Sobre a eficiência do código genético após mutações frameshift

On the efficiency of the genetic code after frameshift mutations

Regine Geyer​, Amir Madany Mamlouk​​

Published May 21, 2018

Author and article information

Institute for Neuro- and Bioinformatics, University of Lübeck, Lübeck, Germany

DOI: 10.7717/peerj.4825

Published 2018-05-21 Accepted 2018-05-02 Received 2017-10-02

Academic Editor Thomas Tullius

Subject Areas Bioinformatics, Evolutionary Studies, Genetics

Keywords Standard genetic code, Overlapping codes, Frameshift mutation, Polar requirement

Copyright

© 2018 Geyer and Madany Mamlouk

Licence

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

Cite this article

Geyer R, Madany Mamlouk A. (2018) On the efficiency of the genetic code after frameshift mutations. PeerJ 6:e4825 https://doi.org/10.7717/peerj.4825

Source/Fonte: NIH - U. S. National Library of Medicine

Abstract

Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes. This work tries to follow the systematic approach on mistranslations and to extend those analyses to the general effect of frameshift mutations on the polarity conservation of amino acids. We generated one million random codes and compared their average polarity change over all triplets and the whole set of possible frameshift mutations. While the natural code—just as for the point mutations—appears to be competitively robust against frameshift mutations as well, we found that both optimizations appear to be independent of each other. For both, better codes can be found, but it becomes significantly more difficult to find candidates that optimize all of these features—just like the SGC does. We conclude that the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.

Cite this as

Geyer R, Madany Mamlouk A. (2018) On the efficiency of the genetic code after frameshift mutations. PeerJ 6:e4825 https://doi.org/10.7717/peerj.4825

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Essas criaturas de 635 milhões de anos eram animais diferentes de quaisquer animais conhecidos hoje

Cambrian petalonamid Stromatoveris phylogenetically links Ediacaran biota to later animals

Jennifer F. Hoyal Cuthill Jian Han

First published: 07 August 2018 https://doi.org/10.1111/pala.12393

Data archiving statementData and supplementary information (including character–taxon matrix and reconstructed phylogenetic trees) for this study are available in MorphoBank: http://morphobank.org/permalink/?P2695 and the Dryad Digital Repository: https://doi.org/10.5061/dryad.5pv4qm3.

Artist’s reconstruction of Stromatoveris, an ancient marine animal

J. HOYAL CUTHILL

Source/Fonte: Science

Abstract

Macro‐organisms of the Ediacaran period (635–541 Ma) were large and morphologically complex, with some living in aphotic habitats, presenting the possibility that they were early animals. However, ‘bizarre’ Ediacaran morphologies and mouldic preservation have frustrated comparison to later taxa. Consequently, both the positions of Ediacaran biota in the tree of life and the origins of the Metazoa have remained disputed. Here we provide phylogenetic evidence to identify Ediacaran macro‐biota as animals, based on 206 new fossils of Stromatoveris psygmoglena from the lower Cambrian Chengjiang Lagerstätte. Exceptionally preserved soft‐tissue anatomy shows that Stromatoveris was a soft‐bodied, radially symmetric animal with multiple, sub‐branched petaloids and a differentiated holdfast. Photo‐referenced morphological character analysis enables phylogenetic reconstruction of a monophyletic clade designated Petalonamae, that unites Stromatoveris with iconic Ediacaran genera (Rangea, Pteridinium, Ernietta, Swartpuntia, Arborea, Pambikalbae and Dickinsonia) and is placed as sister‐group to the Eumetazoa. Therefore, based on phylogenetic bracketing within the Metazoa, the Ediacaran petalonamids are established as animals. From these findings, it follows that petalonamids remained an important component of Cambrian marine ecosystems and that the metazoan radiation can be dated to a minimum age of between 558 and 571 myr.

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Navegação de redes cerebrais: mero acaso, fortuita necessidade ou design inteligente?

Navigation of brain networks

Caio Seguin, Martijn P. van den Heuvel, and Andrew Zalesky

PNAS June 12, 2018. 115 (24) 6297-6302; published ahead of print May 30, 2018. https://doi.org/10.1073/pnas.1801351115

Edited by Edward T. Bullmore, University of Cambridge, Cambridge, United Kingdom, and accepted by Editorial Board Member Michael S. Gazzaniga May 7, 2018 (received for review January 24, 2018)

Significance

We show that the combination of topology and geometry in mammalian cortical networks allows for near-optimal decentralized communication under navigation routing. Following a simple propagation rule based on local knowledge of the distance between cortical regions, we demonstrate that brain networks can be successfully navigated with efficiency that is comparable to shortest paths routing. This finding helps to conciliate the major progress achieved over more than a decade of connectomics research, under the assumption of communication via shortest paths, with recent questions raised by the biologically unrealistic requirements involved in the computation of optimal routes. Our results reiterate the importance of the brain’s spatial embedding, suggesting a three-way relationship between connectome geometry, topology, and communication.

Abstract

Understanding the mechanisms of neural communication in large-scale brain networks remains a major goal in neuroscience. We investigated whether navigation is a parsimonious routing model for connectomics. Navigating a network involves progressing to the next node that is closest in distance to a desired destination. We developed a measure to quantify navigation efficiency and found that connectomes in a range of mammalian species (human, mouse, and macaque) can be successfully navigated with near-optimal efficiency (>80% of optimal efficiency for typical connection densities). Rewiring network topology or repositioning network nodes resulted in 45–60% reductions in navigation performance. We found that the human connectome cannot be progressively randomized or clusterized to result in topologies with substantially improved navigation performance (>5%), suggesting a topological balance between regularity and randomness that is conducive to efficient navigation. Navigation was also found to (i) promote a resource-efficient distribution of the information traffic load, potentially relieving communication bottlenecks, and (ii) explain significant variation in functional connectivity. Unlike commonly studied communication strategies in connectomics, navigation does not mandate assumptions about global knowledge of network topology. We conclude that the topology and geometry of brain networks are conducive to efficient decentralized communication.

connectome neural communication network navigation complex networks

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Pesquisa lança dúvidas sobre a ideia de que o gene FOXP2 - ligado à evolução da linguagem - seja especial para os humanos modernos

Cell

No Evidence for Recent Selection at FOXP2 among Diverse Human Populations

Elizabeth Grace Atkinson 8, 9, 10 Amanda Jane Audesse Julia Adela Palacios Dean Michael Bobo Ashley Elizabeth Webb Sohini Ramachandran Brenna Mariah Henn Show footnotes

Published:August 02, 2018 DOI:https://doi.org/10.1016/j.cell.2018.06.048

Highlights

No support for positive selection at FOXP2 in large genomic datasets

Sample composition and genomic scale significantly affect selection scans

An intronic ROI within FOXP2 is expressed in human brain cells and cortical tissue

This ROI contains a large amount of constrained, human-specific polymorphisms

Summary

FOXP2, initially identified for its role in human speech, contains two nonsynonymous substitutions derived in the human lineage. Evidence for a recent selective sweep in Homo sapiens, however, is at odds with the presence of these substitutions in archaic hominins. Here, we comprehensively reanalyze FOXP2 in hundreds of globally distributed genomes to test for recent selection. We do not find evidence of recent positive or balancing selection at FOXP2. Instead, the original signal appears to have been due to sample composition. Our tests do identify an intronic region that is enriched for highly conserved sites that are polymorphic among humans, compatible with a loss of function in humans. This region is lowly expressed in relevant tissue types that were tested via RNA-seq in human prefrontal cortex and RT-PCR in immortalized human brain cells. Our results represent a substantial revision to the adaptive history of FOXP2, a gene regarded as vital to human evolution.

Keywords

FOXP2 human evolution population structure natural selection language demography human brain

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Darwin não explica a origem e evolução da linguagem humana

Front. Psychol., 07 May 2014 | https://doi.org/10.3389/fpsyg.2014.00401

The mystery of language evolution

Marc D. Hauser1*, Charles Yang2, Robert C. Berwick3, Ian Tattersall4, Michael J. Ryan5, Jeffrey Watumull6, Noam Chomsky7 and Richard C. Lewontin8

1Risk-Eraser, LLC, West Falmouth, MA, USA

2Department of Linguistics and Computer and Information Sciences, University of Pennsylvania, Philadelphia, PA, USA

3Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA

4Division of Anthropology, American Museum of Natural History, New York, NY, USA

5Department of Integrative Biology, University of Texas, Austin, TX, USA

6Department of Theoretical and Applied Linguistics, Cambridge University, Cambridge, UK

7Department of Linguistics and Philosophy, Massachusetts Institute of Technology, Cambridge, MA, USA

8Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA

Source/Fonte

Understanding the evolution of language requires evidence regarding origins and processes that led to change. In the last 40 years, there has been an explosion of research on this problem as well as a sense that considerable progress has been made. We argue instead that the richness of ideas is accompanied by a poverty of evidence, with essentially no explanation of how and why our linguistic computations and representations evolved. We show that, to date, (1) studies of nonhuman animals provide virtually no relevant parallels to human linguistic communication, and none to the underlying biological capacity; (2) the fossil and archaeological evidence does not inform our understanding of the computations and representations of our earliest ancestors, leaving details of origins and selective pressure unresolved; (3) our understanding of the genetics of language is so impoverished that there is little hope of connecting genes to linguistic processes any time soon; (4) all modeling attempts have made unfounded assumptions, and have provided no empirical tests, thus leaving any insights into language's origins unverifiable. Based on the current state of evidence, we submit that the most fundamental questions about the origins and evolution of our linguistic capacity remain as mysterious as ever, with considerable uncertainty about the discovery of either relevant or conclusive evidence that can adjudicate among the many open hypotheses. We conclude by presenting some suggestions about possible paths forward.

FREE PDF GRATIS: Frontiers in Psychology

Escutoides - um bloco de construção de organismos multicellulares: sem ele a vida complexa não poderia ter surgido na Terra! Mero acaso, fortuita necessidade ou design inteligente?

Scutoids are a geometrical solution to three-dimensional packing of epithelia

Pedro Gómez-Gálvez, Pablo Vicente-Munuera, Antonio Tagua, Cristina Forja, Ana M. Castro, Marta Letrán, Andrea Valencia-Expósito, Clara Grima, Marina Bermúdez-Gallardo, Óscar Serrano-Pérez-Higueras, Florencia Cavodeassi, Sol Sotillos, María D. Martín-Bermudo, Alberto Márquez, Javier Buceta & Luis M. Escudero 

Nature Communications volume 9, Article number: 2960 (2018) 

Abstract

As animals develop, tissue bending contributes to shape the organs into complex three-dimensional structures. However, the architecture and packing of curved epithelia remains largely unknown. Here we show by means of mathematical modelling that cells in bent epithelia can undergo intercalations along the apico-basal axis. This phenomenon forces cells to have different neighbours in their basal and apical surfaces. As a consequence, epithelial cells adopt a novel shape that we term “scutoid”. The detailed analysis of diverse tissues confirms that generation of apico-basal intercalations between cells is a common feature during morphogenesis. Using biophysical arguments, we propose that scutoids make possible the minimization of the tissue energy and stabilize three-dimensional packing. Hence, we conclude that scutoids are one of nature's solutions to achieve epithelial bending. Our findings pave the way to understand the three-dimensional organization of epithelial organs.

Acknowledgements

M.D.M.-B. and A.V.-E. work was funded by the Ministerio Español de Ciencia y Tecnología (grants numbers BFU2013-48988-C2-1-P and BFU2016-80797 to M.D.M.-B.). A.V.-E. is supported by a FPI studentship (BES-2014-068850) from the Ministerio de Economía y Competitividad. S.S. is supported by grant of the MICINN/FEDER to J.C.-G. Hombría (BFU2016-76528-P). F.C. work is funded by Spanish Government Grant BFU2014-55918 and BBVA Foundation Personal Grant IN[16]_BBM_BAS_0078. J.B. acknowledges core funding by Lehigh University. L.M.E. and P.G.-G. are supported by the Ramón y Cajal program (PI13/01347); L.M.E., A.M., and C.G. work is funded by the Ministry of Economy, Industry, and Competitiveness grant BFU2016-74975-P co-funded by FEDER funds. P.V.-M. is supported by a contract co-funded by the Asociación Fundación Española contra el Cáncer and the Seville University. A.M.C. is supported by Fundación Pública Andaluza Progreso y Salud (Consejería de Salud), ref. PI-0033-2014. C.F. and A.T. is supported by a contract from Sistema Nacional de Garantía Juvenil and Programa Operativo de Empleo Juvenil 2014–2020. We are thankful to Dr. Nicolas Gompel for the picture of the Cetoniidae: Protaetia (Potosia) speciose to illustrate the term “scutoid”. We thank Dr. Paco Martín, Dr. José López-Barneo, Dr. Alberto Pascual, Dr. Colin Adrain and Dr. Matthew Freeman for helpful comments and corrections to the manuscript.

Author information

Author notes

These authors contributed equally: Pedro Gómez-Gálvez, Pablo Vicente-Munuera.

Affiliations

Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain

Pedro Gómez-Gálvez, Pablo Vicente-Munuera, Antonio Tagua, Cristina Forja, Ana M. Castro, Marta Letrán, Marina Bermúdez-Gallardo, Óscar Serrano-Pérez-Higueras & Luis M. Escudero

CABD, CSIC/JA/UPO, Campus Universidad Pablo de Olavide, 41013, Seville, Spain

Andrea Valencia-Expósito, Sol Sotillos & María D. Martín-Bermudo

Departamento de Matemática Aplicada I, Universidad de Sevilla, 41012, Seville, Spain

Clara Grima & Alberto Márquez

Centro de Biología Molecular Severo Ochoa and CIBER de Enfermedades Raras. C/ Nicolás Cabrera 1, 28049, Madrid, Spain

Florencia Cavodeassi

St. George’s, University of London, Cranmer Terrace, SW17 0RE, London, UK

Florencia Cavodeassi

Bioengineering Department, Lehigh University, Bethlehem, PA, 18018, USA

Javier Buceta

Chemical and Biomolecular Engineering Department, Lehigh University, Bethlehem, PA, 18018, USA

Javier Buceta

Contributions

L.M.E. designed the study with help from A.M., C.G., and J.B. P.G.-G. and P.V.-M. wrote the software for the mathematical model and performed analyses. A.T., C.F., A.M.C., M.L., A.V.-E., M.B.-G., O.S.-P.-H., F.C., S.S., and M.D.M.-B., collaborated in the obtaining, measurement of parameters and analysis of the confocal images. All authors participated in the interpretation of results, discussions, and the development of the project. J.B. and L.M.E. wrote the manuscript with input from all authors.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Javier Buceta or Luis M. Escudero.

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A maquinaria majestosa e complexa do espliceossomo: mero acaso, fortuita necessidade ou design inteligente?

All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome

Lorenzo Casalino, Giulia Palermo, Angelo Spinello, Ursula Rothlisberger, and Alessandra Magistrato

PNAS June 26, 2018. 115 (26) 6584-6589; published ahead of print June 11, 2018. https://doi.org/10.1073/pnas.1802963115

Edited by Michael L. Klein, Temple University, Philadelphia, PA, and approved May 15, 2018 (received for review February 16, 2018)

Significance

Precursor messenger RNA (pre-mRNA) splicing is a crucial step of gene expression, enabling the maturation of pre-mRNA transcripts into protein-coding mRNAs. In humans, a majestic ribonucleoprotein machinery—the spliceosome—governs this fundamental process, the defects and misregulation of which lead to over 200 human diseases. A thorough understanding of splicing is pivotal for biology and medicine, holding the promise of harnessing it for genome modulation applications. Despite the recent breakthroughs gained by cryo-EM, an atomic-resolution picture of the spliceosome functional plasticity is still missing. Here, all-atom simulations elucidate the cooperative motions underlying the functional dynamics of the spliceosome at a late stage of the splicing cycle, suggesting the role of specific proteins involved in the spliceosome disassembly from an atomic-level perspective.

Abstract

The spliceosome (SPL) is a majestic macromolecular machinery composed of five small nuclear RNAs and hundreds of proteins. SPL removes noncoding introns from precursor messenger RNAs (pre-mRNAs) and ligates coding exons, giving rise to functional mRNAs. Building on the first SPL structure solved at near–atomic-level resolution, here we elucidate the functional dynamics of the intron lariat spliceosome (ILS) complex through multi-microsecond-long molecular-dynamics simulations of ∼1,000,000 atoms models. The ILS essential dynamics unveils (i) the leading role of the Spp42 protein, which heads the gene maturation by tuning the motions of distinct SPL components, and (ii) the critical participation of the Cwf19 protein in displacing the intron lariat/U2 branch helix. These findings provide unprecedented details on the SPL functional dynamics, thus contributing to move a step forward toward a thorough understanding of eukaryotic pre-mRNA splicing.

spliceosome splicing molecular dynamics RNA gene maturation

Footnotes

↵1To whom correspondence should be addressed. 

Email: alessandra.magistrato@sissa.it.

Author contributions: A.M. designed research; L.C. performed research; L.C., G.P., and A.S. analyzed data; U.R. participated in the discussion of the results; and L.C., G.P., U.R., and A.M. 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.1802963115/-/DCSupplementa

Published under the PNAS license.

http://www.pnas.org/content/115/26/6584

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O fim do conceito anatômico de homologia da teoria da evolução de Darwin???

Evolution of limb development in cephalopod mollusks

Oscar A. Tarazona, Davys H. Lopez, Leslie A Slota, View ORCID ProfileMartin J. Cohn

doi: https://doi.org/10.1101/379735

This article is a preprint and has not been peer-reviewed [what does this mean?].

Source/Fonte

Abstract

Cephalopod mollusks evolved numerous anatomical innovations, including specialized arms and tentacles, but little is known about the developmental mechanisms underlying the evolution of cephalopod limbs. Here we report that all three axes of cuttlefish limbs are patterned by the same signaling networks that act in vertebrates and arthropods, although they evolved limbs independently. In cuttlefish limb buds, Hedgehog is expressed anteriorly. Posterior transplantation of Hedgehog-expressing cells induced mirror-image limb duplications. Bmp and Wnt signaling, which establishes dorsoventral polarity in vertebrate and arthropod limbs, is similarly polarized in cuttlefish. Inhibition of the dorsal Bmp signal caused ectopic expression of Notum, a ventral sucker field marker, and development of ectopic suckers. Cuttlefish limbs also show proximodistally regionalized expression of Htx, Exd, Dll, Dac, Sp8, and Wnt genes, which delineate arm and tentacle sucker fields. These results suggest that cephalopod limbs evolved by parallel activation of an ancient developmental genetic program that was present in the bilaterian common ancestor

Copyright 

The copyright holder for this preprint is the author/funder. All rights reserved. No reuse allowed without permission.

FREE PREPRINT: bioRxiv

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Comentário de um gigante em Biologia:

"Se os resultados reportados neste trabalho se sustentarem, eles adicionam para a quase completa destruição do conceito neodarwinista de homologia anatômica. Hoje, a homologia significa quase que muita coisa na biologia evolucionária. Este conceito tem se livrado de quaisquer âncoras evidenciais consistentes, por contra-exemplos tão numerosos que eles poderiam encher um livro-texto dedicado simplesmente por sua diversidade taxonômica, abundância, e valor de impacto.

Se você tivesse perguntado um biólogo evolucionário nos anos 1980s se os membros de cefalópodos, artrópodes, e vertebrados usariam os mesmos elementos reguladores de desenvolvimento, ele teria dito “Com os diabos, não! — essas são estruturas classicamente não homólogas.”

Pano rápido!

Carl Woese acreditava em Deus e chamou Darwin de bastardo!!!

BOOKS AND ARTS 31 JULY 2018

The band of biologists who redrew the tree of life

John Archibald praises a compelling guide to the past 3 billion years — and its molecular historians.

John Archibald

Carl Woese discovered the ‘third domain’ of life — the Archaea.

Credit: Jason Lindley/LAS, Univ. Illinois at Urbana-Champaign

The Tangled Tree: A Radical New History of Life David Quammen Simon & Schuster (2018)

In The Tangled Tree, celebrated science writer David Quammen tells perhaps the grandest tale in biology: how scientists used gene sequencing to elucidate the evolutionary relationships between living beings. Charles Darwin called it the ‘great Tree of Life’. But as Quammen reveals, at the molecular level, life’s history is more accurately depicted as a network, a tangled web through which organisms have been exchanging genes for more than 3 billion years. This perspective is indeed radical, and he presents the science — and the scientists involved — with patience, candour and flair.

Centre stage in Quammen’s narrative is Carl Woese (1928–2012), the US microbiologist best known as the discoverer of the Archaea (Archaebacteria) — the ‘third domain’ of life. Inspired by the visionary musings of Francis Crick, Linus Pauling and Emile Zuckerkandl, Woese committed himself to molecular phylogenetics at a time when this powerful approach to the study of evolution was in its infancy. During the 1960s and 1970s, the Woese Laboratory at the University of Illinois at Urbana–Champaign developed and refined techniques for deriving sequence information from molecules of ribosomal RNA (core components of the cell’s protein-synthesizing factory, the ribosome). Sequences were painstakingly obtained from diverse microbes and used as molecular yardsticks to infer how the organisms were related to one another and to animals and plants. Through the following two decades, as molecular sequencing got easier and cheaper, Woese’s ‘three-domains’ tree — comprising archaea, bacteria and the nucleus-containing eukaryotes — served as the definitive road map for the field of comparative genomics. In many ways, it still does.

But life is complicated, and so are the scientists who study it. In his breezy, conversational style, Quammen shepherds us up and down life’s vast timeline, and across 150-plus years of exciting, often controversial discoveries. He handles the complexities with humour and clarity (he’s right: some ribosomes do look like rubber ducks). We learn about the seeds of “tree thinking” in biology, before and after Darwin’s 1859 On the Origin of Species. We learn of a time when a natural classification of microorganisms was considered impossible (they were deemed morphologically too simple, physiologically too variable). We learn how molecular sequencing helped test and eventually prove the endosymbiont hypothesis for the origin of mitochondria and chloroplasts; these eukaryotic organelles are now known to have evolved from once free-living bacteria.

...

Woese’s last months and weeks with pancreatic cancer, as revealed by those closest to him, make for painful, albeit illuminating reading. I was surprised, for instance, to learn that Woese believed in a deity.

Around 2010, Woese and Canadian science historian Jan Sapp began to collaborate on a book tentatively entitled Beyond God and Darwin. The project never moved beyond Sapp’s draft introduction, on which Woese wrote: “Jan, you accord Darwin so much more substance than the bastard deserves.”

FREE PDF GRATIS: Nature

Capacitar revisores paritários com uma lista de verificação para melhorar a transparência

Empowering peer reviewers with a checklist to improve transparency

Timothy H. Parker, Simon C. Griffith, Judith L. Bronstein, Fiona Fidler, Susan Foster, Hannah Fraser, Wolfgang Forstmeier, Jessica Gurevitch, Julia Koricheva, Ralf Seppelt, Morgan W. Tingley & Shinichi Nakagawa 

Nature Ecology & Evolution volume 2, pages929–935 (2018) | Download Citation

Source/Fonte: Editage

Abstract

Peer review is widely considered fundamental to maintaining the rigour of science, but it often fails to ensure transparency and reduce bias in published papers, and this systematically weakens the quality of published inferences. In part, this is because many reviewers are unaware of important questions to ask with respect to the soundness of the design and analyses, and the presentation of the methods and results; also some reviewers may expect others to be responsible for these tasks. We therefore present a reviewers’ checklist of ten questions that address these critical components. Checklists are commonly used by practitioners of other complex tasks, and we see great potential for the wider adoption of checklists for peer review, especially to reduce bias and facilitate transparency in published papers. We expect that such checklists will be well received by many reviewers.

FREE PDF GRATIS: Nature Ecology and Evolution Sup. Info.

Mapeamento das partículas magnéticas no cérebro humano

Distribution of magnetic remanence carriers in the human brain

Stuart A. Gilder, Michael Wack, Leon Kaub, Sophie C. Roud, Nikolai Petersen, Helmut Heinsen, Peter Hillenbrand, Stefan Milz & Christoph Schmitz 

Scientific Reports volume 8, Article number: 11363 (2018) | Download Citation

Abstract

That the human brain contains magnetite is well established; however, its spatial distribution in the brain has remained unknown. We present room temperature, remanent magnetization measurements on 822 specimens from seven dissected whole human brains in order to systematically map concentrations of magnetic remanence carriers. Median saturation remanent magnetizations from the cerebellum were approximately twice as high as those from the cerebral cortex in all seven cases (statistically significantly distinct, p = 0.016). Brain stems were over two times higher in magnetization on average than the cerebral cortex. The ventral (lowermost) horizontal layer of the cerebral cortex was consistently more magnetic than the average cerebral cortex in each of the seven studied cases. Although exceptions existed, the reproducible magnetization patterns lead us to conclude that magnetite is preferentially partitioned in the human brain, specifically in the cerebellum and brain stem.

Acknowledgements

We thank Josef Jezek for advice on the statistical analyses. This work was kindly funded by the Volkswagen Foundation Experiment! program.

Author information

Affiliations

Department of Earth and Environmental Sciences, Ludwig-Maximilians University of Munich, Theresienstrasse 41, Munich, 80333, Germany

Stuart A. Gilder, Michael Wack, Leon Kaub, Sophie C. Roud & Nikolai Petersen

Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital Würzburg, Würzburg, 97080, Germany

Helmut Heinsen

Ageing Brain Study Group, Department of Pathology, LIM 22, University of São Paulo Medical School, São Paulo, Brazil

Helmut Heinsen

Department of Neuroanatomy, Ludwig-Maximilians University of Munich, Pettenkoferstrasse 11, Munich, 80336, Germany

Peter Hillenbrand, Stefan Milz & Christoph Schmitz

Contributions

H.H. provided the brain specimens to C.S., S.M. cut all brains with assistance from P.H., L.K., S.R., S.G. and M.W. S.G. made all magnetic measurements with assistance from P.H., L.K., S.R., M.W. and S.M. Data treatment and interpretation were done by M.W., S.R. and S.G. with contributions from C.S., S.M., P.H., L.K. and N.P. Figures were drafted by S.R., S.G., S.M. and M.W. S.G. wrote the paper and all authors read and contributed comments to the work.

Competing Interests

The authors declare no competing interests.

Corresponding author

Correspondence to Stuart A. Gilder.

FREE PDF GRATIS: Scientific Reports

Difusão anômala, coerência espacial e viscoelasticidade da região energética dos cromossomos humanos: mero acaso, fortuita necessidade ou design inteligente?

Anomalous diffusion, spatial coherence, and viscoelasticity from the energy landscape of human chromosomes

Michele Di Pierro, Davit A. Potoyan, Peter G. Wolynes, and José N. Onuchic

PNAS July 9, 2018. 201806297; published ahead of print July 9, 2018. https://doi.org/10.1073/pnas.1806297115

Contributed by José N. Onuchic, June 8, 2018 (sent for review April 12, 2018; reviewed by Olga K. Dudko and Andrew J. Spakowitz)

Significance

Several active processes operate on eukaryotic genomes, dictating their three-dimensional arrangement and dynamical properties. The combination of structural organization and dynamics is essential to the proper functioning of the cell. We show that an effective energy landscape model for chromatin provides a unifying description of both the structural and dynamical aspects of the genome, recapitulating many of its features. Using this quasi-equilibrium energy landscape model, we demonstrate that the physical interactions accounting for genome architecture also lead to the nontrivial dynamical behavior of genomes previously described in multiple experimental observations.

Abstract

The nucleus of a eukaryotic cell is a nonequilibrium system where chromatin is subjected to active processes that continuously rearrange it over the cell’s life cycle. Tracking the motion of chromosomal loci provides information about the organization of the genome and the physical processes shaping that organization. Optical experiments report that loci move with subdiffusive dynamics and that there is spatially coherent motion of the chromatin. We recently showed that it is possible to predict the 3D architecture of genomes through a physical model for chromosomes that accounts for the biochemical interactions mediated by proteins and regulated by epigenetic markers through a transferable energy landscape. Here, we study the temporal dynamics generated by this quasi-equilibrium energy landscape assuming Langevin dynamics at an effective temperature. Using molecular dynamics simulations of two interacting human chromosomes, we show that the very same interactions that account for genome architecture naturally reproduce the spatial coherence, viscoelasticity, and the subdiffusive behavior of the motion in interphase chromosomes as observed in numerous experiments. The agreement between theory and experiments suggests that even if active processes are involved, an effective quasi-equilibrium landscape model can largely mimic their dynamical effects.

chromatin dynamics anomalous diffusion genome architecture phase separation dynamically associated domains

FREE PDF GRATIS: PNAS Sup. Info.

Nova contagem de genes reacende o debate

NEWS 19 JUNE 2018

New human gene tally reignites debate

Some fifteen years after the human genome was sequenced, researchers still can’t agree on how many genes it contains.

Cassandra Willyard

One of the earliest attempts to estimate the number of genes in the human genome involved tipsy geneticists, a bar in Cold Spring Harbor, New York, and pure guesswork.

That was in 2000, when a draft human genome sequence was still in the works; geneticists were running a sweepstake on how many genes humans have, and wagers ranged from tens of thousands to hundreds of thousands. Almost two decades later, scientists armed with real data still can’t agree on the number — a knowledge gap that they say hampers efforts to spot disease-related mutations.

The latest attempt to plug that gap uses data from hundreds of human tissue samples and was posted on the BioRxiv preprint server on 29 May1. It includes almost 5,000 genes that haven’t previously been spotted — among them nearly 1,200 that carry instructions for making proteins. And the overall tally of more than 21,000 protein-coding genes is a substantial jump from previous estimates, which put the figure at around 20,000.

But many geneticists aren’t yet convinced that all the newly proposed genes will stand up to close scrutiny. Their criticisms underscore just how difficult it is to identify new genes, or even define what a gene is.

“People have been working hard at this for 20 years, and we still don’t have the answer,” says Steven Salzberg, a computational biologist at Johns Hopkins University in Baltimore, Maryland, whose team produced the latest count.

Hard to pin down

In 2000, with the genomics community abuzz over the question of how many human genes would be found, Ewan Birney launched the GeneSweep contest. Birney, now co-director of the European Bioinformatics Institute (EBI) in Hinxton, UK, took the first bets at a bar during an annual genetics meeting, and the contest eventually attracted more than 1,000 entries and a US$3,000 jackpot. Bets on the number of genes ranged from more than 312,000 to just under 26,000, with an average of around 40,000. These days, the span of estimates has shrunk — with most now between 19,000 and 22,000 — but there is still disagreement (See 'Gene Tally').

...

FREE PDF GRATIS: Nature

Taxonomia animal: idênticos por fora, mas distintos

Comparative genomics and the nature of placozoan species

Michael Eitel , Warren R. Francis, Frédérique Varoqueaux, Jean Daraspe, Hans-Jürgen Osigus, Stefan Krebs, Sergio Vargas, Helmut Blum, Gray A. Williams, Bernd Schierwater, Gert Wörheide 

Published: July 31, 2018 https://doi.org/10.1371/journal.pbio.2005359

Abstract

Placozoans are a phylum of nonbilaterian marine animals currently represented by a single described species, Trichoplax adhaerens, Schulze 1883. Placozoans arguably show the simplest animal morphology, which is identical among isolates collected worldwide, despite an apparently sizeable genetic diversity within the phylum. Here, we use a comparative genomics approach for a deeper appreciation of the structure and causes of the deeply diverging lineages in the Placozoa. We generated a high-quality draft genome of the genetic lineage H13 isolated from Hong Kong and compared it to the distantly related T. adhaerens. We uncovered substantial structural differences between the two genomes that point to a deep genomic separation and provide support that adaptation by gene duplication is likely a crucial mechanism in placozoan speciation. We further provide genetic evidence for reproductively isolated species and suggest a genus-level difference of H13 to T. adhaerens, justifying the designation of H13 as a new species, Hoilungia hongkongensis nov. gen., nov. spec., now the second described placozoan species and the first in a new genus. Our multilevel comparative genomics approach is, therefore, likely to prove valuable for species distinctions in other cryptic microscopic animal groups that lack diagnostic morphological characters, such as some nematodes, copepods, rotifers, or mites.

Author summary

Placozoans are a phylum of tiny (approximately 1 mm) marine animals that are found worldwide in temperate and tropical waters. They are characterized by morphological simplicity, with only a handful of cell types, no neurons, no tissue organization, and even no axial polarity. Since the original description of Trichoplax adhaerens 135 years ago, no additional accepted species has been established, leaving the Placozoa as the only animal phylum with only a single formally described species. While classical morphological species identification has failed to reveal further species, single-gene DNA sequence analyses have identified a broad and deep genetic diversity within the Placozoa. To address the significance of this deep genetic diversity in this morphologically uniform phylum, and to better understand its consequences for speciation processes, general biology, and species delimitation in the Placozoa, we sequenced the genome of the placozoan isolate “H13,” a lineage distantly genetically related to T. adhaerens. Our multilevel genomic comparisons with the T. adhaerens genome show considerable differences in the general structure of the genome and the makeup and history of various gene families of biological relevance to habitat adaptation. Based on comparative genomics, we here describe the second placozoan species and show that it belongs to a new genus.

Citation: Eitel M, Francis WR, Varoqueaux F, Daraspe J, Osigus H-J, Krebs S, et al. (2018) Comparative genomics and the nature of placozoan species. PLoS Biol 16(7): e2005359. https://doi.org/10.1371/journal.pbio.2005359

Academic Editor: Chris Tyler-Smith, The Wellcome Trust Sanger Institute, United Kingdom of Great Britain and Northern Ireland

Received: January 5, 2018; Accepted: June 28, 2018; Published: July 31, 2018

Copyright: © 2018 Eitel 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: Python scripts used in this study are available at https://bitbucket.org/wrf/sequences and https://github.com/wrf/lavaLampPlot. Raw genomic short and long reads, as well as RNA-Seq reads, respectively, have been deposited at NCBI Short Read Archive under SRR5311040, SRR5311137, SRR5311041. Bioproject accession is PRJNA377631. A repository has been created that hosts all files related to the genome and performed analyses (https://bitbucket.org/molpalmuc/hoilungia-genome): Masked and unmasked reference genome assembly [fasta] Transcriptome and proteome versions [fasta] Annotation tracks [GFF]: genes, CDS, mapped transcripts, SNPs, unexpressed ab initio gene models, tRNAs, repeats raw genomic sequences alignments of three ribosomal genes (rpl9, rpl32, rpp1) used for phylogenetic tree reconstruction and conspecificity matrix generation H. hongkongensis and T. adhaerens reference coding sequences and alignments of 6,554 orthologs [fasta] H. hongkongensis and T. adhaerens reference protein sequences and alignments of 6,554 orthologs [fasta] H. hongkongensis (reference and allelic variants) and T. adhaerens (reference) coding sequences and alignments of 2,870 orthologs [fasta] H. hongkongensis (reference and allelic variants) and T. adhaerens (reference) protein sequences and alignments of 2,870 orthologs [fasta] Protein matrix used for distance calculations (dataset 1) [phylip] Alignments of selected single marker sequences for distance calculation (16S, cox1, nad1, 18S, 28S) [fasta] Protein alignments for 194 proteins used for phylogenetic inferences [fasta] Protein matrix used for phylogenetic inferences (dataset 2) [phylip] Dayhoff 6-state recoded protein matrix used for phylogenetic inferences (recoded dataset 2) [phylip] Partition files for dataset 1 & 2 [txt] Output files from Phylobayes and RAxML analyses Complete and annotated H. hongkongensis mitochondrial genome [gb, fasta].

Funding: LMUexcellent

https://www.en.uni-muenchen.de/about_lmu/research/excellence_initiative/index.html. Funding through the LMU Munich’s Institutional Strategy LMU excellent within the framework of the German Excellence Initiative to GW and HB. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Deutsche Forschungsgemeinschaft (DFG) www.dfg.de (grant number SCHI 277/26-1, SCHI 277/29-1). Funding to BS. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The University of Hongkong. Funding through a Small Project Fund of The University of Hong Kong to GAW and ME (grant number 201109176175). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Studienstiftung des deutschen Volkes. Doctoral fellowship to HJO. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Deutscher Akademischer Austauschdienst (DAAD) www.daad.de. A postdoctoral research fellowship to M.E. that supported specimen collection and establishment of cultures. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. European Union’s Horizon 2020, Marie Skłodowska-Curie Innovative Training Networks 

https://ec.europa.eu/research/mariecurieactions/actions/get-funding/innovative-training-networks_en (grant number 764840 [ITN IGNITE]). Funding to GW. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Deutsche Forschungsgemeinschaft (DFG) www.dfg.de (grant number Wo896/19-1). Funding to GW within the DFG Priority Program SPP 1991 “TaxonOMICs”. The funder 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.

Abbreviations: CDS, coding sequence; CM, conspecificity matrix; CO1, cytochrome c oxidase subunit 1; dN/dS, nonsynonymous to synonymous nucleotide substitutions; FPKM, fragments per kilobase million; GO, gene ontology; GPCR, G-protein coupled receptor; HMM, hidden Markov model; ITS2, internal transcribed spacer 2; MCL, Markov cluster; ND1, NADH dehydrogenase subunit 1; rDNA, ribosomal DNA; SNP, single nucleotide polymorphism; TPM, transcripts per kilobase million

FREE PDF GRATIS: PLoS Biology

Os olhos das medusas (águas-vivas) evoluíram várias vezes

Prolific Origination of Eyes in Cnidaria with Co-option of Non-visual Opsins

Natasha Picciani Jamie R. Kerlin Noemie Sierra Andrew J.M. Swafford M. Desmond Ramirez Nickellaus G. Roberts Johanna T. Cannon Marymegan Daly Todd H. Oakley 4 Show footnotes

Published:July 19, 2018DOI: https://doi.org/10.1016/j.cub.2018.05.055

Highlights

- Jellyfish eyes (eyespots, pigment cups, and lensed-eyes) originated multiple      times

- Known morphological differences are consistent with multiple eye origins

- Expression of photosensitive proteins supports separate eye origins

Summary

Animal eyes vary considerably in morphology and complexity and are thus ideal for understanding the evolution of complex biological traits [1]. While eyes evolved many times in bilaterian animals with elaborate nervous systems, image-forming and simpler eyes also exist in cnidarians, which are ancient non-bilaterians with neural nets and regions with condensed neurons to process information. How often eyes of varying complexity, including image-forming eyes, arose in animals with such simple neural circuitry remains obscure. Here, we produced large-scale phylogenies of Cnidaria and their photosensitive proteins and coupled them with an extensive literature search on eyes and light-sensing behavior to show that cnidarian eyes originated at least eight times, with complex, lensed-eyes having a history separate from other eye types. Compiled data show widespread light-sensing behavior in eyeless cnidarians, and comparative analyses support ancestors without eyes that already sensed light with dispersed photoreceptor cells. The history of expression of photoreceptive opsin proteins supports the inference of distinct eye origins via separate co-option of different non-visual opsin paralogs into eyes. Overall, our results show eyes evolved repeatedly from ancestral photoreceptor cells in non-bilaterian animals with simple nervous systems, co-opting existing precursors, similar to what occurred in Bilateria. Our study underscores the potential for multiple, evolutionarily distinct visual systems even in animals with simple nervous systems.

FREE PDF GRATIS: Current Biology