Mensagem em uma molécula

Message in a molecule

Tanmay Sarkar, Karuthapandi Selvakumar, Leila Motiei & David Margulies

Affiliations Contributions Corresponding author

Nature Communications 7, Article number: 11374 doi:10.1038/ncomms11374

Received 07 December 2015 Accepted 21 March 2016 Published 03 May 2016

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Abstract

Since ancient times, steganography, the art of concealing information, has largely relied on secret inks as a tool for hiding messages. However, as the methods for detecting these inks improved, the use of simple and accessible chemicals as a means to secure communication was practically abolished. Here, we describe a method that enables one to conceal multiple different messages within the emission spectra of a unimolecular fluorescent sensor. Similar to secret inks, this molecular-scale messaging sensor (m-SMS) can be hidden on regular paper and the messages can be encoded or decoded within seconds using common chemicals, including commercial ingredients that can be obtained in grocery stores or pharmacies. Unlike with invisible inks, however, uncovering these messages by an unauthorized user is almost impossible because they are protected by three different defence mechanisms: steganography, cryptography and by entering a password, which are used to hide, encrypt or prevent access to the information, respectively.

Subject terms: Chemical sciences Organic chemistry Analytical chemistry

FREE PDF GRATIS: Nature Communications

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NOTA DESTE BLOGGER:

Esteganografia é uma ciência de design inteligente!

Eucarioto sem organela mitocondrial???

A Eukaryote without a Mitochondrial Organelle

Anna Karnkowska7, correspondence email, Vojtěch Vacek, Zuzana Zubáčová, Sebastian C. Treitli, Romana Petrželková, Laura Eme, Lukáš Novák, Vojtěch Žárský, Lael D. Barlow, Emily K. Herman, Petr Soukal, Miluše Hroudová, Pavel Doležal, Courtney W. Stairs, Andrew J. Roger, Marek Eliáš, Joel B. Dacks, Čestmír Vlček, Vladimír Hampl correspondence email

7Present address: Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada

Publication stage: In Press Corrected Proof

DOI: http://dx.doi.org/10.1016/j.cub.2016.03.053

Highlights

• Monocercomonoides sp. is a eukaryotic microorganism with no mitochondria

• The complete absence of mitochondria is a secondary loss, not an ancestral feature

• The essential mitochondrial ISC pathway was replaced by a bacterial SUF system

Summary

The presence of mitochondria and related organelles in every studied eukaryote supports the view that mitochondria are essential cellular components. Here, we report the genome sequence of a microbial eukaryote, the oxymonad Monocercomonoides sp., which revealed that this organism lacks all hallmark mitochondrial proteins. Crucially, the mitochondrial iron-sulfur cluster assembly pathway, thought to be conserved in virtually all eukaryotic cells, has been replaced by a cytosolic sulfur mobilization system (SUF) acquired by lateral gene transfer from bacteria. In the context of eukaryotic phylogeny, our data suggest that Monocercomonoides is not primitively amitochondrial but has lost the mitochondrion secondarily. This is the first example of a eukaryote lacking any form of a mitochondrion, demonstrating that this organelle is not absolutely essential for the viability of a eukaryotic cell.

Received: December 23, 2015; Received in revised form: March 5, 2016; Accepted: March 23, 2016; Published: May 12, 2016

© 2016 Elsevier Ltd. Published by Elsevier Inc. All rights reserved.

FREE PDF GRATIS: Current Biology

O que você quer dizer com epigenética?

What Do You Mean, “Epigenetic”?

Carrie Deans, Keith A. Maggert

GENETICS April 1, 2015 vol. 199 no. 4 887-896; 

DOI: 10.1534/genetics.114.173492

Abstract

Interest in the field of epigenetics has increased rapidly over the last decade, with the term becoming more identifiable in biomedical research, scientific fields outside of the molecular sciences, such as ecology and physiology, and even mainstream culture. It has become increasingly clear, however, that different investigators ascribe different definitions to the term. Some employ epigenetics to explain changes in gene expression, others use it to refer to transgenerational effects and/or inherited expression states. This disagreement on a clear definition has made communication difficult, synthesis of epigenetic research across fields nearly impossible, and has in many ways biased methodologies and interpretations. This article discusses the history behind the multitude of definitions that have been employed since the conception of epigenetics, analyzes the components of these definitions, and offers solutions for clarifying the field and mitigating the problems that have arisen due to these definitional ambiguities.

TRANSGENERATIONAL MATERNAL EFFECTS GENE EXPRESSION EPIGENETIC INHERITANCE

FREE PDF GRATIS: Genetics

Green Algae Tree of Life (GrAToL) [Árvore da Vida das Algas Verdes]: uma grande iniciativa científica

O Green Algae Tree of Life (GrAToL) [Árvore da Vida das Algas Verdes] é um projeto envolvendo a colaboração de cinco instituições para compreender as relações evolucionárias de todos os principais grupos de algas verdes, um grupo diverso de mais de 14.000 espécies fotossintéticas. 

GrAToL

Alga marinha estranha reescreve a história das plantas verdes

Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.

Frederik Leliaert, Ana Tronholm, Claude Lemieux, Monique Turmel, Michael S. DePriest, Debashish Bhattacharya, Kenneth G. Karol, Suzanne Fredericq, Frederick W. Zechman & Juan M. Lopez-Bautista

Scientific Reports 6, Article number: 25367 (2016)

doi:10.1038/srep25367

Download Citation

Phylogenetics Phylogenomics Taxonomy

Received: 15 February 2016 Accepted: 15 April 2016 Published online: 09 May 2016

Abstract

The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov.

FREE PDF GRATIS: Scientific Reports

A divergência dos cromossomos Y de Neandertais e Homens modernos

The Divergence of Neandertal and Modern Human Y Chromosomes

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

Open Access

DOI: http://dx.doi.org/10.1016/j.ajhg.2016.02.023

Abstract

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.

FREE PDF GRATIS: AJHG

A equipe do Scripps Research Institute agiliza a pesquisa biomédica: tornou mais fácil o acesso de dados genéticos

High-performance web services for querying gene and variant annotation

Jiwen Xin†, Adam Mark†, Cyrus Afrasiabi†, Ginger Tsueng, Moritz Juchler, Nikhil Gopal, Gregory S. Stupp, Timothy E. Putman, Benjamin J. Ainscough, Obi L. Griffith, Ali Torkamani, Patricia L. Whetzel, Christopher J. Mungall, Sean D. Mooney, Andrew I. SuEmail author and Chunlei WuEmail author

†Contributed equally

Genome Biology201617:91

DOI: 10.1186/s13059-016-0953-9 © Xin et al. 2016

Received: 7 January 2016 Accepted: 14 April 2016 Published: 6 May 2016

Abstract

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://​mygene.​info and http://​myvariant.​info. Both are offered free of charge to the research community.

Keywords Annotation Gene Variant API Cloud Repository Database

FREE PDF GRATIS: Genome Biology

Desafios na descrição do núcleo atômico: unificação e interdisciplinaridade

Open Access

Letter to the Editor

The European Physical Journal A

March 2016, 52:64

Challenges in the description of the atomic nucleus: Unification and interdisciplinarity

P. F. Bortignon, R. A. Broglia

First online: 23 March 2016 Received: 19 February 2016 Accepted: 19 February 2016

DOI: 10.1140/epja/i2016-16064-7

Abstract.

Nuclear physics, in general, and theoretical nuclear physics, in particular, have provided the physics community at large, among other things, with the paradigm of spontaneous symmetry breaking phenomena in finite many-body systems. The study of the associated mechanisms of symmetry restoration has shed light on the microscopic structure of the corresponding condensates, in particular on the superfluid phase, allowing to study Cooper pair tunnelling into superfluid nuclei (related to the Josephson effect), in terms of individual quantum states and reaching, in doing so, a new milestone: that of unifying structure and reactions, these last processes being found at the basis of the formulation of quantum mechanics (probability interpretation, Born). In the process, nuclear physicists have extended the validity of BCS theory of superconductivity to the single Cooper pair situation, let alone discovering unexpected mechanism to break gauge invariance. The insight obtained from pair transfer research is likely to have important consequences in the study of double charge exchange processes, and thus in the determination of the nuclear matrix element associated with neutrinoless double beta decay, eventually providing an important test of the Standard Model. Time, thus, seems ripe for nuclear theorists to take centre stage, backed by a wealth of experimental information and by their interdisciplinary capacity to connect basic physical concepts across the borders. With the help of these elements they can aim at fully revealing the many facets of their femtometer many-body system, from vacuum zero point fluctuations to new exotic modes of nuclear excitations and of their interweaving, resulting in powerful effective field theories. Unless. Unless they are not able to free themselves from words like ab initio or fundamental, and to adapt a relax attitude concerning Skyrme, tensor, etc., forces, as well as regarding the quest for “the” Hamiltonian.

Communicated by N. Alamanos

FREE PDF GRATIS: The European Physical Journal 

Da Árvore da Vida para a Web da Vida: como as imagens do Google podem ajudar no estudo da evolução

Just Google it: assessing the use of Google Images to describe geographical variation in visible traits of organisms

Gabriella R. M. Leighton1,*, Pierre S. Hugo2, Alexandre Roulin3 andArjun Amar4

Article first published online: 11 MAY 2016

DOI: 10.1111/2041-210X.12562

© 2016 The Authors. Methods in Ecology and Evolution © 2016 British Ecological Society

Methods in Ecology and Evolution

Early View (Online Version of Record published before inclusion in an issue)

Keywords: Accipiter melanoleucus ; Corvus cornix ; Corvus corone ; data collection; Google Images; hybrid zone; polymorphism; species distribution; Tyto alba ; Ursus americanus

Summary

Describing spatial patterns of phenotypic traits can be important for evolutionary and ecological studies. However, traditional approaches, such as fieldwork, can be time-consuming and expensive. Information technologies, such as Internet search engines, could facilitate the collection of these data. Google Images is one such technology that might offer an opportunity to rapidly collect information on spatial patterns of phenotypic traits.

We investigated the use of Google Images in extracting data on geographical variation in phenotypic traits visible from photographs. We compared the distribution of visual traits obtained from Google Images with four previous studies: colour morphs of black bear (Ursus americanus); colouration and spottiness in barn owl (Tyto alba); colour morphs of black sparrowhawk (Accipiter melanoleucus) and the distribution of hooded (Corvus corone) and carrion crows (Corvus cornix) across their European hybrid zone. Additionally, we develop and present a web application (morphic), which facilitates the human data capture process of this method.

We found good agreement between fieldwork data and Google Images data across all studies. Indeed, there was strong agreement between the data obtained from the original study and from the Google Images method for the colour morphs of black bear (R2 = 80%) and for two barn owl plumage traits (R2 = 64% and 53%). Our approach also successfully matched the clinal variation of black sparrowhawks morphs across South Africa. Our method also gave a good agreement between the distribution of hooded and carrion crows (with 86% placed on the correct side of the hybrid zone line).

Our results suggest that this method can work well for visible traits of common and widespread species that are objective, binary, and easy to see irrespective of angle. The Google Images method is cost-effective and rapid and can be used with some confidence when investigating patterns of geographical variation, as well as a range of other applications. In many cases, it could therefore supplement or replace fieldwork.

FREE PDF GRATIS: Methods in Ecology and Evolution

Narciso amarelo ajuda na inspiração de "design" de estruturas estáveis

Flow around a helically twisted elliptic cylinder 

Woojin Kim1, Jungil Lee2 and Haecheon Choi1,3,a)

- HIDE AFFILIATIONS

1 Department of Mechanical and Aerospace Engineering, Seoul National University, Seoul 08826, South Korea

2 Department of Mechanical Engineering, Ajou University, Suwon 16499, South Korea

3 Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, South Korea

a) Author to whom correspondence should be addressed. Electronic mail: choi@snu.ac.kr

Phys. Fluids 28, 053602 (2016); http://dx.doi.org/10.1063/1.4948247

Abstract

In the present study, we conduct unsteady three-dimensional simulations of flows around a helically twisted elliptic (HTE) cylinder at the Reynolds numbers of 100 and 3900, based on the free-stream velocity and square root of the product of the lengths of its major and minor axes. A parametric study is conducted for Re = 100 by varying the aspect ratio (AR) of the elliptic cross section and the helical spanwise wavelength (λ). Depending on the values of AR and λ, the flow in the wake contains the characteristic wavelengths of λ, 2λ, 6λ, or even longer than 60λ, showing a wide diversity of flows in the wake due to the shape change. The drag on the optimal (i.e., having lowest drag) HTE cylinder (AR = 1.3 and λ = 3.5d) is lower by 18% than that of the circular cylinder, and its lift fluctuations are zero owing to complete suppression of vortex shedding in the wake. This optimal HTE configuration reduces the drag by 23% for Re = 3900 where the wake is turbulent, showing that the HTE cylinder reduces the mean drag and lift fluctuations for both laminar and turbulent flows.

FREE PDF GRATIS: Physics of Fluids

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NOTA DESTE BLOGGER:

Mas Darwin não tinha eliminado de vez a questão de design na natureza? Richard Dawkins não pontificou que design é ilusão na natureza? Então por que cargas d'água esses cientistas foram buscar "design" em narcisos amarelos para estruturas estáveis??? NOTA BENE: ESTRUTURAS ESTÁVEIS!

Faltou inspiração da natureza nos engenheiros brasileiros que construíram a ciclovia da Av. Niemeyer no Rio de Janeiro em 21/04/2016.

Definindo e quantificando o papel da dinâmica em catálise enzimática

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

Arieh Warshel 1,a) and Ram Prasad Bora1

1 Department of Chemistry, University of Southern California, SGM 418, 3620 McClintock Avenue, Los Angeles, California 90089, USA

a) Author to whom correspondence should be addressed. Electronic mail: warshel@usc.edu

J. Chem. Phys. 144, 180901 (2016); http://dx.doi.org/10.1063/1.4947037

ABSTRACT

Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme’s conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.

FREE PDF GRATIS: The Journal of Chemical Physics

A evolução através do currículo: microbiologia

J Microbiol Biol Educ. 2016 May; 17(2): 252–260.

Published online 2016 May 4. doi: 10.1128/jmbe.v17i2.988

PMCID: PMC4858361

Evolution across the Curriculum: Microbiology

Alita R. Burmeister1,2,3,* and James J. Smith2,3,4,5,6

1Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824

2Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI 48824

3BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824

4Lyman Briggs College, Michigan State University, East Lansing, MI 48825

5Department of Entomology, Michigan State University, East Lansing, MI 48824

6Department of Integrative Biology, Michigan State University, East Lansing, MI 48824

*Corresponding author. Mailing address: 567 Wilson Road, 6176, East Lansing, MI 48824. Phone: 517-884-5396. E-mail: ude.usm@atila.

Abstract

An integrated understanding of microbiology and evolutionary biology is essential for students pursuing careers in microbiology and healthcare fields. In this Perspective, we discuss the usefulness of evolutionary concepts and an overall evolutionary framework for students enrolled in microbiology courses. Further, we propose a set of learning goals for students studying microbial evolution concepts. We then describe some barriers to microbial evolution teaching and learning and encourage the continued incorporation of evidence-based teaching practices into microbiology courses at all levels. Next, we review the current status of microbial evolution assessment tools and describe some education resources available for teaching microbial evolution. Successful microbial evolution education will require that evolution be taught across the undergraduate biology curriculum, with a continued focus on applications and applied careers, while aligning with national biology education reform initiatives.

Journal of Microbiology & Biology Education

FREE PDF GRATIS: NCBI

LMFDB, um site de Matemática ***** (em inglês)

LMFDB

Este blogger recomenda este site de Matemática: *****

A evolução do universo a partir do Big Bang em três minutos de vídeo

Por uma lista de moléculas como gases potenciais de assinatura na busca de vida em exoplanetas e aplicações na bioquímica terrestre

Toward a List of Molecules as Potential Biosignature Gases for the Search for Life on Exoplanets and Applications to Terrestrial Biochemistry

To cite this article:

Seager S., Bains W., and Petkowski J.J.. Astrobiology. April 2016, ahead of print. doi:10.1089/ast.2015.1404.

Online Ahead of Print: April 20, 2016

S. Seager,1,2 W. Bains,1,3 and J.J. Petkowski1

1Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts.

2Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.

3Rufus Scientific, Cambridge, UK.

Address correspondence to:

S. Seager

Department of Earth, Atmospheric, and Planetary Sciences

Massachusetts Institute of Technology

54-1626 77 Massachusetts Ave.

Cambridge, MA 02139

E-mail: seager@mit.edu

Submitted 7 September 2015 Accepted 24 February 2016 

Source/Fonte

Abstract

Thousands of exoplanets are known to orbit nearby stars. Plans for the next generation of space-based and ground-based telescopes are fueling the anticipation that a precious few habitable planets can be identified in the coming decade. Even more highly anticipated is the chance to find signs of life on these habitable planets by way of biosignature gases. But which gases should we search for? Although a few biosignature gases are prominent in Earth's atmospheric spectrum (O2, CH4, N2O), others have been considered as being produced at or able to accumulate to higher levels on exo-Earths (e.g., dimethyl sulfide and CH3Cl). Life on Earth produces thousands of different gases (although most in very small quantities). Some might be produced and/or accumulate in an exo-Earth atmosphere to high levels, depending on the exo-Earth ecology and surface and atmospheric chemistry.

To maximize our chances of recognizing biosignature gases, we promote the concept that all stable and potentially volatile molecules should initially be considered as viable biosignature gases. We present a new approach to the subject of biosignature gases by systematically constructing lists of volatile molecules in different categories. An exhaustive list up to six non-H atoms is presented, totaling about 14,000 molecules. About 2500 of these are CNOPSH compounds. An approach for extending the list to larger molecules is described. We further show that about one-fourth of CNOPSH molecules (again, up to N = 6 non-H atoms) are known to be produced by life on Earth. The list can be used to study classes of chemicals that might be potential biosignature gases, considering their accumulation and possible false positives on exoplanets with atmospheres and surface environments different from Earth's. The list can also be used for terrestrial biochemistry applications, some examples of which are provided. We provide an online community usage database to serve as a registry for volatile molecules including biogenic compounds. Key Words: Astrobiology—Atmospheric gases—Biosignatures—Exoplanets. Astrobiology 16, xxx–xxx.

FREE TILL PDF GRATIS ATÉ: July/Julho 5, 2016  Astrobiology

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

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; 

DOI: 10.1534/genetics.116.187013

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

FRANK WILCZEK — Why Is the World So Beautiful?

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.

http://www.onbeing.org/program/frank-wilczek-why-is-the-world-so-beautiful/8565/audio?embed=1

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

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

DOI: 10.1126/sciadv.1501860

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

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

FREE PDF GRATIS: The British Society of Criminology

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

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.