Epi-Search: seus problemas de buscas por publicações científicas acabaram!

sexta-feira, março 18, 2016

Epi-Search (http://epi-search.com) is the only research tool on the web which allows you to input up to 10,000 words as your search query (i.e. whole articles, papers, book chapters).

Epi-search then runs a "find more like this search" to recommend books from the 5000 volume ISCE.edu library shows you how and why the results shown were recommended AND provides links to "good" related searches from 9 academic databases including:

- Google Scholar related academic results

- PhilPaper related philosophy results

- MIT CogNet related cognitive science results (citations only)

- CiteSeer related academic results

- DeepDyve related articles (abstracts only)

- JSTOR related resources (citations only)

- Taylor and Francis related resources (abstracts only)

- OUP Scholarship Online

Epi-Search is a conceptual search tool that out performs traditional searching algorithms because it is able to make use of concepts that are fully expressed in other documents.

see:


Revelados "tecidos moles" em ossos de répteis do Triássico (200-250 milhões de anos)!

Spectroscopic Studies on Organic Matter from Triassic Reptile Bones, Upper Silesia, Poland

Dawid Surmik , Andrzej Boczarowski , Katarzyna Balin , Mateusz Dulski , Jacek Szade , Barbara Kremer , Roman Pawlicki

Published: March 15, 2016


Abstract

Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted "blood vessels" showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the "blood vessels" was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment.

Citation: Surmik D, Boczarowski A, Balin K, Dulski M, Szade J, Kremer B, et al. (2016) Spectroscopic Studies on Organic Matter from Triassic Reptile Bones, Upper Silesia, Poland. PLoS ONE 11(3): e0151143. doi: 10.1371/journal.pone.0151143

Editor: Steffen Kiel, Naturhistoriska riksmuseet, SWEDEN

Received: October 8, 2015; Accepted: February 24, 2016; Published: March 15, 2016

Copyright: © 2016 Surmik 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: This research project is supported by National Science Center (www.ncn.gov.pl) grant no. 2011/01/N/ST10/06989.

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

FREE PDF GRATIS: PLoS One

A química apoia a identificação de tecido reprodutivo específico de gênero no Tiranossauro rex

quarta-feira, março 16, 2016

Chemistry supports the identification of gender-specific reproductive tissue in Tyrannosaurus rex

Mary Higby Schweitzer, Wenxia Zheng, Lindsay Zanno, Sarah Werning & Toshie Sugiyama

Scientific Reports 6, Article number: 23099 (2016)


Download Citation

Biological techniquesEvolutionPalaeontology

Received: 17 November 2015 Accepted: 01 March 2016

Published online: 15 March 2016


Abstract

Medullary bone (MB), an estrogen-dependent reproductive tissue present in extant gravid birds, is texturally, histologically and compositionally distinct from other bone types. Phylogenetic proximity led to the proposal that MB would be present in non-avian dinosaurs, and recent studies have used microscopic, morphological, and regional homologies to identify this reproductive tissue in both theropod and ornithischian dinosaurs. Here, we capitalize on the unique chemical and histological fingerprint of MB in birds to characterize, at the molecular level, MB in the non-avian theropod Tyrannosaurus rex (MOR 1125), and show that the retention of original molecular components in fossils allows deeper physiological and evolutionary questions to be addressed.

FREE PDF GRATIS: Scientific Reports

Mais complexidade no flagelo bacteriano: diversas capacidades de mobilização

Diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold

Morgan Beebya,1, Deborah A. Ribardob, Caitlin A. Brennanc,2, Edward G. Rubyc,3, Grant J. Jensend,e, and David R. Hendrixsonb,1

Author Affiliations

Edited by Scott J. Hultgren, Washington University School of Medicine, St. Louis, MO, and approved February 8, 2016 (received for review September 24, 2015)

Abstract Full Text Authors & Info Figures SIMetrics PDF PDF + SI

Source/Fonte: 3 bacterial motors, different torque pN mm - Morgan Beeby - Imperial College London.

Significance

Many bacteria swim using helical propellers, flagella. Intriguingly, different bacteria show different swimming abilities, strikingly illustrated by the abilities of some to bore through viscous fluids (e.g., gastrointestinal mucus) in which others are completely immobilized. We used 3D electron microscopy to show that differences can be explained by the structures of the torque-generating motors: two diverse high-torque motors position additional torque-generating complexes at wider radii from the axial driveshaft than in the model enteric bacteria; this positioning is consistent with the exertion of greater leverage to rotate the flagellum and thus greater torque generation. Intriguingly, these torque-generating complexes are scaffolded at wider radii by a conserved but divergent family of structures, suggesting an ancient origin of reconfiguring torque output.

Abstract

Although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. To understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from Campylobacter and Vibrio species. For the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and show that diverse high-torque motors use variants of an ancestrally related family of structures to scaffold incorporation of additional stator complexes at wider radii from the axial driveshaft than in the model enteric motor. We identify the protein components of these additional scaffold structures and elucidate their sequential assembly, demonstrating that they are required for stator-complex incorporation. These proteins are widespread, suggesting that different bacteria have tailored torques to specific environments by scaffolding alternative stator placement and number. Our results quantitatively account for different motor torques, complete the assignment of the locations of the major flagellar components, and provide crucial constraints for understanding mechanisms of torque generation and the evolution of multiprotein complexes.

bacterial flagellar motors electron cryo-tomography macromolecular evolution torque Campylobacter

Footnotes

1To whom correspondence may be addressed. Email: mbeeby@imperial.ac.uk or
david.hendrixson@utsouthwestern.edu.

2Present address: Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115.

3Present address: Kewalo Marine Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI 96813.

Author contributions: M.B., D.A.R., G.J.J., and D.R.H. designed research; M.B. and D.A.R. performed research; M.B., C.A.B., and E.G.R. contributed new reagents/analytic tools; M.B., G.J.J., and D.R.H. analyzed data; and M.B., G.J.J., and D.R.H. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The electron cryo-tomography subtomogram average density maps reported in this paper have been deposited in the Electron Microscopy Data Bank (EMD) (accession nos. Salmonella WT: EMD-3154; Vibrio fischeri WT: EMD-3155; Campylobacter jejuni WT: EMD-3150; V. fischeri motB: EMD-3156; C. jejuni motB: EMD-3157; C. jejuni flgQ: EMD-3158; C. jejuni flgP: EMD-3159; C. jejuni pflA: EMD-3160; C. jejuni pflB: EMD-3161; and V. fischeri flgP: EMD-3162).

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1518952113/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Hierarquias na organização do genoma eucariótico - insights da teoria de polímeros e simulações

Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations

Balaji VS Iyer, Martin Kenward and Gaurav AryaEmail author

BMC Biophysics20114:8

DOI: 10.1186/2046-1682-4-8 © Iyer et al; licensee BioMed Central Ltd. 2011

Received: 7 January 2011Accepted: 15 April 2011Published: 15 April 2011


Source/Fonte: Pearsons Education Inc.

Abstract

Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus. Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function. Elegant microscopy and chromosome conformation capture techniques supported by analysis based on polymer models are important steps in this direction. Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.

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Organização 3D do genoma pode ter guiado a dinâmica da ordem da evolução do gene nos eucariotos

Three dimensional organization of genome might have guided the dynamics of gene order evolution in eukaryotes

Meenakshi Bagadia, Arashdeep Singh and Kuljeet Singh Sandhu*

- Author Affiliations

Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) – Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali

↵* Author for Correspondence: Kuljeet Singh Sandhu, Assistant Professor and Group Leader, Systems Biology Lab, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) – Mohali, Knowledge City, Sector 81, SAS Nagar, Mohali. E-mail: sandhuks@iisermohali.ac.in, Ph: 91-172-2293182, 91-9915013645

Received October 5, 2015. Revision received February 23, 2016. Accepted March 2, 2016.


Abstract

In eukaryotes, genes are non-randomly organized into short gene-dense regions or ‘gene-clusters’ interspersed by long gene-poor regions. How these gene-clusters have evolved is not entirely clear. Gene duplication may not account for all the gene-clusters since the genes in most of the clusters do not exhibit significant sequence similarity. In this study, using genome-wide datasets from budding yeast, fruit-fly and human, we show that: i) long-range evolutionary repositioning of genes strongly associate with their spatial proximity in the nucleus; ii) presence of evolutionary DNA break-points at involved loci hints at their susceptibility to undergo long-range genomic rearrangements; iii) correlated epigenetic and transcriptional states of engaged genes highlight the underlying evolutionary constraints. The significance of observation i, ii & iii are particularly stronger for the instances of inferred evolutionary gain, as compared to loss, of linear gene-clustering. These observations suggest that the long-range genomic rearrangements guided through 3D genome organization might have contributed to the evolution of gene order. We further hypothesize that the evolution of linear gene-clusters in eukaryotic genomes might have been mediated through spatial interactions among distant loci in order to optimize co-ordinated regulation of genes. We model this hypothesis through a heuristic model of gene-order evolution.

Key words

Genome organization gene-clusters genomic rearrangements chromatin interactions

© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

FREE PDF GRATIS: Genome Biol Evol Sup. Info.

A genética de característica humana complexa no século 21

domingo, março 13, 2016

Human Complex Trait Genetics in the 21st Century

View ORCID Profile Peter M. Visscher

GENETICS February 11, 2016 vol. 202 no. 2 377-379; DOI: 10.1534/genetics.115.180513

COMPLEX TRAIT GENOMICS POPULATION GENETICS QUANTITATIVE GENETICS


I moved into the field of human complex trait genetics less than 20 years ago, from a background in quantitative genetics and animal breeding. Even in this period of time, major changes have occurred that were hard to predict back in the 1990s. Driven by enormous advances in DNA sequencing technologies, one can now sequence and analyze an entire human genome for a few thousand dollars. Some may argue that the cost of a sequenced genome is much lower than that, but that usually ignores the expense of storage, analysis, and interpretation. Sequencing technology has facilitated easy and fast discovery of Mendelian disease mutations and coding variants with high penetrance (a high probability of disease given genotype), and has led to precise estimates of the per-generation mutation rate (1000 Genomes Project Consortium et al. 2010). In the same period, development of array genotyping technology has made it possible to genotype hundreds of thousands of DNA variants for less than $100. Millions of samples have been genotyped using such arrays to study the genetic basis of complex traits such as common disease and quantitative traits, which has led to the discovery of many thousands of genes, gene variants, and biological pathways that are associated with one or more complex traits (Visscher et al. 2012). The traits vary widely, from psychiatric disorders to autoimmune disease, cancer, anthropometric traits such as height and weight, traits measured in blood such as platelet size and counts, and behavioral traits such as intelligence and years of schooling. In addition to trait-variant discovery, the technologies have led to new discoveries in human evolution and population genetics.

These mostly unpredicted rapid developments were not just taking place in human complex trait genetics. In plant and animal breeding, a revolution has been taking place in the last 15 years. In 2001, a theoretical paper in this journal showed that with a sufficiently dense marker map, linkage disequilibrium could be exploited to predict breeding values and speed up genetic gain by radically changing the structure of breeding programs (Meuwissen et al. 2001). This paper was published well before the first commercial SNP chips were available, and within 10 years of publication, the method, called “genomic selection” (or “genomic prediction”), was implemented in dairy cattle breeding programs around the world; breeders of other livestock species and crops are following the same route. The update of this technology has led to a doubling of the rate of genetic gain in dairy cattle (Veerkamp 2015), an astounding increase and an incredibly rapid update of new technology.

My main thesis is that the relentless pace of technological innovation will cause a change in how science is conducted. Instead of the model-based hypothesis-testing science that dominated the last century, the next will be hypothesis-generating-discovery science that is driven by data. I believe that this change will not be confined to human complex trait genetics, but will apply to all areas of research in genetics. Genomics will become synonymous with biology, a trend already occurring.

...

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Examinando a revolução epigenética

sábado, março 12, 2016

BioSocieties (2014) 9, 431–456. 
doi:10.1057/biosoc.2014.22; published online 4 August 2014

Scrutinizing the epigenetics revolution

OPEN

Maurizio Melonia,b,† and Giuseppe Testac,†

a School of Sociology and Social Policy, University of Nottingham, Law and Social Sciences Building, University Park, Nottingham NG7 2RD UK.

b Honorary, College of Social Sciences and International Studies, University of Exeter, EX4 4RJ, Exeter, UK.

c European Institute of Oncology, Via Adamello 16, Milan 20139, Italy.

Correspondence: Maurizio Meloni, E-mails: maurizio.meloni@nottingham.ac.uk; m.meloni@exeter.ac.uk; Giuseppe Testa, E-mail: giuseppe.testa@ieo.eu

†Both the authors contributed equally.

Top


Abstract

Epigenetics is one of the most rapidly expanding fields in the life sciences. Its rise is frequently framed as a revolutionary turn that heralds a new epoch both for gene-based epistemology and for the wider discourse on life that pervades knowledge-intensive societies of the molecular age. The fundamentals of this revolution remain however to be scrutinized, and indeed the very contours of what counts as ‘epigenetic’ are often blurred. This is reflected also in the mounting discourse on the societal implications of epigenetics, in which vast expectations coexist with significant uncertainty about what aspects of this science are most relevant for politics or policy alike. This is therefore a suitable time to reflect on the directions that social theory could most productively take in the scrutiny of this revolution. Here we take this opportunity in both its scholarly and normative dimension, that is, proposing a roadmap for social theorizing on epigenetics that does not shy away from, and indeed hopefully guides, the framing of its most socially relevant outputs. To this end, we start with an epistemological reappraisal of epigenetic discourse that valorizes the blurring of meanings as a critical asset for the field and privileged analytical entry point. We then propose three paths of investigation. The first looks at the structuring elements of controversies and visions around epigenetics. The second probes the mutual constitution between the epigenetic reordering of living phenomena and the normative settlements that orient individual and collective responsibilities. The third highlights the material import of epigenetics and the molecularization of culture that it mediates. We suggest that these complementary strands provide both an epistemically and socially self-reflective framework to advance the study of epigenetics as a molecular juncture between nature and nurture and thus as the new critical frontier in the social studies of the life sciences.

Keywords: epigenetics; imaginaries; molecularization; plasticity; responsibility; social policy

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A vantagem dos abstracts simples de artigos científicos

Journal of Informetrics
Volume 10, Issue 1, February 2016, Pages 1–8

The advantage of simple paper abstracts

Adrian Letchford, , Tobias Preis, Helen Susannah Moat

Data Science Lab, Behavioural Science, Warwick Business School, University of Warwick, CV4 7AL, Coventry, UK

Received 16 June 2015, Revised 1 November 2015, Accepted 1 November 2015, Available online 13 December 2015


Get rights and content

Open Access funded by Engineering and Physical Sciences Research Council

Under a Creative Commons license


Highlights

• We investigate whether or not the style of a scientific paper's abstract bears any relation to the number of times that paper is cited.

• We find that papers whose abstracts contain more frequently used words tend to receive slightly more citations.

• We find that journals which publish papers whose abstracts are shorter and contain more frequently used words receive slightly more citations per paper.

Abstract

Each year, researchers publish an immense number of scientific papers. While some receive many citations, others receive none. Here we investigate whether any of this variance can be explained by the choice of words in a paper's abstract. We find that doubling the word frequency of an average abstract increases citations by 0.70%. We also find that journals which publish papers whose abstracts are shorter and contain more frequently used words receive slightly more citations per paper. Specifically, adding a 5 letter word to an abstract decreases the number of citations by 0.02%. These results are consistent with the hypothesis that the style in which a paper's abstract is written bears some relation to its scientific impact.

Keywords: Citation analysis; Scientific writing; Computational social science; Science of science

FREE PDF GRATIS: Journal of Informetrics

A vantagem dos títulos curtos de artigos científicos

The advantage of short paper titles

Adrian Letchford, Helen Susannah Moat, Tobias Preis

Published 26 August 2015.DOI: 10.1098/rsos.150266



Abstract

Vast numbers of scientific articles are published each year, some of which attract considerable attention, and some of which go almost unnoticed. Here, we investigate whether any of this variance can be explained by a simple metric of one aspect of the paper's presentation: the length of its title. Our analysis provides evidence that journals which publish papers with shorter titles receive more citations per paper. These results are consistent with the intriguing hypothesis that papers with shorter titles may be easier to understand, and hence attract more citations.

FREE PDF GRATIS: Royal Society Open Science

Expressão gênica: aumentando através do ciclo celular

quinta-feira, março 10, 2016

Gene expression: Bursting through the cell cycle

Shani Ben-Moshe Shalev Itzkovitz 

Weizmann Institute of Science, Israel


Published March 7, 2016

Cite as eLife 2016;5:e14953


Abstract

How are cells able to maintain constant levels of mRNA when the number of genes in a cell doubles ahead of cell division?

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Explorando cérebros miniaturas de insetos utilizando técnicas de exploração micro-CT

Exploring miniature insect brains using micro-CT scanning techniques

Dylan B. Smith, Galina Bernhardt, Nigel E. Raine, Richard L. Abel, Dan Sykes, Farah Ahmed, Inti Pedroso & Richard J. Gill

Scientific Reports 6, Article number: 21768 (2016)


Download Citation

3-D reconstructionAnimal physiologyX-ray tomography

Received: 20 May 2015 Accepted: 29 January 2016

Published online: 24 February 2016


Abstract

The capacity to explore soft tissue structures in detail is important in understanding animal physiology and how this determines features such as movement, behaviour and the impact of trauma on regular function. Here we use advances in micro-computed tomography (micro-CT) technology to explore the brain of an important insect pollinator and model organism, the bumblebee (Bombus terrestris). Here we present a method for accurate imaging and exploration of insect brains that keeps brain tissue free from trauma and in its natural stereo-geometry, and showcase our 3D reconstructions and analyses of 19 individual brains at high resolution. Development of this protocol allows relatively rapid and cost effective brain reconstructions, making it an accessible methodology to the wider scientific community. The protocol describes the necessary steps for sample preparation, tissue staining, micro-CT scanning and 3D reconstruction, followed by a method for image analysis using the freeware SPIERS. These image analysis methods describe how to virtually extract key composite structures from the insect brain, and we demonstrate the application and precision of this method by calculating structural volumes and investigating the allometric relationships between bumblebee brain structures.

FREE PDF GRATIS: Scientific Reports

Evolução inteligente - uma teoria evolucionária alternativa

Intelligent Evolution: An Alternate Theory of Evolution Kindle Edition

by Claire Quinn (Author)

Intelligent design is often depicted as science versus religion but this is not always the case. I have a Ph.D. in molecular biology, don't follow any specific religion, and have come to the conclusion that the complexity of life suggests intelligent design. I believe microbes were designed by an intelligent entity and then released into the cold, vastness of space. Some haphazardly landed on our warm, wet planet and went on to evolve into everything we see here today, including us. This is 'Intelligent Evolution' because we evolved from intelligently designed microbes. Evidence of this and how these microbes took our planet from a barren, wet rock to a thriving, rich ecosystem is outlined in detail, essentially rewriting the entire theory of evolution. 

About the Author: 

I have a B.Sc. in Genetics from the University of Western Ontario, a Masters in Physiology and Pharmacology from the University of Western Ontario, and a Ph.D. in Molecular Biology from the University of Toronto.

Source/Fonte: Amazon

Taxa individual de publicação de pesquisadores não cresceu em um século!!!

quarta-feira, março 09, 2016

Researchers’ Individual Publication Rate Has Not Increased in a Century

Daniele Fanelli , Vincent Larivière

Published: March 9, 2016


Abstract

Debates over the pros and cons of a “publish or perish” philosophy have inflamed academia for at least half a century. Growing concerns, in particular, are expressed for policies that reward “quantity” at the expense of “quality,” because these might prompt scientists to unduly multiply their publications by fractioning (“salami slicing”), duplicating, rushing, simplifying, or even fabricating their results. To assess the reasonableness of these concerns, we analyzed publication patterns of over 40,000 researchers that, between the years 1900 and 2013, have published two or more papers within 15 years, in any of the disciplines covered by the Web of Science. The total number of papers published by researchers during their early career period (first fifteen years) has increased in recent decades, but so has their average number of co-authors. If we take the latter factor into account, by measuring productivity fractionally or by only counting papers published as first author, we observe no increase in productivity throughout the century. Even after the 1980s, adjusted productivity has not increased for most disciplines and countries. These results are robust to methodological choices and are actually conservative with respect to the hypothesis that publication rates are growing. Therefore, the widespread belief that pressures to publish are causing the scientific literature to be flooded with salami-sliced, trivial, incomplete, duplicated, plagiarized and false results is likely to be incorrect or at least exaggerated.

Citation: Fanelli D, Larivière V (2016) Researchers’ Individual Publication Rate Has Not Increased in a Century. PLoS ONE 11(3): e0149504. 

Editor: Pablo Dorta-González, Universidad de Las Palmas de Gran Canaria, SPAIN

Received: November 2, 2015; Accepted: January 29, 2016; Published: March 9, 2016

Copyright: © 2016 Fanelli, Larivière. 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: The authors have no support or funding to report.

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

FREE PDF GRATIS: PLoS One

O particionamento da energia elástica na deformação e ligação do DNA às proteínas

Elastic Energy Partitioning in DNA Deformation and Binding to Proteins

Xiaojing Teng† and Wonmuk Hwang*†‡§

† Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States

‡ Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States

§ School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea 02455

ACS Nano, 2016, 10 (1), pp 170–180


Publication Date (Web): December 05, 2015

Copyright © 2015 American Chemical Society

*E-mail: hwm@tamu.edu.


Abstract

We study the elasticity of DNA based on local principal axes of bending identified from over 0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order parameters describe motion of DNA as an elastic rod. In 10 possible dinucleotide steps, bending about the two principal axes is anisotropic yet linearly elastic. Twist about the centroid axis is largely decoupled from bending, but DNA tends to overtwist for unbending beyond the typical range of thermal motion, which is consistent with experimentally observed twist–stretch coupling. The calculated elastic stiffness of dinucleotide steps yield sequence-dependent persistence lengths consistent with previous single-molecule experiments, which is further analyzed by performing coarse-grained simulations of DNA. Flexibility maps of oligos constructed from simulation also match with those from the precalculated stiffness of dinucleotide steps. These support the premise that base pair interaction at the dinucleotide-level is mainly responsible for the elasticity of DNA. Furthermore, we analyze 1381 crystal structures of protein–DNA complexes. In most structures, DNAs are mildly deformed and twist takes the highest portion of the total elastic energy. By contrast, in structures with the elastic energy per dinucleotide step greater than about 4.16 kBT (kBT: thermal energy), the major bending becomes dominant. The extensional energy of dinucleotide steps takes at most 35% of the total elastic energy except for structures containing highly deformed DNAs where linear elasticity breaks down. Such partitioning between different deformational modes provides quantitative insights into the conformational dynamics of DNA as well as its interaction with other molecules and surfaces.

Keywords: DNA flexibility; DNA−protein complex; DNA nanostructure; principal axis; molecular dynamics; type-II topoisomerase

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Rastreando a transmissão interespécies e a evolução a longo prazo de um retrovírus antigo usando os genomas de mamíferos modernos

Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals

William E Diehl Nirali Patel Kate Halm Welkin E Johnson 

Boston College, United States


Published March 8, 2016

Cite as eLife 2016;5:e12704


Abstract

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections.


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A extinção de répteis marinhos em forma de peixe associada a taxas evolutivas reduzidas e a volatilidade ambiental global

Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility

Valentin Fischer, Nathalie Bardet, Roger B. J. Benson, Maxim S. Arkhangelsky & Matt Friedman

Affiliations Contributions Corresponding author

Nature Communications 7, Article number: 10825 doi:10.1038/ncomms10825

Received 12 August 2015 Accepted 22 January 2016 Published 08 March 2016


Abstract

Despite their profound adaptations to the aquatic realm and their apparent success throughout the Triassic and the Jurassic, ichthyosaurs became extinct roughly 30 million years before the end-Cretaceous mass extinction. Current hypotheses for this early demise involve relatively minor biotic events, but are at odds with recent understanding of the ichthyosaur fossil record. Here, we show that ichthyosaurs maintained high but diminishing richness and disparity throughout the Early Cretaceous. The last ichthyosaurs are characterized by reduced rates of origination and phenotypic evolution and their elevated extinction rates correlate with increased environmental volatility. In addition, we find that ichthyosaurs suffered from a profound Early Cenomanian extinction that reduced their ecological diversity, likely contributing to their final extinction at the end of the Cenomanian. Our results support a growing body of evidence revealing that global environmental change resulted in a major, temporally staggered turnover event that profoundly reorganized marine ecosystems during the Cenomanian.

Subject terms: Biological sciences Evolution Palaeontology

FREE PDF GRATIS: Nature Communications

Desenvolvimento molecular da redução fibular em aves e sua evolução a partir de dinossauros

Molecular development of fibular reduction in birds and its evolution from dinosaurs

João Francisco Botelho1, Daniel Smith-Paredes1, Sergio Soto-Acuña1,2, Jingmai O'Connor3, Verónica Palma4 andAlexander O. Vargas1

Article first published online: 4 MAR 2016


Source/Fonte: Internet

Abstract

Keywords: Bird–dinosaur transition; fibula, IHH; mesozoic birds; PTHrP; zeugopod

Birds have a distally reduced, splinter-like fibula that is shorter than the tibia. In embryonic development, both skeletal elements start out with similar lengths. We examined molecular markers of cartilage differentiation in chicken embryos. We found that the distal end of the fibula expresses Indian hedgehog (IHH), undergoing terminal cartilage differentiation, and almost no Parathyroid-related protein (PTHrP), which is required to develop a proliferative growth plate (epiphysis). Reduction of the distal fibula may be influenced earlier by its close contact with the nearby fibulare, which strongly expresses PTHrP. The epiphysis-like fibulare however then separates from the fibula, which fails to maintain a distal growth plate, and fibular reduction ensues. Experimental downregulation of IHH signaling at a postmorphogenetic stage led to a tibia and fibula of equal length: The fibula is longer than in controls and fused to the fibulare, whereas the tibia is shorter and bent. We propose that the presence of a distal fibular epiphysis may constrain greater growth in the tibia. Accordingly, many Mesozoic birds show a fibula that has lost its distal epiphysis, but remains almost as long as the tibia, suggesting that loss of the fibulare preceded and allowed subsequent evolution of great fibulo–tibial disparity.

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A plasticidade esqueletal em resposta à atividade muscular embrionária está subjacente ao desenvolvimento e evolução do dígito empoleirador das aves

Skeletal plasticity in response to embryonic muscular activity underlies the development and evolution of the perching digit of birds

João Francisco Botelho, Daniel Smith-Paredes, Sergio Soto-Acuña, Jorge Mpodozis, Verónica Palma & Alexander O. Vargas

Scientific Reports 5, Article number: 9840 (2015)


Evolutionary developmental biology Palaeontology

Received: 02 November 2014 Accepted: 11 March 2015

Published online: 14 May 2015

Abstract

Most birds have an opposable digit 1 (hallux) allowing the foot to grasp, which evolved from the non-opposable hallux of early theropod dinosaurs. An important morphological difference with early theropods is the twisting of the long axis of its metatarsal. Here, we show how embryonic musculature and the onset of its activity are required for twisting of metatarsal 1 (Mt1) and retroversion of the hallux. Pharmacologically paralyzed embryos do not fully retrovert the hallux and have a straight Mt1 shaft, phenocopying the morphology of early tetanuran dinosaurs. Molecular markers of cartilage maturation and ossification show that differentiation of Mt1 is significantly delayed compared to Mt2-4. We hypothesize on how delayed maturation may have increased plasticity, facilitating muscular twisting. Our experimental results emphasize the importance of embryonic muscular activity in the evolutionary origin of a crucial adaptation.

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Fósseis em âmbar do Cretáceo intermediário ilumina a diversidade passada dos lagartos tropicais

segunda-feira, março 07, 2016

Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards

Juan D. Daza1,*, Edward L. Stanley2,3, Philipp Wagner4, Aaron M. Bauer5 and David A. Grimaldi6

- Author Affiliations

1Department of Biological Sciences, Sam Houston State University, 1900 Avenue I, Lee Drain Building Suite 300, Huntsville, TX 77341, USA.

2Department of Herpetology, Florida Museum of Natural History, 3215 Hull Road, Gainesville, FL 31611, USA.

3Department of Herpetology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA.

4Zoologische Staatssammlung München, Münchhausenstraße 21, 81247 Munich, Germany.

5Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA.

6Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024–5192, USA.

↵*Corresponding author. E-mail: jdd054@shsu.edu

Science Advances 04 Mar 2016:

Vol. 2, no. 3, e1501080 DOI: 10.1126/sciadv.1501080


Abstract

Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships.

Keywords Mesozoic period fossils  lizards paleobiology

Copyright © 2016, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

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