A dimensionalidade da informação genômica e seu efeito sobre a predição genômica

quinta-feira, maio 05, 2016

The Dimensionality of Genomic Information and Its Effect on Genomic Prediction

Ivan Pocrnic, Daniela A. L. Lourenco, Yutaka Masuda, Andres Legarra, Ignacy Misztal

GENETICS May 1, 2016 vol. 203 no. 1 573-581; 


Abstract

The genomic relationship matrix (GRM) can be inverted by the algorithm for proven and young (APY) based on recursion on a random subset of animals. While a regular inverse has a cubic cost, the cost of the APY inverse can be close to linear. Theory for the APY assumes that the optimal size of the subset (maximizing accuracy of genomic predictions) is due to a limited dimensionality of the GRM, which is a function of the effective population size (Ne). The objective of this study was to evaluate these assumptions by simulation. Six populations were simulated with approximate effective population size (Ne) from 20 to 200. Each population consisted of 10 nonoverlapping generations, with 25,000 animals per generation and phenotypes available for generations 1–9. The last 3 generations were fully genotyped assuming genome length L = 30. The GRM was constructed for each population and analyzed for distribution of eigenvalues. Genomic estimated breeding values (GEBV) were computed by single-step GBLUP, using either a direct or an APY inverse of GRM. The sizes of the subset in APY were set to the number of the largest eigenvalues explaining x% of variation (EIGx, x = 90, 95, 98, 99) in GRM. Accuracies of GEBV for the last generation with the APY inverse peaked at EIG98 and were slightly lower with EIG95, EIG99, or the direct inverse. Most information in the GRM is contained in ∼NeL largest eigenvalues, with no information beyond 4NeL. Genomic predictions with the APY inverse of the GRM are more accurate than by the regular inverse.

GENPRED SHARED DATA RESOURCE GENOMIC SELECTION GENOMIC RELATIONSHIP MATRIX INVERSION RECURSION EFFECTIVE POPULATION SIZE SINGLE-STEP GBLUP

FREE PDF GRATIS: Genetics

A sobrevivência dos mais antigos - por que algumas espécies mais antigas sobrevivem mais do que outras?

Why are some species older than others? A large-scale study of vertebrates

Laure Cattin, Johan Schuerch, Nicolas Salamin and Sylvain DubeyEmail author

BMC Evolutionary BiologyBMC series – open, inclusive and trusted201616:90

DOI: 10.1186/s12862-016-0646-8 © Cattin et al. 2016

Received: 21 October 2015Accepted: 30 March 2016Published: 4 May 2016



Abstract

Background

Strong variations are observed between and within taxonomic groups in the age of extant species and these differences can clarify factors that render species more vulnerable to extinction. Understanding the factors that influence the resilience of species is thus a key component of evolutionary biology, but it is also of prime importance in a context of climate change and for conservation in general. We explored the effect of extrinsic and intrinsic factors on the timing of the oldest diversification event in over 600 vertebrate species distributed worldwide. We used phylogenetic comparative methods to show that color polymorphism, latitude and reproduction (the latter through its interaction with latitude) affected the timing of the oldest diversification event within a species.

Results

Species from higher latitudes tended to be younger, and colour-polymorphic species were older than monomorphic species. Mode of reproduction was important also, in that the age of oviparous species decreased with latitude, whereas no pattern was apparent for viviparous species. Organisms which have already persisted for a long time may be more likely to deal with future modifications of their environment.

Conclusions

Species that are colour polymorphic, viviparous, and/or live at low latitudes have exhibited resilience to past environmental changes, and hence may be better able to deal with current climate change.

Keywords

Species age Intraspecific diversification Latitude Viviparity Oviparity Colour polymorphism

FREE PDF GRATIS: BMC Evolutionary Biology

Leandro Russovski Tessler, professor de Física da Unicamp, ouça o que Frank Wilczek, prêmio Nobel em Física, disse porque o mundo é tão lindo




Nobel physicist Frank Wilczek sees beauty as a compass for truth, discovery, and meaning. His book, A Beautiful Question, is a long meditation on the question: “Does the world embody beautiful ideas?” He’s the unusual scientist willing to analogize his discoveries about the deep structure of reality with deep meaning in the human everyday.

Um trilhão de espécies e 99.99% delas desconhecidas!!!

terça-feira, maio 03, 2016

Scaling laws predict global microbial diversity

Kenneth J. Loceya,1 and Jay T. Lennona,1

Author Affiliations

a Department of Biology, Indiana University, Bloomington, IN 47405

Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved March 30, 2016 (received for review October 27, 2015)


Significance

Ecological scaling laws are intensively studied for their predictive power and universal nature but often fail to unify biodiversity across domains of life. Using a global-scale compilation of microbial and macrobial data, we uncover relationships of commonness and rarity that scale with abundance at similar rates for microorganisms and macroscopic plants and animals. We then show a unified scaling law that predicts the abundance of dominant species across 30 orders of magnitude to the scale of all microorganisms on Earth. Using this scaling law combined with the lognormal model of biodiversity, we predict that Earth is home to as many as 1 trillion (1012) microbial species.

Abstract

Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ∼35,000 sites and ∼5.6⋅106 species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we show similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upward of 1 trillion (1012) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome.

biodiversity microbiology macroecology microbiome rare biosphere

FREE PDF GRATIS: PNAS

Descoberto um limite fundamental para a evolução do código genético

Saturation of recognition elements blocks evolution of new tRNA identities

Adélaïde Saint-Léger1, Carla Bello2,3, Pablo D. Dans1,4, Adrian Gabriel Torres1, Eva Maria Novoa1,5,6, Noelia Camacho1, Modesto Orozco1,4,7, Fyodor A. Kondrashov2,3,8 and Lluís Ribas de Pouplana1,8,*

- Author Affiliations

1Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain.

2Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 88 Dr. Aiguader, 08003 Barcelona, Catalonia, Spain.

3Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.

4Joint BSC-IRB Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Catalonia, Spain.

5Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.

6Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02139, USA.

7Departament de Bioquimica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avgda Diagonal 647, 08028 Barcelona, Catalonia, Spain.

8Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Catalonia, Spain.

↵*Corresponding author. Email: lluis.ribas@irbbarcelona.org

Science Advances 29 Apr 2016:

Vol. 2, no. 4, e1501860



Abstract

Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure.

Key words tRNA identities genetic code evolution ADA TtRNA Gly

FREE PDF GRATIS: Science Advances

As consequências de erros nas pesquisas científicas

segunda-feira, maio 02, 2016

The consequence of errors

From memory molecules to the criminal chromosome, erroneous conclusions continue to blight scientific research

Katrin Weigmann

Author Affiliations

OI 10.1038/sj.embor.7400389 | Published online 01.04.2005

EMBO reports (2005) 6, 306-309



Article

Ancient Greek philosophers laid the groundwork for the scientific tradition of critical inquiry, but they nevertheless missed out on one aspect important to modern science. Many philosophers obtained their results through a tradition of contemplation and thought rather than experimental procedure, which, not surprisingly, led to errors. Aristotle's belief that the brain is a cooling organ for the blood was definitely not based on anything that scientists today would consider scientific evidence. He also thought that in humans, goats and pigs, males have more teeth than females, a notion easy enough to correct. His statement that flies have four legs was repeated in natural history texts for more than a thousand years despite the fact that a little counting would have proven otherwise.

Today, these errors are anecdotal, and science prides itself on having progressed from intuition‐driven to solid, experiment‐based reasoning. But modern science is not as infallible as it seems—it has erred in the recent past and still does today. To err is human. Given the increasing influence of science on nearly all aspects of daily life, the important question is how efficiently such errors are recognized and corrected.

The basis of every experiment is the acquisition of data. But even if this merely involves counting, it can be astonishingly difficult to obtain reliable data. In the 1950s and 1960s—centuries after the number of fly legs and male teeth had been corrected—James McConnell at Ann Arbor University (MI, USA) carried out experiments to condition planarians to associate a light stimulus with an electric shock so they would scrunch up their bodies in response to light. The educated worm was then ground up and fed to untrained littermates. Once they had cannibalized their brethren, these worms learned to contract in response to light twice as fast as compared with controls, according to McConnell. He concluded that the conditioned memory was stored in a molecule that could be transferred by ingestion (Rose, 1993). Today, we know that memory is not transferable in this way. But the implications of McConnell's experiment—that specific memories are stored in isolatable molecules—caused quite a stir at the time. “Eat your professor”, the New York Times suggested (Zankl, 2004), and TIME Magazine discussed potential misuses, such as a police state or government brainwashing a whole population by lacing tap water.


"…modern science is not as infallible as it seems—it has erred in the recent past and still does today".

FREE PDF GRATIS: EMBO Reports

Lendas urbanas acadêmicas

Academic urban legends

Ole Bjørn Rekdal

Faculty of Health and Social Sciences, Bergen University College, Bergen, Norway

Ole Bjørn Rekdal, Faculty of Health and Social Sciences, Bergen University College, PO Box 7030, 5020 Bergen, Norway. Email: obr@hib.no

Next Section


Abstract

Many of the messages presented in respectable scientific publications are, in fact, based on various forms of rumors. Some of these rumors appear so frequently, and in such complex, colorful, and entertaining ways that we can think of them as academic urban legends. The explanation for this phenomenon is usually that authors have lazily, sloppily, or fraudulently employed sources, and peer reviewers and editors have not discovered these weaknesses in the manuscripts during evaluation. To illustrate this phenomenon, I draw upon a remarkable case in which a decimal point error appears to have misled millions into believing that spinach is a good nutritional source of iron. Through this example, I demonstrate how an academic urban legend can be conceived and born, and can continue to grow and reproduce within academia and beyond.

academic shortcuts academic urban legends citation practices iron spinach

FREE PDF GRATIS: Social Studies of Science

Impeachment de Darwin e Wallace na História da Ciência: crime de pedalada teórica da seleção natural de Patrick Matthew

Papers from the British Criminology Conference

© 2014 the authors and the British Society of Criminology

www.britsoccrim.org

ISSN 1759-0043; Vol. 14: 49-64

Panel Paper

The hi-tech detection of Darwin’s and Wallace’s possible science fraud:

Big data criminology re-writes the history of contested discovery

Mike Sutton, Nottingham Trent University


Abstract

Priority for discoveries is awarded to those who are first to publish. If a scholar writes claiming to have discovered something or originated a theory that has been earlier published, or presented in public by another who got their first, then the peer review process, professional and public disapproval is relied upon to identify and correct the self-serving irregularity. Thereafter, the pretender to the throne of discovery is expected to retract and apologise. If there is evidence that such a counterfeit originator had prior knowledge of their supposedly independent discovery being first discovered by another, the professional repercussions are likely to be catastrophic. This article is about the devastating Big Data facilitated 2014 discovery that the world’s most celebrated and studied natural scientist Charles Darwin, and his lesser known associate Alfred Russel Wallace, more likely than not committed the world’s greatest science fraud by apparently plagiarising the entire theory of natural selection from a book written by Patrick Matthew and then claiming to have had no prior-knowledge of it.

Key Words: science fraud; plagiarism; Darwin; Matthew

Em 1997 Deamer 'falou e disse' sobre os primeiros sistemas vivos a partir de uma perspectiva bioenergética

domingo, maio 01, 2016

The first living systems: a bioenergetic perspective.

D W Deamer

- Author Affiliations

Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA. deamer@hydrogen.ucsc.edu


Source/Fonte: U. S. Department of Energy



SUMMARY

The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.

NASA Discipline Exobiology Non-NASA Center

FREE PDF GRATIS: Microbiol Mol Biol Rev.

Os cientistas capturaram o momento extraordinário "uau" da fertilização

sexta-feira, abril 29, 2016

The zinc spark is an inorganic signature of human egg activation

Francesca E. Duncan, Emily L. Que, Nan Zhang, Eve C. Feinberg, Thomas V. O’Halloran & Teresa K. Woodruff

Scientific Reports 6, Article number: 24737 (2016) doi:10.1038/srep24737

Download Citation 

Predictive markers Reproductive biology

Received: 03 December 2015 Accepted: 01 April 2016 Published online: 26 April 2016



Abstract

Egg activation refers to events required for transition of a gamete into an embryo, including establishment of the polyspermy block, completion of meiosis, entry into mitosis, selective recruitment and degradation of maternal mRNA, and pronuclear development. Here we show that zinc fluxes accompany human egg activation. We monitored calcium and zinc dynamics in individual human eggs using selective fluorophores following activation with calcium-ionomycin, ionomycin, or hPLCζ cRNA microinjection. These egg activation methods, as expected, induced rises in intracellular calcium levels and also triggered the coordinated release of zinc into the extracellular space in a prominent “zinc spark.” The ability of the gamete to mount a zinc spark response was meiotic-stage dependent. Moreover, chelation of intracellular zinc alone was sufficient to induce cell cycle resumption and transition of a meiotic cell into a mitotic one. Together, these results demonstrate critical functions for zinc dynamics and establish the zinc spark as an extracellular marker of early human development.

FREE PDF GRATIS: Scientific Reports

50 anos de desafios científicos à teoria da evolução: Relembrando o Simpósio de Wistar

quinta-feira, abril 28, 2016





A teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários de A a Z (vai que um falhe), não fecha na matemática! Leiam este livro de 50 anos atrás (e a Nomenklatura científica e a Galera de meninos e meninas de Darwin dizem que não houve e nem há crise epistêmica na teoria da evolução?): Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution (US$ 199,95), e vejam que os problemas não foram respondidos no contexto de justificação teórica, e aumentaram cada vez mais!

Porta de entrada para o cérebro: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, abril 27, 2016

Structural insights into the transport mechanism of the human sodium-dependent lysophosphatidylcholine transporter Mfsd2a

Debra Q.Y. Quek1, Long N. Nguyen2, Hao Fan3 and David L. Silver1*

- Author Affiliations

1 Duke-NUS Medical School, Singapore;

2 National University of Singapore, Singapore;

3 A*STAR, Singapore

↵* Corresponding author; email: david.silver@duke-nus.edu.sg

Author contributions: D.L.S., D.Q.Q., and H.F. designed research; D.Q.Q. and H.F. performed research; L.N.N performed experiments for Fig. 3H; D.Q.Q. and H.F. performed structural modelling and analysis. D.Q.Q., D.L.S., and H.F. wrote the paper.



Abstract

Major Facilitator Superfamily Domain containing 2A (Mfsd2a) was recently characterized as a sodium-dependent lysophosphatidylcholine (LPC) transporter expressed at the blood-brain barrier endothelium. It is the primary route for importation of docosohexaenoic acid and other long-chain fatty acids into foetal and adult brain, and is essential for mouse and human brain growth and function. Remarkably, Mfsd2a is the first identified MFS family member that uniquely transports lipids, implying that Mfsd2a harbours unique structural features and transport mechanism. Here, we present three 3D structural models of human Mfsd2a derived by homology modelling using MelB- and LacY-based crystal structures, and refined by biochemical analysis. All models revealed 12 transmembrane helices and connecting loops, and represented the partially outward-open, outward-partially occluded, and inward-open states of the transport cycle. In addition to a conserved sodium-binding site, three unique structural features were identified: A phosphate headgroup binding site, a hydrophobic cleft to accommodate a hydrophobic hydrocarbon tail, and three sets of ionic locks that stabilize the outward-open conformation. Ligand docking studies and biochemical assays identified Lys436 as a key residue for transport. It is seen forming a salt bridge with the negative charge on the phosphate headgroup. Importantly, Mfsd2a transported structurally related acylcarnitines but not a lysolipid without a negative charge, demonstrating the necessity of a negative charged headgroup interaction with Lys436 for transport. These findings support a novel transport mechanism by which LPCs are flipped within the transporter cavity by pivoting about Lys436 leading to net transport from the outer to the inner leaflet of the plasma membrane.

brain metabolism drug transport lysophospholipid membrane protein polyunsaturated fatty acid (PUFA) X-ray crystallography blood-brain barrier docosahexaenoic acid membrane transporter microcephaly

Received February 9, 2016. Accepted March 4, 2016.

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

Mutação e o excepcionalismo humano: nossa carga genética futura

Mutation and Human Exceptionalism: Our Future Genetic Load

Michael Lynch

GENETICS March 1, 2016 vol. 202 no. 3 869-875; 


Abstract

Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.

FREE PDF GRATIS: Genetics


Porque a evolução humana deve ser uma ciência básica para estudantes de medicina e psicologia

Why human evolution should be a basic science for medicine and psychology students

Paola Palanza & Stefano Parmigiani

Department of Neuroscience, Unit of Behavioral Biology, University of Parma, Viale delle Scienze 11A, 43100 Parma, Italy

e-mail: paola.palanza@unipr.it



Summary

Based on our teaching experience in medicine and psychology degree programs, we examine different aspects of human evolution that can help students to understand how the human body and mind work and why they are vulnerable to certain diseases. Three main issues are discussed: 1) the necessity to consider not only the mechanisms, i.e. the “proximate causations”, implicated in biological processes but also why these mechanisms have evolved, i.e. the “ultimate causations” or “adaptive significance”, to understand the functioning and malfunctioning of human body and mind; 2) examples of how human vulnerabilities to disease are caused by phylogenetic constraints, evolutionary tradeoffs reflecting the combined actions of natural and sexual selection, and/or mismatch between past and present environment (i.e., evolution of the eye, teeth and diets, erect posture and their consequences); 3) human pair-bonding and parent-offspring relationships as the result of socio-sexual selection and evolutionary compromises between cooperation and conflict. These psychobiological mechanisms are interwoven with our brain developmental plasticity and the effects of culture in shaping our behavior and mind, and allow a better understanding of functional (normal) and dysfunctional (pathological) behaviors. Thus, because the study of human evolution offers a powerful framework for clinical practice and research, the curriculum studiorum of medical and psychology students should include evolutionary biology and human phylogeny.

Keywords - Science education, Natural selection, Sexual selection, Ultimate causation, Human health, Darwinian medicine.

Novos insights na regulação de genes através da caracterização do complexo NuRD de repressão

The structure of the core NuRD repression complex provides insights into its interaction with chromatin

Christopher J Millard Niranjan Varma Almutasem Saleh Kyle Morris Peter J Watson Andrew R Bottrill Louise Fairall Corinne J Smith John WR Schwabe 

University of Leicester, United Kingdom; University of Warwick, United Kingdom


Published April 21, 2016 Cite as eLife 2016;5:e13941



Abstract

The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.


eLife digest

The correct regulation of our genes is essential for life. Genes are actively switched on or off through the action of assemblies of proteins that act together as molecular machines. Some of these machines alter the way that DNA is packaged inside cells. Packaged DNA – called chromatin – consists of DNA wrapped around proteins called histones, which together form structures called nucleosomes. Changing how tightly nucleosomes are packed together can alter whether a gene is active: tighter packing makes it harder to access the genes in that stretch of DNA and therefore inactivates them.

In humans, an assembly of proteins called the NuRD complex makes chromatin more compact by removing acetyl groups from nucleosomes. This complex is important for early development and for the stability and repair of our genes. Three proteins make up its core: HDAC1, which removes the acetyl group from the nucleosome; MTA1, which acts as a scaffold to hold the complex together; and RBBP4, which enables the complex to interact with nucleosomes.

Understanding how protein complexes are assembled tells us a lot about how they work. Millard et al. have therefore used a number of structural techniques to investigate the three-dimensional architecture of the three core proteins in the NuRD complex. The resulting structures have revealed how the HDAC1, MTA1 and RBBP4 proteins interact to influence how the complex is recruited to nucleosomes. The next step will be to assemble all the remaining proteins of the NuRD complex to understand its architecture as a whole.


FREE PDF GRATIS: eLIFE

Novos fósseis do Mioceno e a história dos pinguins na Austrália

New Miocene Fossils and the History of Penguins in Australia

Travis Park , Erich M. G. Fitzgerald, Stephen J. Gallagher, Ellyn Tomkins, Tony Allan

Published: April 26, 2016http://dx.doi.org/10.1371/journal.pone.0153915



Abstract

Australia has a fossil record of penguins reaching back to the Eocene, yet today is inhabited by just one breeding species, the little penguin Eudyptula minor. The description of recently collected penguin fossils from the re-dated upper Miocene Port Campbell Limestone of Portland (Victoria), in addition to reanalysis of previously described material, has allowed the Cenozoic history of penguins in Australia to be placed into a global context for the first time. Australian pre-Quaternary fossil penguins represent stem taxa phylogenetically disparate from each other and E. minor, implying multiple dispersals and extinctions. Late Eocene penguins from Australia are closest to contemporaneous taxa in Antarctica, New Zealand and South America. Given current material, the Miocene Australian fossil penguin fauna is apparently unique in harbouring ‘giant penguins’ after they went extinct elsewhere; and including stem taxa until at least 6 Ma, by which time crown penguins dominated elsewhere in the southern hemisphere. Separation of Australia from Antarctica during the Palaeogene, and its subsequent drift north, appears to have been a major event in Australian penguin biogeography. Increasing isolation through the Cenozoic may have limited penguin dispersal to Australia from outside the Australasian region, until intensification of the eastwards-flowing Antarctic Circumpolar Current in the mid-Miocene established a potential new dispersal vector to Australia.

Citation: Park T, Fitzgerald EMG, Gallagher SJ, Tomkins E, Allan T (2016) New Miocene Fossils and the History of Penguins in Australia. PLoS ONE 11(4): e0153915. doi:10.1371/journal.pone.0153915

Editor: Nicholas Pyenson, Smithsonian Institution, UNITED STATES

Received: July 24, 2015; Accepted: April 6, 2016; Published: April 26, 2016

Copyright: © 2016 Park et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: Grant number: DP0558150, Australian Research Council, funder's website: www.arc.gov.au, author who received funding: SJG and ET. Funding was for fieldwork associated with geologic data collection and subsequent stratigraphic analyses only. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

FREE PDF GRATIS: PLoS One

Os elos perdidos na origem da vida podem ter se desenvolvido em poças d'água

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

Brian J. Cafferty, David M. Fialho, Jaheda Khanam, Ramanarayanan Krishnamurthy & Nicholas V. Hud

Affiliations Contributions Corresponding author

Nature Communications 7, Article number: 11328 doi:10.1038/ncomms11328

Received 02 August 2015 Accepted 16 March 2016 Published 25 April 2016



Abstract

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

Subject terms: Chemical sciences Organic chemistry Chemical biology

FREE PDF GRATIS: Nature Communications

Como e porque os organismos unicelulares evoluíram em vida multicelular

The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity

Erik R. Hanschen, Tara N. Marriage, Patrick J. Ferris, Takashi Hamaji, Atsushi Toyoda, Asao Fujiyama, Rafik Neme, Hideki Noguchi, Yohei Minakuchi, Masahiro Suzuki, Hiroko Kawai-Toyooka, David R. Smith, Halle Sparks, Jaden Anderson, Robert Bakarić, Victor Luria, Amir Karger, Marc W. Kirschner, Pierre M. Durand, Richard E. Michod et al.

Affiliations Contributions Corresponding authors

Nature Communications 7, Article number: 11370 doi:10.1038/ncomms11370

Received 26 January 2016 Accepted 18 March 2016 Published 22 April 2016


Abstract

The transition to multicellularity has occurred numerous times in all domains of life, yet its initial steps are poorly understood. The volvocine green algae are a tractable system for understanding the genetic basis of multicellularity including the initial formation of cooperative cell groups. Here we report the genome sequence of the undifferentiated colonial alga, Gonium pectorale, where group formation evolved by co-option of the retinoblastoma cell cycle regulatory pathway. Significantly, expression of the Gonium retinoblastoma cell cycle regulator in unicellular Chlamydomonas causes it to become colonial. The presence of these changes in undifferentiated Gonium indicates extensive group-level adaptation during the initial step in the evolution of multicellularity. These results emphasize an early and formative step in the evolution of multicellularity, the evolution of cell cycle regulation, one that may shed light on the evolutionary history of other multicellular innovations and evolutionary transitions.

Subject terms: Biological sciences Evolution Genetics

FREE PDF GRATIS: Nature Communications

Celebrando o Dia do DNA 2016: mais de 100 artigos acesso livre!

segunda-feira, abril 25, 2016

Celebrating DNA Day 2016

Read top articles published in Springer Nature Genetics Journals

We are pleased to announce that we are supporting the DNA Day 2016 celebrated on April 25. This annual event commemorates the discovery of DNA's double helix back in 1953 and celebrates the completion of the Human Genome Project in 2003.
Springer Nature is opening top research articles about key scientific developments in Genetics. The selected articles are published in Springer, BioMed Central and Nature Publishing Group journals

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A divergência dos cromossomos Y de neandertais e humanos modernos

sábado, abril 23, 2016

The Divergence of Neandertal and Modern Human Y Chromosomes

Fernando L. Mendez correspondence email, G. David Poznik, Sergi Castellano, Carlos D. Bustamante correspondence email

Open Access


Publication History Published: April 7, 2016 Accepted: February 26, 2016 Received: December 22, 2015

User License

Creative Commons Attribution (CC BY 4.0)


Relationship of Neandertal Y Chromosome to Those of Modern Humans

The genealogy (red tree) can be parsimoniously explained as mirroring the population divergence (gray tree). We find no evidence for (a) a highly divergent super-archaic origin of the Neandertal Y chromosome, (b) ancient gene flow post-dating the population split, or (c) relatively recent introgression of a modern human Y chromosome into the Neandertal population.


Summary

Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447–806 kya). This is ∼2.1 (95% CI: 1.7–2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

Received: December 22, 2015; Accepted: February 26, 2016; Published: April 7, 2016

© 2016 The Authors. Published by Elsevier Inc.

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Novos módulos para ensinar medicina evolucionária: uma experiência australiana e suíça

sexta-feira, abril 22, 2016

Novel Modules to Teach Evolutionary Medicine: an Australian and a Swiss Experience

Frank Rühli, Martin Haeusler, Arthur Saniotis, Maciej Henneberg

First online: 18 April 2016




Abstract

Objectives

Evolutionary medicine is a growing field focusing on the evolutionary basis of human diseases and their changes through time. The introduction of concepts of long- and short-term evolution into the medical curricula is essential to acknowledge the variability of human biology.

Methods

Three courses of the EM taught at the University of Zurich and the University of Adelaide are presented by giving their general descriptions, full curricula, and the results of anonymized student evaluations.

Results

The presented courses meet a growing need and were positively received by the students. Most importantly, they seem to stimulate critical thinking about issues relating to health and evolution.

Conclusions

The incorporation of these topics into curricula will allow future practitioners of health-related professions to apply principles of human evolution and its forces in their work.

Keywords Disease Curricula Evolutionary medicine Medical school

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Construção de árvores filogenéticas de alunos de um curso de introdução à biologia

Student construction of phylogenetic trees in an introductory biology course

Jonathan Dees and Jennifer L. Momsen Email author

Evolution: Education and Outreach20169:3

DOI: 10.1186/s12052-016-0054-y© Dees and Momsen. 2016

Received: 25 November 2015Accepted: 14 April 2016Published: 21 April 2016



Abstract

Background

Phylogenetic trees have become increasingly essential across biology disciplines. Consequently, learning about phylogenetic trees has become an important component of biology education and an area of interest for biology education research. Construction tasks, in which students generate phylogenetic trees from some type of data, are often used for instruction. However, the impact of these exercises on student learning is uncertain, in part due to our fragmented knowledge of what students construct during the tasks. The goal of this project was to develop a more robust method for describing student-generated phylogenetic trees, which will support future investigations that attempt to link construction tasks with student learning.

Results

Through iterative examination of data from an introductory biology course, we developed a method for describing student-generated phylogenetic trees in terms of style, conventionality, and accuracy. Students used the diagonal style more often than the bracket style for construction tasks. The majority of phylogenetic trees were constructed conventionally, and variable orientation of branches was the most common unconventional feature. In addition, the majority of phylogenetic trees were generated correctly (no errors) or adequately (minor errors only) in terms of accuracy. Suggesting extant taxa are descended from other extant taxa was the most common major error, while empty branches and extra nodes were very common minor errors.

Conclusions

The method we developed to describe student-constructed phylogenetic trees uncovered several trends that warrant further investigation. For example, while diagonal and bracket phylogenetic trees contain equivalent information, student preference for using the diagonal style could impact comprehension. In addition, despite a lack of explicit instruction, students generated phylogenetic trees that were largely conventional and accurate. Surprisingly, accuracy and conventionality were also dependent on each other. Our method for describing phylogenetic trees constructed by students is based on data from one introductory biology course at one institution, and the results are likely limited. We encourage researchers to use our method as a baseline for developing a more generalizable tool, which will support future investigations that attempt to link construction tasks with student learning.

Keywords

Phylogenetic trees Cladograms Conceptual models Construction tasks Evolution Tree thinking

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