2014; Accepted: April 30, 2015; Published: June 19, 2015

Copyright: © 2015 Sadeh 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: Funded by the German Ministry of Education and Research (BMBF, grant BFNT 01GQ0830) and the German Research Foundation (DFG, grant EXC 1086). The article processing charge was covered by the open access publication fund of the University of Freiburg. 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 Computational Biology

E Darwin não era racista... SQN!!!

“Eu poderia mostrar o combate na seleção natural tendo feito e fazendo mais para o progresso da civilização do que você pareça inclinado a admitir. Lembre-se do risco que as nações da Europa correram, não muitos séculos atrás de serem suplantadas pelos turcos, e quão ridícula tal ideia é hoje!

As mais civilizadas das tão chamadas raças caucasianas derrotaram a tentativa turca vazia na luta pela existência. Olhando o mundo em uma data não mui distante, quando um grande número de raças inferiores terão sido eliminadas pelas raças civilizadas superiores por todo o mundo.”

“I could show fight on natural selection having done and doing more for the progress of civilisation than you seem inclined to admit. Remember what risk the nations of Europe ran, not so manày centuries ago of being overwhelmed by the Turks, and how ridiculous such an idea now is!

The more civilised so-called Caucasian races have beaten the Turkish hollow in the struggle for existence. Looking to the world at no very distant date, what an endless number of the lower races will have been eliminated by the higher civilised races throughout the world.” (“The Life and Letters of Charles Darwin”, by Francis Darwin, Vol.I, 1888. New York D. Appleton and Company, pp.285-286).

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NOTA DESTE BLOGGER:

Alguém viu o grupo que quis censurar Monteiro Lobato pelo "racismo" velado encontrado na sua literatura infantil, ter censurado Darwin pelo seu racismo declarado nos seus escritos para os adultos? Eu não vi. Alguém viu?

Dois pesos, duas medidas!!!

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Foto de Darwin: Biblioteca do Congresso Americano

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


Abstract

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.



Keywords:

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

Abstract

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

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





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PERGUNTA CÁUSTICA DESTE BLOGGER:

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

Abstract

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

FREE PDFGRATIS: Sci Adv

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



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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

ACCEPTED MANUSCRIPT

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.

ABSTRACT

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. 

FREE PDF GRATIS: eLife

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


Abstract

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.

Copyright 

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

FREE PDF GRATIS: bioRxiv

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.


Abstract

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

LUIZ FELIPE PONDÉ


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.
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Leia mais aqui: Folha de São Paulo (Assinantes)


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NOTA DESTE BLOGGER:

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

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.

Abstract

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.

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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



Highlights

• 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

Summary

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.

FREE PDF GRATIS: Cell

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

Highlights

•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



Summary

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.

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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.