Descoberto o elo entre a estrutura e função das proteínas: mero acaso, fortuita necessidade ou design inteligente?

The early history and emergence of molecular functions and modular scale-free network behavior

M. Fayez Aziz, Kelsey Caetano-Anollés & Gustavo Caetano-Anollés

Scientific Reports 6, Article number: 25058 (2016)

doi:10.1038/srep25058

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Molecular evolution Power law Protein function predictions

Received: 01 October 2015 Accepted: 08 April 2016 Published online: 28 April 2016

Abstract

The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop sequences and domain structures defined at the fold superfamily level of SCOP classification. The resulting ‘elementary functionome’ network and its loop motif and structural domain graph projections create evolutionary ‘waterfalls’ describing the emergence of primordial functions. Waterfalls reveal how ancient loops are shared by domain structures in two initial waves of functional innovation that involve founder ‘p-loop’ and ‘winged helix’ domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers ‘preferential’ cooption properties of ancient loops to emerging domains. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the network of motifs and structures expand metabolic pathways and translation.

FREE PDF GRATIS: Scientific Reports

De simples células à multicelularidade foi muito fácil há 1.5 bilhões de anos atrás: zip, zap!

Decimetre-scale multicellular eukaryotes from the 1.56-billion-year-old Gaoyuzhuang Formation in North China

Shixing Zhu, Maoyan Zhu, Andrew H. Knoll, Zongjun Yin, Fangchen Zhao, Shufen Sun, Yuangao Qu, Min Shi & Huan Liu

Affiliations Contributions Corresponding author

Nature Communications 7, Article number: 11500 doi:10.1038/ncomms11500

Received 21 November 2015 Accepted 04 April 2016 Published 17 May 2016

Article tools

Abstract

Fossils of macroscopic eukaryotes are rarely older than the Ediacaran Period (635–541 million years (Myr)), and their interpretation remains controversial. Here, we report the discovery of macroscopic fossils from the 1,560-Myr-old Gaoyuzhuang Formation, Yanshan area, North China, that exhibit both large size and regular morphology. Preserved as carbonaceous compressions, the Gaoyuzhuang fossils have statistically regular linear to lanceolate shapes up to 30 cm long and nearly 8 cm wide, suggesting that the Gaoyuzhuang fossils record benthic multicellular eukaryotes of unprecedentedly large size. Syngenetic fragments showing closely packed ~10 μm cells arranged in a thick sheet further reinforce the interpretation. Comparisons with living thalloid organisms suggest that these organisms were photosynthetic, although their phylogenetic placement within the Eukarya remains uncertain. The new fossils provide the strongest evidence yet that multicellular eukaryotes with decimetric dimensions and a regular developmental program populated the marine biosphere at least a billion years before the Cambrian Explosion.

Subject terms: Biological sciences Evolution Palaeontology

FREE PDF GRATIS: Nature Communications Sup. Info Sup. Info

WhatsApp? Messenger? Quimiocinas transmembranares atuam como receptores em um novo mecanismo denominado sinalização inversa

Transmembrane chemokines act as receptors in a novel mechanism termed inverse signaling

Kirsten Hattermann Henrike Gebhardt Sebastian Krossa Andreas Ludwig Ralph Lucius Janka Held-Feindt Rolf Mentlein 

University of Kiel, Germany; Institute of Zoology, Germany; RWTH Aachen University, Germany; University Medical Center Schleswig-Holstein, Germany

DOI: http://dx.doi.org/10.7554/eLife.10820

Published January 21, 2016

Cite as eLife 2016;5:e10820

Abstract

The transmembrane chemokines CX3CL1/fractalkine and CXCL16 are widely expressed in different types of tumors, often without an appropriate expression of their classical receptors. We observed that receptor-negative cancer cells could be stimulated by the soluble chemokines. Searching for alternative receptors we detected that all cells expressing or transfected with transmembrane chemokine ligands bound the soluble chemokines with high affinity and responded by phosphorylation of intracellular kinases, enhanced proliferation and anti-apoptosis. This activity requires the intracellular domain and apparently the dimerization of the transmembrane chemokine ligand. Thus, shed soluble chemokines can generate auto- or paracrine signals by binding and activating their transmembrane forms. We term this novel mechanism “inverse signaling”. We suppose that inverse signaling is an autocrine feedback and fine-tuning system in the communication between cells that in tumors supports stabilization and proliferation.

DOI: http://dx.doi.org/10.7554/eLife.10820.001

eLife digest

The cells that make up an animal need to communicate with each other for a variety of purposes, including controlling the growth and repair of tissues. Commonly, such signaling involves ‘ligand’ molecules binding to specific ‘receptor’ proteins embedded in the cell membrane. When a ligand docks to the right receptor protein, the parts of the receptor inside the cell change shape. This activates signaling pathways within that cell.

Types of ligands called transmembrane ligands are found embedded in cell membranes. Some cancer cells have high levels of transmembrane ligands called CXCL16 and CX3CL1 but do not produce the corresponding receptors for these molecules. The part of these ligands that sits outside of the cells can also be separated from the rest of the molecule to produce a soluble ligand that can move around outside the cell.

By studying cancer cells using microscopy and biochemical approaches, Hattermann, Gebhardt et al. now show that the soluble forms of CXCL16 and CX3CL1 bind to their transmembrane equivalents. This activates signaling pathways that promote cell growth and make the cancer cells more resistant to cell death. However, this signaling did not occur if the transmembrane ligands were altered to lack the part normally found inside the cell, which suggests that transmembrane CXCL16 and CX3CL1 act as receptors.

It was not previously known that a soluble ligand could activate its transmembrane equivalent. Hattermann, Gebhardt et al. have named this process “inverse signaling”, and suggest that it helps to fine-tune the communication between cells. Future experiments will need to study the importance of inverse signaling in living animals and investigate how it works alongside other signaling methods.

DOI: http://dx.doi.org/10.7554/eLife.10820.002

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Plantas exibem maquinaria optofluídica natural

Optofluidics of plants 

Demetri Psaltis1,a), Andreas E. Vasdekis1,2,b) and Jae-Woo Choi1

1 Optics Laboratory, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland

2 Department of Physics, University of Idaho, Moscow, Idaho 83844, USA

a) Author to whom correspondence should be addressed. Electronic mail: demetri.psaltis@epfl.ch.

b) Electronic mail: andreasv@uidaho.edu

APL Photonics 1, 020901 (2016); http://dx.doi.org/10.1063/1.4947228

ABSTRACT

Optofluidics is a tool for synthesizing optical systems, making use of the interaction of light with fluids. In this paper we explore optofluidic mechanisms that have evolved in plants where sunlight and fluidic control combine to define most of the functionality of the plan. We hope that the presentation of how plants function, from an optofluidics point of view, will open a window for the optics community to the vast literature of plant physiology and provide inspiration for new ideas for the design of bio-mimetic optofluidic devices.

FREE PDF GRATIS: APL Photonics

Resenha de Feduccia: fantasia vs realidade da evolução das aves

FANTASY VS REALITY: A Critique of Smith et al.'s Bird Origins

Alan Feduccia*

Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280, United States of America

Abstract

Adherents of the current orthodoxy of a derivation of birds from theropod dinosaurs, criticize the commentary by Feduccia (2013, Auk, 130) [1-12] entitled “Bird Origins Anew” as well as numerous papers by Lingham-Soliar on theropod dermal fibers, using numerous mischaracterizations and misstatements of content, and illustrate their own misconceptions of the nature of the debate, which are here clarified. While there is general agreement with the affinity of birds and maniraptorans, the widely accepted phylogeny, advocating derived earth-bound maniraptorans giving rise to more primitive avians (i.e. Archaeopteryx), may be “topsy-turvy.” The current primary debate concerns whether maniraptorans are ancestral or derived within the phylogeny, and whether many maniraptorans and birds form a clade distinct from true theropods. Corollaries of the current scheme show largely terrestrial maniraptoran theropods similar to the Late Cretaceous Velociraptor giving rise to avians, and flight originating via a terrestrial (cursorial) “gravity-resisted,” as opposed to an arboreal “gravity-assisted” model. The current dogma posits pennaceous flight remiges in earth-bound theropods having evolved in terrestrial theropods that never flew. As part of the orthodoxy, fully feathered maniraptorans such as the tetrapteryx gliders Microraptor and allies, are incorrectly reconstructed as terrestrial cursors, when in reality their anatomy and elongate hindlimb feathers would be a hindrance to terrestrial locomotion.The same is true of many early birds, exemplified by reconstruction of the arboreally adapted Confuciusornis as a terrestrial predator, part of the overall theropodan scheme of birds evolving from terrestrial dinosaurs, and flight from the ground up. Both sides of this contentious debate must be constantly aware that new fossil or even molecular discoveries on birds may change current conclusions.

Keywords: Bird origins, cladistic, flight origins, maniraptoran, phylogenomics, theropod.

FREE PEDF GRATIS: The Open Ornithology Journal

Sequência do genoma da girafa revela indícios de sua morfologia e fisiologia exclusivas

Giraffe genome sequence reveals clues to its unique morphology and physiology

Morris Agaba, Edson Ishengoma, Webb C. Miller, Barbara C. McGrath, Chelsea N. Hudson, Oscar C. Bedoya Reina, Aakrosh Ratan, Rico Burhans, Rayan Chikhi, Paul Medvedev, Craig A. Praul, Lan Wu-Cavener, Brendan Wood, Heather Robertson, Linda Penfold & Douglas R. Cavener

Affiliations Contributions Corresponding author

Nature Communications 7, Article number: 11519 doi:10.1038/ncomms11519

Received 30 November 2015 Accepted 01 April 2016 Published 17 May 2016

Source/Fonte

Abstract

The origins of giraffe’s imposing stature and associated cardiovascular adaptations are unknown. Okapi, which lacks these unique features, is giraffe’s closest relative and provides a useful comparison, to identify genetic variation underlying giraffe’s long neck and cardiovascular system. The genomes of giraffe and okapi were sequenced, and through comparative analyses genes and pathways were identified that exhibit unique genetic changes and likely contribute to giraffe’s unique features. Some of these genes are in the HOX, NOTCH and FGF signalling pathways, which regulate both skeletal and cardiovascular development, suggesting that giraffe’s stature and cardiovascular adaptations evolved in parallel through changes in a small number of genes. Mitochondrial metabolism and volatile fatty acids transport genes are also evolutionarily diverged in giraffe and may be related to its unusual diet that includes toxic plants. Unexpectedly, substantial evolutionary changes have occurred in giraffe and okapi in double-strand break repair and centrosome functions.

Subject terms: Biological sciences Evolution Genetics Zoology

FREE PDF GRATIS: Nature Communications

Pesquisa associa malformações congênitas à idade e estilo de vida do pai

Am J Stem Cells 2016;5(1):11-18

www.AJSC.us /ISSN:2160-4150/AJSC0030217

Review Article

Influence of paternal preconception exposures on their offspring: through epigenetics to phenotype

Jonathan Day1, Soham Savani1, Benjamin D Krempley1, Matthew Nguyen1, Joanna B Kitlinska2

1Georgetown University Medical Center, Georgetown University Special Master’s Program in Physiology,

Washington, DC, USA; 2Department of Biochemistry and Molecular & Cellular Biology, Georgetown University

Medical Center, Washington, DC, USA

Received April 10, 2016; Accepted April 28, 2016; Epub May 15, 2016; Published May 30, 2016

Source/Fonte: Georgetown Medical Center

Abstract: 

Historically, research into congenital defects has focused on maternal impacts on the fetal genome during gestation and prenatal periods. However, recent findings have sparked interest in epigenetic alterations of paternal genomes and its effects on offspring. This emergent field focuses on how environmental influences can epigenetically alter gene expression and ultimately change the phenotype and behavior of progeny. There are three primary mechanisms implicated in these changes: DNA methylation, histone modification, and miRNA expression. This paper provides a summary and subsequent review of past research, which highlights the significant impact of environmental factors on paternal germ cells during the lifetime of an individual as well as those of future generations. These findings support the existence of transgenerational epigenetic inheritance of paternal experiences. Specifically, we

explore epidemiological and laboratory studies that demonstrate possible links between birth defects and paternal age, environmental factors, and alcohol consumption. Ultimately, our review highlights the clinical importance of these factors as well as the necessity for future research in the field.

Keywords: Transgenerational effects, paternal preconception exposures, epigenetics

FREE PDF GRATIS: American Journal of Stem Cells

A identificação e caracterização de RNAs circulares como uma nova classe putativa de biomarcadores no sangue humano

Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood

Sebastian Memczak , Panagiotis Papavasileiou , Oliver Peters, Nikolaus Rajewsky 

Published: October 20, 2015 http://dx.doi.org/10.1371/journal.pone.0141214

Abstract

Covalently closed circular RNA molecules (circRNAs) have recently emerged as a class of RNA isoforms with widespread and tissue specific expression across animals, oftentimes independent of the corresponding linear mRNAs. circRNAs are remarkably stable and sometimes highly expressed molecules. Here, we sequenced RNA in human peripheral whole blood to determine the potential of circRNAs as biomarkers in an easily accessible body fluid. We report the reproducible detection of thousands of circRNAs. Importantly, we observed that hundreds of circRNAs are much higher expressed than corresponding linear mRNAs. Thus, circRNA expression in human blood reveals and quantifies the activity of hundreds of coding genes not accessible by classical mRNA specific assays. Our findings suggest that circRNAs could be used as biomarker molecules in standard clinical blood samples.

Citation: Memczak S, Papavasileiou P, Peters O, Rajewsky N (2015) Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood. PLoS ONE 10(10): e0141214. doi:10.1371/journal.pone.0141214

Editor: Sebastien Pfeffer, French National Center for Scientific Research - Institut de biologie moléculaire et cellulaire, FRANCE

Received: September 3, 2015; Accepted: October 5, 2015; Published: October 20, 2015

Copyright: © 2015 Memczak 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: Sequencing data have been deposited at NCBI GEO under accession number GSE73570.

Funding: SM was supported by the grant DFG RA 838/7-1, PP was supported by the NYU/MDC Exchange Program, OP and NR were supported by the grant BIH CRG 2a TP7.

Competing interests: The authors NR, SM, and PP filed a patent (patent EP15187446) covering the use of blood circular RNAs as biomarkers in neurological diseases. This did not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

FREE PDF GRATIS: PLoS One

Microtúbulos duplos são ferrovias de via dupla para comboios de transporte intraflagelar: mero acaso, fortuita necessidade ou design inteligente???

Microtubule doublets are double-track railways for intraflagellar transport trains

Ludek Stepanek, Gaia Pigino*

+ Author Affiliations

↵*Corresponding author. Email: pigino@mpi-cbg.de

Science 06 May 2016:

Vol. 352, Issue 6286, pp. 721-724

DOI: 10.1126/science.aaf4594

Source/Fonte

Stay on the right track

Cilia contain a well-ordered array of microtubule doublets along their length. A longstanding question in cilium structure and function is why the microtubule arrangement in cilia is so complex. Stepanek and Pigino developed a time-resolved correlative fluorescence and three-dimensional electron microscopy method to show that the doublets provide directionality to intraflagellar transport. One microtubule in the pair moves cargoes up to the ciliary tip. Meanwhile, the other microtubule moves cargoes back to the cell body. These results explain why the axoneme is built out of microtubule doublets and suggest a mechanistic picture of how the logistics of bidirectional intraflagellar transport are regulated.

Science, this issue p. 721

Abstract

The cilium is a large macromolecular machine that is vital for motility, signaling, and sensing in most eukaryotic cells. Its conserved core structure, the axoneme, contains nine microtubule doublets, each comprising a full A-microtubule and an incomplete B-microtubule. However, thus far, the function of this doublet geometry has not been understood. We developed a time-resolved correlative fluorescence and three-dimensional electron microscopy approach to investigate the dynamics of intraflagellar transport (IFT) trains, which carry ciliary building blocks along microtubules during the assembly and disassembly of the cilium. Using this method, we showed that each microtubule doublet is used as a bidirectional double-track railway: Anterograde IFT trains move along B-microtubules, and retrograde trains move along A-microtubules. Thus, the microtubule doublet geometry provides direction-specific rails to coordinate bidirectional transport of ciliary components.

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site Portal de Periódicos CAPES/MEC podem acessar gratuitamente este artigo da Science e de mais 30.000 publicações científicas.

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NOTA DESTE BLOGGER:

Pesquisas como esta aqui deixam cada vez mais robusta a teoria do Design Inteligente na questão de complexidade especificada de Michael Behe.

Science and Human Origins (A ciência e as origens humanas)

Science and Human Origins

Ann Gauger, Casey Luskin, Douglas Axe

126 pages 

Science & Human Origins, the provocative new book from Discovery Institute Press, boldly addresses some of the most popular evolutionary arguments pertaining to controversial claims that humans and apes are related through common ancestry.

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Tempo, (inverso) temperatura e inflação cosmológica como entrelaçamento

Time, (Inverse) Temperature and Cosmological Inflation as Entanglement

Vlatko Vedral

(Submitted on 29 Aug 2014)

We present arguments to the effect that time and temperature can be viewed as a form of quantum entanglement. Furthermore, if temperature is thought of as arising from the quantum mechanical tunneling probability this then offers us a way of dynamically "converting" time into temperature based on the entanglement between the transmitted and reflected modes. We then show how similar entanglement-based logic can be applied to the dynamics of cosmological inflation and discuss the possibility of having observable effects of the early gravitational entanglement at the level of the universe.

Comments: 8 pages, no figures

Subjects: Quantum Physics (quant-ph)

Cite as: arXiv:1408.6965 [quant-ph]

(or arXiv:1408.6965v1 [quant-ph] for this version)

Submission history

From: Vlatko Vedral [view email] 

[v1] Fri, 29 Aug 2014 09:47:40 GMT (14kb)

FREE PDF GRATIS: ArXiv

Vlatko Vedral 'falou e disse': a informação é mais fundamental na definição da realidade

“A definição mais fundamental da realidade não é matéria ou energia, mas informação – e é o processamento da informação que está na raiz de todos os fenômenos físicos, biológicos, econômicos e sociais.”

Vlatko Vedral – Professor de Física na Universidade de Oxford, e no CQT (Centre for Quantum Technologies Centro de Tecnologias Quânticas) na Universidade Nacional de Singapura, e um Fellow do Wolfson College – um líder reconhecido no campo de mecânica quântica.

“The most fundamental definition of reality is not matter or energy, but information–and it is the processing of information that lies at the root of all physical, biological, economic, and social phenomena.”

Vlatko Vedral – Professor of Physics at the University of Oxford, and CQT (Centre for Quantum Technologies) at the National University of Singapore, and a Fellow of Wolfson College – a recognized leader in the field of quantum mechanics.

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   Amazon 

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A teoria do Design Inteligente tem no seu arcabouço teórico a informação complexa e especificada...

A expressão gênica depende de constante "diálogo"entre o núcleo e o citoplasma

Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex

Ishaan Gupta 6, Zoltan Villanyi 6, Sari Kassem, Christopher Hughes, Olesya O. Panasenko, Lars M. Steinmetz, Martine A. Collart correspondence email

6Co-first author

Publication stage: In Press Corrected Proof

Open Access

DOI: http://dx.doi.org/10.1016/j.celrep.2016.04.055

Highlights

• Inhibition of transcription elongation is balanced by enhanced translation

• Co-transcriptional Not1 mRNA imprinting regulates mRNA stability and translatability

• Not5 determines global ribosomal protein gene mRNA imprinting

• Not5 determines the translational capacity of the cells

Summary

The current understanding of gene expression considers transcription and translation to be independent processes. Challenging this notion, we found that translation efficiency is determined during transcription elongation through the imprinting of mRNAs with Not1, the central scaffold of the Ccr4-Not complex. We determined that another subunit of the complex, Not5, defines Not1 binding to specific mRNAs, particularly those produced from ribosomal protein genes. This imprinting mechanism specifically regulates ribosomal protein gene expression, which in turn determines the translational capacity of cells. We validate our model by SILAC and polysome profiling experiments. As a proof of concept, we demonstrate that enhanced translation compensates for transcriptional elongation stress. Taken together, our data indicate that in addition to defining mRNA stability, components of the Ccr4-Not imprinting complex regulate RNA translatability, thus ensuring global gene expression homeostasis.

Received: October 23, 2015; Received in revised form: February 8, 2016; Accepted: April 4, 2016; Published: May 12, 2016

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

FREE PDF GRATIS: Cell Reports   Sup. Info

Visita Virtual ao Laboratório ThoMSon de MS UNICAMP

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

Article tools

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

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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

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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.

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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.