Suzana Herculano-Houzel 'falou e disse': o cérebro humano é extraordinário, mas não é excepcional.

sexta-feira, agosto 12, 2016

No relative expansion of the number of prefrontal neurons in primate and human evolution

Mariana Gabi a,b,c, Kleber Neves a,b, Carolinne Masseron a,b, Pedro F. M. Ribeiro a,b, Lissa Ventura-Antunes a,b, Laila Torres d,e, Bruno Mota f, Jon H. Kaas c,1, and Suzana Herculano-Houzel a,b,c,g,1

Author Affiliations

aInstituto de Ciências Morfológicas, Universidade Federal do Rio De Janeiro, 21941-901, Rio de Janeiro, Brazil;

bInstituto Nacional de Neurociência Translacional, 04023-900, Sao Paulo, Brazil;

cDepartment of Psychology, Vanderbilt University, Nashville, TN 37240;

dUniversidade Federal de São Paulo, 04021-001, Sao Paulo, Brazil;

eMuseu Paraense Emílio Goeldi, 66040-170, Belem, Brazil;

fInstituto de Física, Universidade Federal do Rio De Janeiro, 21941-901, Rio de Janeiro, Brazil;

gDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235

Contributed by Jon H. Kaas, June 29, 2016 (sent for review February 29, 2016; reviewed by Robert A. Barton and Randy L. Buckner)


Significance

Human brain evolution is often considered synonymous with cortical expansion, in particular of the prefrontal cortex, a cortical region required for our remarkable cognitive abilities such as personality expression, planning, and decision making. In this study, we show that the expansion of numbers of cortical neurons in human and nonhuman primate evolution occurred in a similar manner across the cortex, without an increase in the relative number of neurons in the prefrontal region, and without a relative increase in the number of cells in the prefrontal white matter. One thing that distinguishes the human brain from other primate brains is thus not the relative size of its prefrontal cortex but its absolute number of neurons.

Abstract

Human evolution is widely thought to have involved a particular expansion of prefrontal cortex. This popular notion has recently been challenged, although controversies remain. Here we show that the prefrontal region of both human and nonhuman primates holds about 8% of cortical neurons, with no clear difference across humans and other primates in the distribution of cortical neurons or white matter cells along the anteroposterior axis. Further, we find that the volumes of human prefrontal gray and white matter match the expected volumes for the number of neurons in the gray matter and for the number of other cells in the white matter compared with other primate species. These results indicate that prefrontal cortical expansion in human evolution happened along the same allometric trajectory as for other primate species, without modification of the distribution of neurons across its surface or of the volume of the underlying white matter. We thus propose that the most distinctive feature of the human prefrontal cortex is its absolute number of neurons, not its relative volume.

cortical expansion evolution number of neurons primate prefrontal cortex

Footnotes

1To whom correspondence may be addressed. Email: jon.h.kaas@vanderbilt.edu or suzana.herculano@vanderbilt.edu.

Author contributions: M.G., J.H.K., and S.H.-H. designed research; M.G., K.N., C.M., P.F.M.R., and L.V.-A. performed research; L.T., J.H.K., and S.H.-H. contributed new reagents/analytic tools; M.G., B.M., and S.H.-H. analyzed data; and M.G., J.H.K., and S.H.-H. wrote the paper.

Reviewers: R.A.B., Durham University; R.L.B., Harvard University.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1610178113/-/DCSupplemental.

FREE PDF GRATIS: PNAS

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EXCERPT FROM SCIENCE DAILY/EXCERTO DO SCIENCE DAILY:

"People need to drop the idea that the human brain is exceptional," said Vanderbilt University neuroscientist Suzana Herculano-Houzel, who directed the study. "Our brain is basically a primate brain. Because it is the largest primate brain, it does have one distinctive feature: It has the highest number of cortical neurons of any primate. Humans have 16 billion compared with 9 billion in gorillas and orangutans and six-to-seven billion in chimpanzees. It is remarkable, but it is not exceptional."

Navegando a fronteira do fenótipo: a Inciativa Monarca

quinta-feira, agosto 11, 2016

Navigating the Phenotype Frontier: The Monarch Initiative

Julie A. McMurry, Sebastian Köhler, Nicole L. Washington, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine, Julius O.B. Jacobsen, Daniel Keith, Bryan Laraway, Jeremy Nguyen Xuan, Kent Shefchek, Nicole A. Vasilevsky, Zhou Yuan, Suzanna E. Lewis, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel

GENETICS August 1, 2016 vol. 203 no. 4 1491-1495; 


Abstract

The principles of genetics apply across the entire tree of life. At the cellular level we share biological mechanisms with species from which we diverged millions, even billions of years ago. We can exploit this common ancestry to learn about health and disease, by analyzing DNA and protein sequences, but also through the observable outcomes of genetic differences, i.e. phenotypes. To solve challenging disease problems we need to unify the heterogeneous data that relates genomics to disease traits. Without a big-picture view of phenotypic data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) provides tools for genotype-phenotype analysis, genomic diagnostics, and precision medicine across broad areas of disease.

COMPARATIVE MEDICINE DATA INTEGRATION DISEASE DIAGNOSIS DISEASE DISCOVERY PHENOTYPE ONTOLOGIES

FREE PDF GRATIS: Genetics

Saccharomyces cerevisiae - levedura de cervejeiro - faz um salto evolutivo em poucas gerações no laboratório

Evolution of simple multicellularity increases environmental complexity

Maria Rebolleda-Gomez, William C. Ratcliff, Fankhauser Jonathon, Michael Travisano


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



Abstract

Multicellularity - the integration of previously autonomous cells into a new, more complex organism- is one of the major transitions in evolution. Multicellularity changed evolutionary possibilities and facilitated the evolution of increased complexity. Transitions to multicellularity are associated with rapid diversification and increased ecological opportunity but the potential mechanisms are not well understood. In this paper we explore the ecological mechanisms of multicellular diversification during experimental evolution of the brewer's yeast, Saccharomyces cerevisiae. The evolution from single cells into multicellular clusters modifies the structure of the environment, changing the fluid dynamics and creating novel ecological opportunities. This study demonstrates that even in simple conditions, incipient multicellularity readily changes the environment, facilitating the origin and maintenance of diversity.

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 

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NOTA DESTE BLOGGER:

Já estão alardeando que isso fornece prova experimental de que quando a evolução dá um grande passo adiante – como na origem da multicelularidade -os organismos podem diversificar rapidamente para tirar vantagem da mudança.

Será que com este experimento com a "simples" levedura de cervejeiro, a Nomenklatura científica está querendo dizer que acharam A PROVA de como ocorreu a Explosão Cambriana??? É muita imaginação e pouca ciência!

Pesquisa explica a formação da boca durante o desenvolvimento embrionário de sapo

Formation of a “Pre-mouth Array” from the Extreme Anterior Domain Is Directed by Neural Crest and Wnt/PCP Signaling

Laura Jacox, Justin Chen, Alyssa Rothman, Hillary Lathrop-Marshall, Hazel Sive correspondence email

Open Access




Highlights

• A Xenopus pre-mouth cell array splits down the midline to surround the oral opening

• The pre-mouth array forms by convergent extension of EAD ectoderm

• EAD morphogenesis is directed by adjacent cranial neural crest

• Wnt/PCP signaling is necessary and sufficient to elicit EAD convergent extension

Summary

The mouth arises from the extreme anterior domain (EAD), a region where the ectoderm and endoderm are directly juxtaposed. Here, we identify a “pre-mouth array” in Xenopus that forms soon after the cranial neural crest has migrated to lie on either side of the EAD. Initially, EAD ectoderm comprises a wide and short epithelial mass that becomes narrow and tall with cells and nuclei changing shape, a characteristic of convergent extension. The resulting two rows of cells—the pre-mouth array—later split down the midline to surround the mouth opening. Neural crest is essential for convergent extension and likely signals to the EAD through the Wnt/planar cell polarity (PCP) pathway. Fzl7 receptor is locally required in EAD ectoderm, while Wnt11 ligand is required more globally. Indeed, heterologous cells expressing Wnt11 can elicit EAD convergent extension. The study reveals a precise cellular mechanism that positions and contributes to the future mouth.

Received: June 12, 2015; Received in revised form: May 18, 2016; Accepted: June 16, 2016; Published: July 14, 2016

© 2016 The Author(s). Published by Elsevier Inc.

FREE PDF GRATIS: Cell Reports

A inevitabilidade de parasitas genéticos

Inevitability of genetic parasites

Jaime Iranzo, Pere Puigbo, Alexander E. Lobkovsky, Yuri I. Wolf and Eugene V. Koonin*

- Author Affiliations

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894

↵*For correspondence: Eugene V. Koonin, koonin@ncbi.nlm.nih.gov

Received June 1, 2016. Revision received July 20, 2016. Accepted August 2, 2016.


Source/Fonte: University of Michigan

Abstract

Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites (‘cheaters’) necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given the (near) ubiquity, abundance and diversity of genetic parasites, the question becomes pertinent: are such parasites intrinsic to life? At least in prokaryotes, the persistence of parasites is linked to the rate of horizontal gene transfer (HGT). We mathematically derive the threshold value of the minimal transfer rate required for selfish element persistence, depending on the element duplication and loss rates as well as the cost to the host. Estimation of the characteristic gene duplication, loss and transfer rates for transposons, plasmids and virus-related elements in multiple groups of diverse bacteria and archaea indicates that most of these rates are compatible with the long term persistence of parasites. Notably, a small but non-zero rate of HGT is also required for the persistence of non-parasitic genes. We hypothesize that cells cannot tune their horizontal transfer rates to be below the threshold required for parasite persistence without experiencing highly detrimental side-effects. As a lower boundary to the minimum DNA transfer rate that a cell can withstand, we consider the process of genome degradation and mutational meltdown of populations through Muller’s ratchet. A numerical assessment of this hypothesis suggests that microbial populations cannot purge parasites while escaping Muller’s ratchet. Thus, genetic parasites appear to be virtually inevitable in cellular organisms.

Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2016. This work is written by US Government employees and are in the public domain in the US.

Charles Dawson, o único responsável pela fraude do Homem de Piltdown???

quarta-feira, agosto 10, 2016

New genetic and morphological evidence suggests a single hoaxer created ‘Piltdown man’

Isabelle De Groote, Linus Girdland Flink, Rizwaan Abbas, Silvia M. Bello, Lucia Burgia, Laura Tabitha Buck, Christopher Dean, Alison Freyne, Thomas Higham, Chris G. Jones, Robert Kruszynski, Adrian Lister, Simon A. Parfitt, Matthew M. Skinner, Karolyn Shindler, Chris B. Stringer

Published 10 August 2016.DOI: 10.1098/rsos.160328



Abstract

In 1912, palaeontologist Arthur Smith Woodward and amateur antiquarian and solicitor Charles Dawson announced the discovery of a fossil that supposedly provided a link between apes and humans: Eoanthropus dawsoni (Dawson's dawn man). The publication generated huge interest from scientists and the general public. However, ‘Piltdown man's’ initial celebrity has long been overshadowed by its subsequent infamy as one of the most famous scientific frauds in history. Our re-evaluation of the Piltdown fossils using the latest scientific methods (DNA analyses, high-precision measurements, spectroscopy and virtual anthropology) shows that it is highly likely that a single orang-utan specimen and at least two human specimens were used to create the fake fossils. The modus operandi was found consistent throughout the assemblage (specimens are stained brown, loaded with gravel fragments and restored using filling materials), linking all specimens from the Piltdown I and Piltdown II sites to a single forger—Charles Dawson. Whether Dawson acted alone is uncertain, but his hunger for acclaim may have driven him to risk his reputation and misdirect the course of anthropology for decades. The Piltdown hoax stands as a cautionary tale to scientists not to be led by preconceived ideas, but to use scientific integrity and rigour in the face of novel discoveries.

Abstract

Data accessibility

All DNA sequences are available on NCBI GenBank (KX533938-KX533939). The CT scans can be obtained from the Anthropology Curator at the Natural History Museum, London.

Authors' contributions

All authors provided written sections and feedback on the manuscript. L.G.F. carried out the DNA analyses. R.A. and M.M.S. contributed the geometric morphometric analyses. I.D.G. and C.D. performed the morphometric analyses. I.D.G., C.D., S.M.B., L.T.B., L.B. and C.G.J. carried out the Modus Operandi analyses. C.B.S., C.D., S.A.P., R.K., K.S., A.F. and A.L. provided the historical context. Dating analyses were performed by T.H. All authors authorize the publication of this work.

Competing interests

We declare that we have no competing interests.

Funding

The research of S.M.B., L.T.B., A.F., S.A.P. and C.B.S. is supported by the Calleva Foundation and the Human Origins Research Fund of the Natural History Museum.

Acknowledgements

There are too many people to thank individually for their assistance and engaging discussions on the topic of Piltdown, but we express special thanks for the assistance provided by the librarians and archivists at the Natural History Museum, and especially to John Farrant for drawing our attention to Mrs Dawson's letter held in the British Library.

Received May 11, 2016. Accepted July 14, 2016.

© 2016 The Authors.

http://creativecommons.org/licenses/by/4.0/

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

FREE PDF GRATIS: Royal Society Open Science

Proteínas grandes com vários domínios podem ter conformações mais estáveis do que se pensava

Single-molecule force-spectroscopy reveals the calcium dependency of the alternative conformations in the native state of a βγ-crystallin protein

Zackary Nathan Scholl, Qing Li, Weitao Yang and Piotr E. Marszalek*

- Author Affiliations

Duke University, United States

↵* Corresponding author; email: pemar@duke.edu

Author contributions: All authors helped design experiments. ZNS and QL performed the experiments. ZNS analyzed the data. All authors helped to write the manuscript.

To better understand the structure and stability of Protein S, researchers slowly pulled it apart. The red protein is Protein S and the blue proteins are used as "ties" for each end of the protein.
Source/Fonte: Duke University


Abstract

Though multidomain proteins predominate the proteome of all organisms, and are expected to display complex folding behaviors and significantly greater structural dynamics as compared to single-domain proteins, their conformational heterogeneity and its impact on their interaction with ligands is poorly understood due to lack of experimental techniques. The multidomain calcium-binding β γ-crystallin proteins are particularly important, as their deterioration and misfolding/aggregation is associated with melanoma tumors and cataracts. Here we investigate the mechanical stability and conformational dynamics of a model calcium-binding β γ-crystallin protein, Protein S, and elaborate on its interactions with calcium. We ask whether domain interactions and calcium binding affect Protein S folding and potential structural heterogeneity. Our results from single-molecule force-spectroscopy (SMFS) show that the N-terminal (but not the C-terminal) domain is in equilibrium with an alternative conformation in the absence of Ca2+, which is mechanically stable in contrast to other proteins that were observed to sample a molten globule under similar conditions. Mutagenesis experiments and computer simulations reveal that the alternative conformation of the N-terminal domain is caused by structural instability produced by the high charge density of a calcium binding site. We find that this alternative conformation in the N-terminal domain is diminished in the presence of calcium and can also be partially eliminated with a hitherto unrecognized compensatory mechanism that uses the interaction of the C-terminal domain to neutralize the electronegative site. We find that up to 1% of all identified multidomain calcium-binding proteins contain a similarly high-charged site and therefore may exploit a similar compensatory mechanism to prevent structural instability in the absence of ligand.

atomic force microscopy (AFM) calcium crystallin molecular dynamics protein folding

Received March 28, 2016. Accepted July 4, 2016.

Copyright © 2016, The American Society for Biochemistry and Molecular Biology

A evolução da epigenética: de procariontes a humanos e suas consequências biológicas

segunda-feira, agosto 08, 2016

The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences

Amber Willbanks, Meghan Leary, Molly Greenshields, Camila Tyminski, Sarah Heerboth, Karolina Lapinska, Kathryn Haskins and Sibaji Sarkar

Genetics & Epigenetics 2016:8 25-36

Review

Published on 03 Aug 2016


Further metadata provided in PDF

Source/Fonte:


Abstract

The evolution process includes genetic alterations that started with prokaryotes and now continues in humans. A distinct difference between prokaryotic chromosomes and eukaryotic chromosomes involves histones. As evolution progressed, genetic alterations accumulated and a mechanism for gene selection developed. It was as if nature was experimenting to optimally utilize the gene pool without changing individual gene sequences. This mechanism is called epigenetics, as it is above the genome. Curiously, the mechanism of epigenetic regulation in prokaryotes is strikingly different from that in eukaryotes, mainly higher eukaryotes, like mammals. In fact, epigenetics plays a significant role in the conserved process of embryogenesis and human development. Malfunction of epigenetic regulation results in many types of undesirable effects, including cardiovascular disease, metabolic disorders, autoimmune diseases, and cancer. This review provides a comparative analysis and new insights into these aspects.

FREE PDF GRATIS: Genetics and Epigenetics

CERN confirma o sumiço de indícios de partícula hipotética

domingo, agosto 07, 2016

Available on the CERN CDS information server CMS PAS EXO-16-027

CMS Physics Analysis Summary

Contact: cms-pag-conveners-exotica@cern.ch 2016/08/05

Search for resonant production of high mass photon pairs using 12.9 fb−1 of proton-proton collisions at √s = 13 TeV and combined interpretation of searches at 8 and 13 TeV

The CMS Collaboration


Abstract

We report on a search for resonant production of high mass photon pairs. The search employs 12.9 fb−1 of pp collision data collected by the CMS experiment in 2016 at a centre-of-mass energy of 13 TeV. It is aimed at spin-0 and spin-2 resonances of mass between 0.5 and 4.5 TeV and width, relative to the mass, up to 5.6 × 10−2

The results of the search are combined statistically with those previously obtained by the CMS collaboration at √s = 8 and 13 TeV. Limits are set on scalar resonances produced through gluon-gluon fusion, and on Randall–Sundrum gravitons. No significant excess is observed over the standard model predictions.

FREE PDF GRATIS: CERN

A esfera de vírus da cadeia dupla do DNA como uma rede modular hierárquica de compartilhamento de gene

sexta-feira, agosto 05, 2016

The Double-Stranded DNA Virosphere as a Modular Hierarchical Network of Gene Sharing

Jaime Iranzo a, Mart Krupovic b, Eugene V. Koonin a

- Author Affiliations

a National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA

b Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, France

Address correspondence to Eugene V. Koonin, koonin@ncbi.nlm.nih.gov.

Editor Roger Hendrix, University of Pittsburgh


ABSTRACT

Virus genomes are prone to extensive gene loss, gain, and exchange and share no universal genes. Therefore, in a broad-scale study of virus evolution, gene and genome network analyses can complement traditional phylogenetics. We performed an exhaustive comparative analysis of the genomes of double-stranded DNA (dsDNA) viruses by using the bipartite network approach and found a robust hierarchical modularity in the dsDNA virosphere. Bipartite networks consist of two classes of nodes, with nodes in one class, in this case genomes, being connected via nodes of the second class, in this case genes. Such a network can be partitioned into modules that combine nodes from both classes. The bipartite network of dsDNA viruses includes 19 modules that form 5 major and 3 minor supermodules. Of these modules, 11 include tailed bacteriophages, reflecting the diversity of this largest group of viruses. The module analysis quantitatively validates and refines previously proposed nontrivial evolutionary relationships. An expansive supermodule combines the large and giant viruses of the putative order “Megavirales” with diverse moderate-sized viruses and related mobile elements. All viruses in this supermodule share a distinct morphogenetic tool kit with a double jelly roll major capsid protein. Herpesviruses and tailed bacteriophages comprise another supermodule, held together by a distinct set of morphogenetic proteins centered on the HK97-like major capsid protein. Together, these two supermodules cover the great majority of currently known dsDNA viruses. We formally identify a set of 14 viral hallmark genes that comprise the hubs of the network and account for most of the intermodule connections.

IMPORTANCE

Viruses and related mobile genetic elements are the dominant biological entities on earth, but their evolution is not sufficiently understood and their classification is not adequately developed. The key reason is the characteristic high rate of virus evolution that involves not only sequence change but also extensive gene loss, gain, and exchange. Therefore, in the study of virus evolution on a large scale, traditional phylogenetic approaches have limited applicability and have to be complemented by gene and genome network analyses. We applied state-of-the art methods of such analysis to reveal robust hierarchical modularity in the genomes of double-stranded DNA viruses. Some of the identified modules combine highly diverse viruses infecting bacteria, archaea, and eukaryotes, in support of previous hypotheses on direct evolutionary relationships between viruses from the three domains of cellular life. We formally identify a set of 14 viral hallmark genes that hold together the genomic network.

FOOTNOTES

Citation Iranzo J, Krupovic M, Koonin EV. 2016. The double-stranded DNA virosphere as a modular hierarchical network of gene sharing. mBio 7(4):e00978-16. doi:10.1128/mBio.00978-16.

This article is a direct contribution from a Fellow of the American Academy of Microbiology. External solicited reviewers: Sergei Maslov, University of Illinois-Urbana-Champagne; Anca Segall, San Diego State University.

Received 31 May 2016 Accepted 14 June 2016 Published 2 August 2016

Copyright © 2016 Iranzo et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

FREE PDF GRATIS: mBio

DNA fóssil datado em 1.4 milhões de anos deixa cientistas atordoados

Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales

John B. Kirkpatrick, Emily A. Walsh and Steven D’Hondt

- Author Affiliations

Graduate School of Oceanography, University of Rhode Island, 215 South Ferry Road, Narragansett, Rhode Island 02882, USA


Source/Fonte: Illuminating Fossils

Abstract

DNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given >150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y.

Acknowledgments

We thank the IODP; the staff, crew, and science party of Expedition 323; and Heather Schrum, Nils Risgaard-Petersen, Dennis Graham, Victoria Fulfer, Paul Johnson, and Janet Atoyan. We thank the National Science Foundation (NSF)–funded Center for Dark Energy Biosphere Investigations (C-DEBI: NSF grant OCE-0939564). We used the Rhode Island Marine Science Research Facility and the Genomics and Sequencing Center, supported in part by NSF under EPSCoR Grants Nos. 0554548 and EPS-1004057. This is C-DEBI contribution #329. We thank the editor and reviewers for their contributions to this manuscript.

Footnotes

↵1GSA Data Repository item 2016199, details of methods protocols, taxa-specific depth and site profiles, comparative trees, and a table of sample data, is available online at www.geosociety.org/pubs/ft2016.htm, or on request from editing@geosociety.org.

Received 25 March 2016. Revision received 31 May 2016. Accepted 3 June 2016.

© The Authors

Gold Open Access: This paper is published under the terms of the CC-BY license.

FREE PAPER GRATIS: Geologyy

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DESTAQUE DESTE BLOGGER:

"We do not know the mechanism behind the apparent relative slowdown of DNA degradation with age. Whether this decreased turnover is due to decreased lability of residual DNA, an overall decrease in enzyme activity, a decrease in spontaneous decay rates, or some combination of these and other factors remains presently unknown."

Gregory Radick 'falou e disse': Ensinem para os seus alunos a Biologia atual!!!

quinta-feira, agosto 04, 2016

Teach students the biology of their time

An experiment in genetics education reveals how Mendel’s legacy holds back the teaching of science, says Gregory Radick.

17 May 2016

Historians study the causes and consequences of past events, but also consider alternative scenarios. What might have happened, for example, if Britain had stayed out of the war in Europe in 1914? Science historians also ask such counterfactual questions, and the results can be surprisingly instructive.

Take genetics. The past year has seen prolonged celebrations of the work of Gregor Mendel, linked to the 150th anniversary of the paper that reported his experiments with hybrid peas. Mendel’s experiments are central to biology curricula across the world. By contrast, the criticisms levelled at Mendel’s ideas by W. F. R. Weldon, Linacre professor at the University of Oxford, UK, are a footnote.

From 1902, Weldon’s views brought him into increasingly bad-tempered conflict with Mendel’s followers. In basic terms, the Mendel­i­­­­ans believed that inherited factors (later called ‘genes’) determine the visible characters of an organism, whereas Weldon saw context — developmental and environmental — as being just as important, with its influence making characters variable in ways that Mendelians ignored. The Mendelians won — helped by Weldon’s sudden death in 1906, before he published his ideas fully — and the teaching of genetics has emphasized the primacy of the gene ever since.

The problem is that the Mendelian ‘genes for’ approach is increasingly seen as out of step with twenty-first-century biology. If we are to realize the potential of the genomic age, critics say, we must find new concepts and language better matched to variablebiological reality. This is important in education, where the reliance on simple examples may even promote an outmoded determinism about the power of genes.

But what if Mendelism had never come to dominate genetics in the first place? What if Weldon’s perspective had emerged as the winner in that historical battle, and his interactionism, allied to his vivid sense of how variable the real characters of real organisms are (never just yellow or green, round or wrinkled, or any other Mendelian binary), had become the core of the subject? This is where I, and colleagues, have tried to run an experiment.

In a recent two-year project, we taught university students a curriculum that was altered to reflect what genetics textbooks might be like now if biology circa 1906 had taken the Weldonian rather than the Mendelian route. These students encountered genetics as funda­mentally tied to development and environment. Genes were not presented to them as what inheritance is ‘really about’, with everything else relegated to ignorable supporting roles. For example, they were taught that although genes can affect the heart directly, they also affect blood pressure, the body’s activity levels and other influential factors, themselves often influenced by non-genetic factors (such as smoking). Where in this tangle, we ask them, is a gene for heart disease? In effect, this revised curriculum seeks to take what is peripheral in the existing teaching of genetics and make it central, and to make what is central peripheral.

...

FREE PDF GRATIS: Nature

Scientific Inheritance - an Inaugural Lecture from Gregory Radick (University of Leeds)



1:01:52

Fósseis de lampreia e enguia de 300 milhões de anos derrubam teoria da evolução dos olhos de vertebrados

quarta-feira, agosto 03, 2016

Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye

Sarah E. Gabbott, Philip C. J. Donoghue, Robert S. Sansom, Jakob Vinther, Andrei Dolocan, Mark A. Purnell

Published 3 August 2016.DOI: 10.1098/rspb.2016.1151


Abstract

The success of vertebrates is linked to the evolution of a camera-style eye and sophisticated visual system. In the absence of useful data from fossils, scenarios for evolutionary assembly of the vertebrate eye have been based necessarily on evidence from development, molecular genetics and comparative anatomy in living vertebrates. Unfortunately, steps in the transition from a light-sensitive ‘eye spot’ in invertebrate chordates to an image-forming camera-style eye in jawed vertebrates are constrained only by hagfish and lampreys (cyclostomes), which are interpreted to reflect either an intermediate or degenerate condition. Here, we report—based on evidence of size, shape, preservation mode and localized occurrence—the presence of melanosomes (pigment-bearing organelles) in fossil cyclostome eyes. Time of flight secondary ion mass spectrometry analyses reveal secondary ions with a relative intensity characteristic of melanin as revealed through principal components analyses. Our data support the hypotheses that extant hagfish eyes are degenerate, not rudimentary, that cyclostomes are monophyletic, and that the ancestral vertebrate had a functional visual system. We also demonstrate integument pigmentation in fossil lampreys, opening up the exciting possibility of investigating colour patterning in Palaeozoic vertebrates. The examples we report add to the record of melanosome preservation in Carboniferous fossils and attest to surprising durability of melanosomes and biomolecular melanin.

FREE PDF GRATIS: Proc. R. Soc. B

O status da educação da medicina evolucionária nas faculdades de medicina dos Estados Unidos

terça-feira, agosto 02, 2016

The status of evolutionary medicine education in North American medical schools

Brandon H Hidaka Email author, Anila Asghar, C Athena Aktipis, Randolph M Nesse, Terry M Wolpaw, Nicole K Skursky, Katelyn J Bennett, Matthew W Beyrouty and Mark D Schwartz

BMC Medical Education 2015 15:38

DOI: 10.1186/s12909-015-0322-5 © Hidaka et al.; licensee BioMed Central. 2015

Received: 26 November 2014Accepted: 20 February 2015Published: 8 March 2015


Abstract

Background

Medical and public health scientists are using evolution to devise new strategies to solve major health problems. But based on a 2003 survey, medical curricula may not adequately prepare physicians to evaluate and extend these advances. This study assessed the change in coverage of evolution in North American medical schools since 2003 and identified opportunities for enriching medical education.

Methods

In 2013, curriculum deans for all North American medical schools were invited to rate curricular coverage and perceived importance of 12 core principles, the extent of anticipated controversy from adding evolution, and the usefulness of 13 teaching resources. Differences between schools were assessed by Pearson’s chi-square test, Student’s t-test, and Spearman’s correlation. Open-ended questions sought insight into perceived barriers and benefits.

Results

Despite repeated follow-up, 60 schools (39%) responded to the survey. There was no evidence of sample bias. The three evolutionary principles rated most important were antibiotic resistance, environmental mismatch, and somatic selection in cancer. While importance and coverage of principles were correlated (r = 0.76, P < 0.01), coverage (at least moderate) lagged behind importance (at least moderate) by an average of 21% (SD = 6%). Compared to 2003, a range of evolutionary principles were covered by 4 to 74% more schools. Nearly half (48%) of responders anticipated igniting controversy at their medical school if they added evolution to their curriculum. The teaching resources ranked most useful were model test questions and answers, case studies, and model curricula for existing courses/rotations. Limited resources (faculty expertise) were cited as the major barrier to adding more evolution, but benefits included a deeper understanding and improved patient care.

Conclusion

North American medical schools have increased the evolution content in their curricula over the past decade. However, coverage is not commensurate with importance. At a few medical schools, anticipated controversy impedes teaching more evolution. Efforts to improve evolution education in medical schools should be directed toward boosting faculty expertise and crafting resources that can be easily integrated into existing curricula.

KeywordsEvolutionary biology Evolutionary medicine Medical education Medical school curriculum Curriculum dean Survey

FREE PDF GRATIS: BMC Medical Education

Câncer em hominini mais antigo: um osteosarcoma de 1.7 milhões de anos

Earliest hominin cancer: 1.7-million-year-old osteosarcoma from Swartkrans Cave, South Africa

Type: Research Article

Authors: Edward J. Odes Patrick S. Randolph-Quinney (contact author) Maryna Steyn Zach Throckmorton Jacqueline S. Smilg Bernhard Zipfel Tanya Augustine Frikkie De Beer Jakobus W. Hoffman Ryan D. Franklin Lee R. Berger

Issue: July/August 2016

Number of pages: 5


Published: 28 July 2016

Source/Fonte: SciNews

Abstract: 

The reported incidence of neoplasia in the extinct human lineage is rare, with only a few confirmed cases of Middle or Later Pleistocene dates reported. It has generally been assumed that pre-modern incidence of neoplastic disease of any kind is rare and limited to benign conditions, but new fossil evidence suggests otherwise. We here present the earliest identifiable case of malignant neoplastic disease from an early human ancestor dated to 1.8–1.6 million years old. The diagnosis has been made possible only by advances in 3D imaging methods as diagnostic aids. We present a case report based on re-analysis of a hominin metatarsal specimen (SK 7923) from the cave site of Swartkrans in the Cradle of Humankind, South Africa. The expression of malignant osteosarcoma in the Swartkrans specimen indicates that whilst the upsurge in malignancy incidence is correlated with modern lifestyles, there is no reason to suspect that primary bone tumours would have been any less frequent in ancient specimens. Such tumours are not related to lifestyle and often occur in younger individuals. As such, malignancy has a considerable antiquity in the fossil record, as evidenced by this specimen.

Keywords: palaeopathology; oncology; malignant neoplasia; metatarsal; micro-computed tomography

A origem evolucionária do orgasmo feminino

Perspective and Hypothesis

The Evolutionary Origin of Female Orgasm

Authors: MIHAELA PAVLIČEV, GÜNTER WAGNER

First published: 31 July 2016Full publication history


Funding Information

Grant sponsor: March of Dimes Prematurity Research Center Ohio Collaborative; grant number: 22-FY14-470; grant sponsor: John Templeton Foundation; grant number: 54860.

Conflicts of interest: None.

Source/Fonte: EvMedReview

ABSTRACT

The evolutionary explanation of female orgasm has been difficult to come by. The orgasm in women does not obviously contribute to the reproductive success, and surprisingly unreliably accompanies heterosexual intercourse. Two types of explanations have been proposed: one insisting on extant adaptive roles in reproduction, another explaining female orgasm as a byproduct of selection on male orgasm, which is crucial for sperm transfer. We emphasize that these explanations tend to focus on evidence from human biology and thus address the modification of a trait rather than its evolutionary origin. To trace the trait through evolution requires identifying its homologue in other species, which may have limited similarity with the human trait. Human female orgasm is associated with an endocrine surge similar to the copulatory surges in species with induced ovulation. We suggest that the homolog of human orgasm is the reflex that, ancestrally, induced ovulation. This reflex became superfluous with the evolution of spontaneous ovulation, potentially freeing female orgasm for other roles. This is supported by phylogenetic evidence showing that induced ovulation is ancestral, while spontaneous ovulation is derived within eutherians. In addition, the comparative anatomy of female reproductive tract shows that evolution of spontaneous ovulation is correlated with increasing distance of clitoris from the copulatory canal. In summary, we suggest that the female orgasm-like trait may have been adaptive, however for a different role, namely for inducing ovulation. With the evolution of spontaneous ovulation, orgasm was freed to gain secondary roles, which may explain its maintenance, but not its origin.

Pode a Teoria da Evolução Moderna explicar a macroevolução?

segunda-feira, agosto 01, 2016

Futuyma, D. J. 2015. "Can Modern Evolutionary Theory Explain Macroevolution?" In Macroevolution: Explanation, Interpretation and Evidence. Serrelli, E and N. Gontier, eds. Cham, Switzerland: Springer International Publishing, 29-58.


Abstract

Ever since the Evolutionary Synthesis of the 1930s and 1940s, some biologists have expressed doubt that the Synthetic Theory, based principally on mutation, genetic variation, and natural selection, adequately accounts for macroevolution, or evolution above the species level. Some questions pertain to the history of biological diversity, but the greatest argument has concerned the evolution of major changes in organisms’ form and function. Such changes have been the subject of debate on the nature and phenotypic effect of mutations (especially the role of “macromutations” or saltations), the role of developmental mechanisms and processes, and the importance of internal constraints on adaptive evolution. Bridging the two major macroevolutionary themes, the hypothesis of punctuated equilibria invoked constraints on phenotypic evolution and the role of speciation in both diversification and the evolution of form. This chapter describes the Evolutionary Synthesis and the challenges to it and addresses the extent to which the modern formulation of the Synthetic Theory (ST) adequately addresses the observations that have prompted skeptical challenge. I conclude that although several proposed extensions and seemingly unorthodox ideas have some merit, the observations they purport to explain can mostly be interpreted within the framework of the Synthetic Theory.

Keywords: 

Evolutionary synthesis Punctuated equilibria Evolutionary developmental Biology Epigenetics Genetic constraints Adaptation

EXCERPT/EXCERTO:

"Ever since the Evolutionary Synthesis of the 1930s and 1940s, some biologists have expressed doubt that the Synthetic Theory [the prevailing modern version of evolution, also called neo-Darwinism], based principally on mutation, genetic variation, and natural selection, adequately accounts for macroevolution, or evolution above the species level."

FREE PDF GRATIS: Springer

Papel da estrutura de mRNA no controle da dobragem de proteínas

Role of mRNA structure in the control of protein folding

Guilhem Faure, Aleksey Y. Ogurtsov, Svetlana A. Shabalina and Eugene V. Koonin*

- Author Affiliations

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

↵*To whom correspondence should be addressed. Tel: +1 301 435 5913; Fax: +1 301 435 7793; Email: koonin@ncbi.nlm.nih.gov

Received May 3, 2016. Revision received July 12, 2016. Accepted July 14, 2016.



Source/Fonte: ISaude

Abstract

Specific structures in mRNA modulate translation rate and thus can affect protein folding. Using the protein structures from two eukaryotes and three prokaryotes, we explore the connections between the protein compactness, inferred from solvent accessibility, and mRNA structure, inferred from mRNA folding energy (ΔG). In both prokaryotes and eukaryotes, the ΔG value of the most stable 30 nucleotide segment of the mRNA (ΔGmin) strongly, positively correlates with protein solvent accessibility. Thus, mRNAs containing exceptionally stable secondary structure elements typically encode compact proteins. The correlations between ΔG and protein compactness are much more pronounced in predicted ordered parts of proteins compared to the predicted disordered parts, indicative of an important role of mRNA secondary structure elements in the control of protein folding. Additionally, ΔG correlates with the mRNA length and the evolutionary rate of synonymous positions. The correlations are partially independent and were used to construct multiple regression models which explain about half of the variance of protein solvent accessibility. These findings suggest a model in which the mRNA structure, particularly exceptionally stable RNA structural elements, act as gauges of protein co-translational folding by reducing ribosome speed when the nascent peptide needs time to form and optimize the core structure.

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

FREE PDF GRATIS: Nucleic Acids Research Sup Info