Pesquisa pioneira faz imagens de atividade em cérebros fetais antes do nascimento

domingo, janeiro 22, 2017

Weak functional connectivity in the human fetal brain prior to preterm birth

Moriah E. Thomason, Dustin Scheinost, Janessa H. Manning, Lauren E. Grove, Jasmine Hect, Narcis Marshall, Edgar Hernandez-Andrade, Susan Berman, Athina Pappas, Lami Yeo, Sonia S. Hassan, R. Todd Constable, Laura R. Ment & Roberto Romero

Scientific Reports 7, Article number: 39286 (2017)


Download Citation

Disease model Neural patterning

Received: 08 June 2016 Accepted: 21 November 2016 Published online: 09 January 2017

Figure 1: Comparison of preterm (PT) - and term (T) -born fetuses using voxel-level connectivity.

Abstract

It has been suggested that neurological problems more frequent in those born preterm are expressed prior to birth, but owing to technical limitations, this has been difficult to test in humans. We applied novel fetal resting-state functional MRI to measure brain function in 32 human fetuses in utero and found that systems-level neural functional connectivity was diminished in fetuses that would subsequently be born preterm. Neural connectivity was reduced in a left-hemisphere pre-language region, and the degree to which connectivity of this left language region extended to right-hemisphere homologs was positively associated with the time elapsed between fMRI assessment and delivery. These results provide the first evidence that altered functional connectivity in the preterm brain is identifiable before birth. They suggest that neurodevelopmental disorders associated with preterm birth may result from neurological insults that begin in utero.

Additional Information

How to cite this article: Thomason, M. E. et al. Weak functional connectivity in the human fetal brain prior to preterm birth. Sci. Rep. 7, 39286; doi: 10.1038/srep39286 (2017).

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Acknowledgements

This project was supported by awards to M.E.T. from the National Institutes of Health, MH110793 and ES026022, and by a NARSAD Young Investigator Award. This project was also supported in part by NIH contract HHSN 275201300006 C. The authors thank Pavan Jella, Saige Rutherford, Sophia Neuenfeldt, and Ki-Jana Malone for their assistance in acquiring the scan data; Farrah Elrahal, Jamie Pierce, Jordan Boeve, Gillian Grace Spitzley, Sydney Rooks, and Joi Webb for their assistance in participant recruitment, screening, and conducting behavioral testing; and Tarek Bazzi, Alison Li, Kassem Soufan, and Baldish Oberoi for their help with data processing. The authors also thank participant families who generously shared their time.

Author information

Affiliations

Merrill Palmer Skillman Institute for Child and Family Development, Wayne State University, Detroit, MI 48202, USA

Moriah E. Thomason, Janessa H. Manning, Lauren E. Grove, Jasmine Hect & Narcis Marshall

Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI 48202, USA

Moriah E. Thomason & Athina Pappas

Perinatology Research Branch, NICHD/NIH/DHHS, Detroit, Michigan, and Bethesda, Maryland, USA

Moriah E. Thomason, Janessa H. Manning, Lauren E. Grove, Narcis Marshall, Edgar Hernandez-Andrade, Athina Pappas, Lami Yeo, Sonia S. Hassan & Roberto Romero

Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, 48104, USA

Moriah E. Thomason

Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06520, USA

Dustin Scheinost & R. Todd Constable

Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48202, USA

Edgar Hernandez-Andrade, Susan Berman, Lami Yeo & Sonia S. Hassan

Department of Neurosurgery, Yale School of Medicine, New Haven, CT 06520, USA

R. Todd Constable

Department of Pediatrics, Yale School of Medicine, New Haven, CT 06520, USA

Laura R. Ment

Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA

Laura R. Ment

Center for Molecular Medicine, Wayne State University, Detroit, MI 48202, USA

Roberto Romero

Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, MI, 48104, USA

Roberto Romero

Department of Epidemiology, Michigan State University, East Lansing, MI 48825, USA.

Roberto Romero

Contributions

M.E.T., D.S., R.R., L.R.M., S.S.H., and L.Y. designed research; A.P., S.B., and E.H.A. performed research; M.E.T., D.S., J.H.M., L.E.G., J.H., N.M., and T.C. analyzed data; and M.E.T., D.S., R.R., L.Y. and L.M. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Moriah E. Thomason.

Nova espécie de mariposa "batizada" com o nome de Donald Trump

sexta-feira, janeiro 20, 2017

ZooKeys 646: 79-94 (17 Jan 2017)


Review of Neopalpa Povolný, 1998 with description of a new species from California and Baja California, Mexico (Lepidoptera, Gelechiidae)

expand article infoVazrick Nazari‡

‡ Unaffiliated, Ottawa, Canada

Corresponding author: Vazrick Nazari ( nvazrick@yahoo.com )

Academic editor: Donald Lafontaine

© 2017 Vazrick Nazari.

This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Citation: Nazari V (2017) Review of Neopalpa Povolný, 1998 with description of a new species from California and Baja California, Mexico (Lepidoptera, Gelechiidae). ZooKeys 646: 79-94. https://doi.org/10.3897/zookeys.646.11411

ZooBank: urn:lsid:zoobank.org:pub:3175884F-5A42-4662-8F09-7639C0FDE708

Open Access


Abstract

The monotypic genus Neopalpa was described in 1998 by Czech entomologist Dalibor Povolný based on two male specimens from Santa Catalina Island, California, which he named N. neonata. The female of this species was discovered recently based on a DNA barcode match and is described. In addition, a new species with marked differences in morphology and DNA barcodes from southern California and Baja California Mexico is described as Neopalpa donaldtrumpi sp. n. Adults and genitalia of both species are illustrated, new diagnosis for the genus Neopalpa is provided, and its position within Gelechiidae is briefly discussed.

Keywords Microlepidoptera, new species, nomenclature, taxonomy, Donald J. Trump

FREE PDF GRATIS: ZooKeys

Cientistas alertam sobre a iminente perda mundial da população de primatas

Impending extinction crisis of the world’s primates: Why primates matter

Alejandro Estrada1,*, Paul A. Garber2,*, Anthony B. Rylands3, Christian Roos4, Eduardo Fernandez-Duque5, Anthony Di Fiore6, K. Anne-Isola Nekaris7, Vincent Nijman7, Eckhard W. Heymann8, Joanna E. Lambert9, Francesco Rovero10, Claudia Barelli10, Joanna M. Setchell11, Thomas R. Gillespie12, Russell A. Mittermeier3, Luis Verde Arregoitia13, Miguel de Guinea7, Sidney Gouveia14, Ricardo Dobrovolski15, Sam Shanee16,17, Noga Shanee16,17, Sarah A. Boyle18, Agustin Fuentes19, Katherine C. MacKinnon20, Katherine R. Amato21, Andreas L. S. Meyer22, Serge Wich23,24, Robert W. Sussman25, Ruliang Pan26, Inza Kone27 and Baoguo Li28

+ Author Affiliations

↵*Corresponding author. Email: aestradaprimates@gmail.com (A.E.); p-garber@illinois.edu (P.A.G.)

Science Advances 18 Jan 2017: Vol. 3, no. 1, e1600946




Abstract

Nonhuman primates, our closest biological relatives, play important roles in the livelihoods, cultures, and religions of many societies and offer unique insights into human evolution, biology, behavior, and the threat of emerging diseases. They are an essential component of tropical biodiversity, contributing to forest regeneration and ecosystem health. Current information shows the existence of 504 species in 79 genera distributed in the Neotropics, mainland Africa, Madagascar, and Asia. Alarmingly, ~60% of primate species are now threatened with extinction and ~75% have declining populations. This situation is the result of escalating anthropogenic pressures on primates and their habitats—mainly global and local market demands, leading to extensive habitat loss through the expansion of industrial agriculture, large-scale cattle ranching, logging, oil and gas drilling, mining, dam building, and the construction of new road networks in primate range regions. Other important drivers are increased bushmeat hunting and the illegal trade of primates as pets and primate body parts, along with emerging threats, such as climate change and anthroponotic diseases. Often, these pressures act in synergy, exacerbating primate population declines. Given that primate range regions overlap extensively with a large, and rapidly growing, human population characterized by high levels of poverty, global attention is needed immediately to reverse the looming risk of primate extinctions and to attend to local human needs in sustainable ways. Raising global scientific and public awareness of the plight of the world’s primates and the costs of their loss to ecosystem health and human society is imperative.

Keywords nonhuman primates tropical forests deforestation hunting illegal trade primate conservation sustainable land use industrial agriculture ecosystem health rural livelihoods

Copyright © 2017, 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.

FREE PDF GRATIS: Science Advances

Imagem de proteínas ao nível de uma única molécula revela mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, janeiro 19, 2017

Imaging proteins at the single-molecule level

Jean-Nicolas Longchamp a,1, Stephan Rauschenbach b, Sabine Abb b, Conrad Escher a, Tatiana Latychevskaia a, Klaus Kern b,c,1, and Hans-Werner Fink a,1

Author Affiliations

a Physics Department of the University of Zurich, CH-8057 Zurich, Switzerland;

b Max Planck Institute for Solid State Research, DE-70569 Stuttgart, Germany;

c Institut de Physique, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland

Edited by R. Graham Cooks, Purdue University, West Lafayette, IN, and approved December 13, 2016 (received for review September 2, 2016)


Fig. 4.
Low-energy electron micrographs of BSA in different orientations on graphene. (Top) Low-energy electron micrographs of BSA. (Bottom) The atomic model of BSA (PDB ID: 3V03) in the corresponding orientations. (Scale bars, 5 nm.)

Significance

We report a method to image and reveal structural details of proteins on a truly single-molecule level. Low-energy electron holography is used to image individual proteins electrospray deposited on freestanding graphene. In contrast to the current state of the art in structural biology, we do away with the need for averaging over many molecules. This is crucial because proteins are flexible objects that can assume distinct conformations often associated with different functions. Proteins are also the targets of almost all the currently known and available drugs. The design of new and more effective drugs relies on the knowledge of the targeted proteins structure in all its biologically significant conformations at the best possible resolution.

Abstract

Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics, and molecular nanotechnology. In particular, revealing the distinct conformations of an individual protein is of utmost importance. Here, we show the imaging of individual proteins and protein complexes by low-energy electron holography. Samples of individual proteins and protein complexes on ultraclean freestanding graphene were prepared by soft-landing electrospray ion beam deposition, which allows chemical- and conformational-specific selection and gentle deposition. Low-energy electrons do not induce radiation damage, which enables acquiring subnanometer resolution images of individual proteins (cytochrome C and BSA) as well as of protein complexes (hemoglobin), which are not the result of an averaging process.

low-energy electron holography single protein imaging preparative mass spectrometry microscopy structural biology

Footnotes

1 To whom correspondence may be addressed. Email: longchamp@physik.uzh.ch, k.kern@fkf.mpg.de, or hwfink@physik.uzh.ch.

Author contributions: J.-N.L. had the original idea to combine ES-IBD and low-energy electron holography and further elaborated the concept with K.K. and H.-W.F. J.-N.L. prepared the ultraclean freestanding graphene supports and recorded the holograms. J.-N.L. and S.R. planned the deposition experiments and along with S.A. performed the electrospray deposition of the proteins onto graphene. T.L. performed the hologram reconstructions with her self-developed software package. J.-N.L. and S.R. interpreted the data. H.-W.F. invented the technology of lens-less holography with low-energy electrons based on atomic sized coherent electron point sources. J.-N.L., C.E., T.L., and H.-W.F. further developed the low-energy electron holographic microscope used in this study. S.R. and K.K. developed the ES-IBD technique. J.-N.L, C.E., and H.-W.F. wrote the manuscript main text and with S.R. the supplementary information, in discussions with all remaining authors.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1614519114/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

Design inteligente em engenharia

Access Volume 42, Issue 1 (Material Functionalities from Molecular Rigidity) January 2017, pp. 18-22

Material functionalities from molecular rigidity: Maxwell’s modern legacy

Matthieu Micoulaut (a1) and Yuanzheng Yue (a2) 


Published online: 10 January 2017


Figure 1. Detail of Gustave Eiffel’s plan shows that the well-known Paris construction is a node and bar framework. An analogy can be made at the microscopic scale, where the nodes are replaced by atoms and the bars by covalent bonds. For ease of calculation, rather than focusing on ordered networks, the authors of the initial rigidity approach preferred averaging over disorder to achieve mean-field rigidity.

Abstract

We provide an overview of the field of rigidity theory applied at the atomic scale. This theoretical approach, initially designed for macroscopic structures such as bridges or buildings, has gained renewed interest in the past few years thanks to new methodological developments and to attractive applications in a variety of materials, such as scratch-resistant glassy sheets for mobile phones, phase-change memory, tough cement, dielectrics, and photonic devices. In parallel, basic phenomena associated with the onset of rigidity have been discovered, which have challenged our current understanding of the structural modification induced by changes in composition. This has led to the identification of “smart” glasses with multiple functionalities and superior mechanical performances. Topological prediction and engineering of physical properties are also enabling intelligent design of new disordered materials.

FREE PDF GRATIS: MRS Bulletin

Cientistas precisam dar ferramentas para a sociedade confiar neles!


Give the public the tools to trust scientists

Anita Makri argues that the form of science communicated in popular media leaves the public vulnerable to false certainty.

17 January 2017


What is truth? How do we find it and does it still carry weight in public debate? Given recent political events, these are important and urgent questions. But of the two industries I work in that are concerned with truth — science and journalism — only the latter has seriously engaged and looked for answers. Scientists need to catch up, or they risk further marginalization in a society that is increasingly weighing evidence and making decisions without them.

Whereas journalists are debating facts and falsehood, their own role and possible ways to react, scientists seem to see themselves as victims of, rather than active players in, the new political scene. Most debate centres on how the new political order threatens scientific knowledge and research funding, or downgrades climate-change policy.

All are important, but what's overlooked by many is how science is losing its relevance as a source of truth. To reclaim this relevance, scientists, communicators, institutions and funders must work to change the way that socially relevant science is presented to the public. This is not about better media training for researchers. It demands a rethink about the kind of science that we want to communicate to broader society. This message may sound familiar but the new focus on post-truth shows there is now a tangible danger that must be addressed.

Much of the science that the public knows about and admires imparts a sense of wonder and fun about the world, or answers big existential questions. It's in the popularization of physics through the television programmes of physicist Brian Cox and in articles about new fossils and quirky animal behaviour on the websites of newspapers. It is sellable and familiar science: rooted in hypothesis testing, experiments and discovery.

Although this science has its place, it leaves the public (not to mention policymakers) with a different, outdated view to that of scientists of what constitutes science. People expect science to offer authoritative conclusions that correspond to the deterministic model. When there's incomplete information, imperfect knowledge or changing advice — all part and parcel of science — its authority seems to be undermined. We see this in the public debate over food and health: first, fat was bad and now it's sugar. A popular conclusion of that shifting scientific ground is that experts don't know what they're talking about.

...

FULL PDF GRATIS: Nature

As moscas Drosofila melanogaster escolhem "racionalmente" os parceiros sexuais

quarta-feira, janeiro 18, 2017

Mate choice in fruit flies is rational and adaptive

Devin Arbuthnott, Tatyana Y. Fedina, Scott D. Pletcher & Daniel E. L. Promislow

Nature Communications 8, Article number: 13953 (2017)


Download Citation

Animal behaviour Sexual selection

Received: 05 May 2016 Accepted: 16 November 2016 Published online: 17 January 2017

Source/Fonte: Texas A & M University


Abstract

According to rational choice theory, beneficial preferences should lead individuals to sort available options into linear, transitive hierarchies, although the extent to which non-human animals behave rationally is unclear. Here we demonstrate that mate choice in the fruit fly Drosophila melanogaster results in the linear sorting of a set of diverse isogenic female lines, unambiguously demonstrating the hallmark of rational behaviour, transitivity. These rational choices are associated with direct benefits, enabling males to maximize offspring production. Furthermore, we demonstrate that female behaviours and cues act redundantly in mate detection and assessment, as rational mate choice largely persists when visual or chemical sensory modalities are impaired, but not when both are impaired. Transitivity in mate choice demonstrates that the quality of potential mates varies significantly among genotypes, and that males and females behave in such a way as to facilitate adaptive mate choice.

Acknowledgements

We thank Erin Tudor, Quynh Tran, Sharon Ornels, Alexandria McCarthy, Laurie Huang, William Gordon, Nick Force, Erika Gajda, Jake Mouser, Cindy Tseng and Eric Vanderbilt-Mathews for experimental help. Howard Rundle and Julie Colpitts performed gas chromatography for CHC extractions. Carly Ziegler provided valuable comments on an earlier draft. This work was funded by NIH grant GM102279 to S.D.P. and D.E.L.P and NIA Training Grant AG000114 to T.Y.F.

Author information

Affiliations

Department of Pathology, University of Washington, 1959 NE Pacific Street, Box 357705, Seattle, Washington 98195, USA

Devin Arbuthnott & Daniel E. L. Promislow

Department of Zoology, University of British Columbia, 4200-6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4

Devin Arbuthnott

Department of Molecular and Integrative Physiology, and Geriatrics Center, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA

Tatyana Y. Fedina & Scott D. Pletcher

Department of Biology, University of Washington, Seattle, Washington 98195, USA

Daniel E. L. Promislow

Contributions

All authors devised and planned experiments. D.A. and T.Y.F. carried out experiments. D.A. and D.E.L.P. analysed the data. All authors wrote the paper. S.D.P. and D.E.L.P. funded the work.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Devin Arbuthnott.

FREE PDF GRATIS: Nature Communications Sup. Info.1 Peer-review file

Rumo à descoberta de cartéis de citação em redes de citações de artigos científicos

Front. Phys., 15 December 2016 | https://doi.org/10.3389/fphy.2016.00049

Toward the Discovery of Citation Cartels in Citation Networks

Iztok Fister Jr.1, Iztok Fister1 and Matjaž Perc2,3*

1Faculty of Electrical Engineering and Computer Science, University of Maribor, Maribor, Slovenia

2Faculty of Natural Sciences and Mathematics, Institute of Physics, University of Maribor, Maribor, Slovenia

3Center for Applied Mathematics and Theoretical Physics, University of Maribor, Maribor, Slovenia


Abstract

In this perspective, our goal is to present and elucidate a thus far largely overlooked problem that is arising in scientific publishing, namely the identification and discovery of citation cartels in citation networks. Taking from the well-known definition of a community in the realm of network science, namely that people within a community share significantly more links with each other as they do outside of this community, we propose that citation cartels are defined as groups of authors that cite each other disproportionately more than they do other groups of authors that work on the same subject. Evidently, the identification of citation cartels is somewhat different, although similar to the identification of communities in networks. We systematically expose the problem, provide theoretical examples, and outline an algorithmic guide on how to approach the subject.

Author Contributions

IF Jr., IF, and MP designed and performed the research as well as wrote the paper.

Funding

This research was supported by the Slovenian Research Agency (Grants P5-0027 and J1-7009).

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Keywords: citation network, citation cartel, network science, community detection, cooperation

Citation: Fister I Jr., Fister I and Perc M (2016) Toward the Discovery of Citation Cartels in Citation Networks. Front. Phys. 4:49. doi: 10.3389/fphy.2016.00049

Received: 02 November 2016; Accepted: 29 November 2016; Published: 15 December 2016.

Edited by: Antonio F. Miguel, University of Évora, Portugal

Reviewed by: Zoran Levnajic, Institute Jozef Stefan, Slovenia, Marija Mitrovic Dankulov, Institute of Physics Belgrade, Serbia, Walter Quattrociocchi, IMT Lucca, Italy

Copyright © 2016 Fister, Fister and Perc. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: Matjaž Perc, matjaz.perc@uni-mb.si

FREE PDF GRATIS: Frontiers in Physics

Mecanismos de controle de qualidade excluem polimerases incorretas da forquilha de replicação eucariótica: mero acaso, fortuita necessidade ou design inteligente?

Quality control mechanisms exclude incorrect polymerases from the eukaryotic replication fork

Grant D. Schauer a and Michael E. O’Donnell a,1

Author Affiliations

Contributed by Michael E. O'Donnell, December 2, 2016 (sent for review November 21, 2016; reviewed by Daniel L. Kaplan and R. Stephen Lloyd)



Significance

DNA replication is a central life process and is performed by numerous proteins that orchestrate their actions to separate the strands of duplex DNA and produce two new copies of the genome for cell division. While the antiparallel architecture of DNA is elegant in its simplicity, replication of DNA still holds many mysteries. For example, many essential replication proteins still have unknown functions. In eukaryotes the two DNA strands are duplicated by different DNA polymerases. The mechanism by which these different polymerases target to their respective strands is understood. This report examines the mechanisms that eject incorrect polymerases when they associate with the wrong strand.

Abstract

The eukaryotic genome is primarily replicated by two DNA polymerases, Pol ε and Pol δ, that function on the leading and lagging strands, respectively. Previous studies have established recruitment mechanisms whereby Cdc45-Mcm2-7-GINS (CMG) helicase binds Pol ε and tethers it to the leading strand, and PCNA (proliferating cell nuclear antigen) binds tightly to Pol δ and recruits it to the lagging strand. The current report identifies quality control mechanisms that exclude the improper polymerase from a particular strand. We find that the replication factor C (RFC) clamp loader specifically inhibits Pol ε on the lagging strand, and CMG protects Pol ε against RFC inhibition on the leading strand. Previous studies show that Pol δ is slow and distributive with CMG on the leading strand. However, Saccharomyces cerevisiae Pol δ–PCNA is a rapid and processive enzyme, suggesting that CMG may bind and alter Pol δ activity or position it on the lagging strand. Measurements of polymerase binding to CMG demonstrate Pol ε binds CMG with a Kd value of 12 nM, but Pol δ binding CMG is undetectable. Pol δ, like bacterial replicases, undergoes collision release upon completing replication, and we propose Pol δ–PCNA collides with the slower CMG, and in the absence of a stabilizing Pol δ–CMG interaction, the collision release process is triggered, ejecting Pol δ on the leading strand. Hence, by eviction of incorrect polymerases at the fork, the clamp machinery directs quality control on the lagging strand and CMG enforces quality control on the leading strand.

replisome replication clamp loader PCNA DNA polymerase

Footnotes

1To whom correspondence should be addressed. Email: odonnel@rockefeller.edu.

Author contributions: G.D.S. and M.E.O. designed research; G.D.S. performed research; G.D.S. analyzed data; and G.D.S. and M.E.O. wrote the paper.

Reviewers: D.L.K., Florida State University College of Medicine; and R.S.L., Oregon Health & Sciences University.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1619748114/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS 

Cinco grandes mistérios sobre a origem de CRISPRs

terça-feira, janeiro 17, 2017

Five big mysteries about CRISPR’s origins

Where did it come from? How do organisms use it without self-destructing? And what else can it do?

Heidi Ledford

12 January 2017 Corrected: 13 January 2017


Francisco Mojica was not the first to see CRISPR, but he was probably the first to be smitten by it. He remembers the day in 1992 when he got his first glimpse of the microbial immune system that would launch a biotechnology revolution. He was reviewing genome-sequence data from the salt-loving microbe Haloferax mediterranei and noticed 14 unusual DNA sequences, each 30 bases long. They read roughly the same backwards and forwards, and they repeated every 35 bases or so. Soon, he saw more of them. Mojica was entranced, and made the repeats a focus of his research at the University of Alicante in Spain.

It wasn't a popular decision. His lab went years without funding. At meetings, Mojica would grab the biggest bigwigs he could find and ask what they thought of the strange little repeats. “Don't care about repeats so much,” he says that they would warn him. “There are many repeats in many organisms — we've known about them for years and still don't know how many of them work.”

Today, much more is known about the clustered, regularly interspaced short palindromic repeats that give CRISPR its name and help the CRISPR–Cas microbial immune system to destroy invading viruses. But although most in biomedicine have come to revere the mechanics of the system — particularly of a version called CRISPR–Cas9 — for the ways in which it can be harnessed to edit genes, Mojica and other microbiologists are still puzzling over some basic questions about the system and how it works. How did it evolve, and how did it shape microbial evolution? Why do some microbes use it, whereas others don't? And might it have other, yet-to-be-appreciated roles in their basic biology?

“A lot of the attention paid to CRISPR systems in the media has really been around its use as a technology — and with good reason. That's where we're seeing incredible impact and opportunities,” says Jennifer Doudna, a molecular biologist at the University of California, Berkeley, and one of the first scientists to reveal CRISPR–Cas's agility as a gene-editing tool. “At the same time, there's a lot of interesting fundamental biology research to be done.”

Where did it come from?

The biological advantages of something like CRISPR–Cas are clear. Prokaryotes — bacteria and less-well-known single-celled organisms called archaea, many of which live in extreme environments — face a constant onslaught of genetic invaders. Viruses outnumber prokaryotes by ten to one and are said to kill half of the world's bacteria every two days. Prokaryotes also swap scraps of DNA called plasmids, which can be parasitic — draining resources from their host and forcing it to self-destruct if it tries to expel its molecular hitch-hiker. It seems as if nowhere is safe: from soil to sea to the most inhospitable places on the planet, genetic invaders are present.

Prokaryotes have evolved a slew of weapons to cope with these threats. Restriction enzymes, for example, are proteins that cut DNA at or near a specific sequence. But these defences are blunt. Each enzyme is programmed to recognize certain sequences, and a microbe is protected only if it has a copy of the right gene. CRISPR–Cas is more dynamic. It adapts to and remembers specific genetic invaders in a similar way to how human antibodies provide long-term immunity after an infection. “When we first heard about this hypothesis, we thought that would be way too sophisticated for simple prokaryotes,” says microbiologist John van der Oost of Wageningen University in the Netherlands.

Mojica and others deduced the function of CRISPR–Cas when they saw that DNA in the spaces between CRISPR's palindromic repeats sometimes matches sequences in viral genomes. Since then, researchers have worked out that certain CRISPR-associated (Cas) proteins add these spacer sequences to the genome after bacteria and archaea are exposed to specific viruses or plasmids. RNA made from those spacers directs other Cas proteins to chew up any invading DNA or RNA that matches the sequence (see 'Lasting protection').

How did bacteria and archaea come to possess such sophisticated immune systems? That question has yet to be answered, but the leading theory is that the systems are derived from transposons — 'jumping genes' that can hop from one position to another in the genome. Evolutionary biologist Eugene Koonin of the US National Institutes of Health in Bethesda, Maryland, and his colleagues have found1 a class of these mobile genetic elements that encodes the protein Cas1, which is involved in inserting spacers into the genome. These 'casposons', he reasons, could have been the origin of CRISPR–Cas immunity. Researchers are now working to understand how these bits of DNA hop from one place to another — and then to track how that mechanism may have led to the sophistication of CRISPR–Cas.
...

FREE PDF GRATIS: Nature

Os primeiros humanos chegaram mais cedo à América do Norte do que antes "crido" pelos cientistas

Earliest Human Presence in North America Dated to the Last Glacial Maximum: New Radiocarbon Dates from Bluefish Caves, Canada

Lauriane Bourgeon , Ariane Burke, Thomas Higham

Published: January 6, 2017


Fig 1. Cut marks on a horse mandible from Cave II.

Abstract

The timing of the first entry of humans into North America is still hotly debated within the scientific community. Excavations conducted at Bluefish Caves (Yukon Territory) from 1977 to 1987 yielded a series of radiocarbon dates that led archaeologists to propose that the initial dispersal of human groups into Eastern Beringia (Alaska and the Yukon Territory) occurred during the Last Glacial Maximum (LGM). This hypothesis proved highly controversial in the absence of other sites of similar age and concerns about the stratigraphy and anthropogenic signature of the bone assemblages that yielded the dates. The weight of the available archaeological evidence suggests that the first peopling of North America occurred ca. 14,000 cal BP (calibrated years Before Present), i.e., well after the LGM. Here, we report new AMS radiocarbon dates obtained on cut-marked bone samples identified during a comprehensive taphonomic analysis of the Bluefish Caves fauna. Our results demonstrate that humans occupied the site as early as 24,000 cal BP (19,650 ± 130 14C BP). In addition to proving that Bluefish Caves is the oldest known archaeological site in North America, the results offer archaeological support for the “Beringian standstill hypothesis”, which proposes that a genetically isolated human population persisted in Beringia during the LGM and dispersed from there to North and South America during the post-LGM period.

Fig 2. Cut marks on a caribou coxal bone from Cave II.

Citation: Bourgeon L, Burke A, Higham T (2017) Earliest Human Presence in North America Dated to the Last Glacial Maximum: New Radiocarbon Dates from Bluefish Caves, Canada. PLoS ONE 12(1): e0169486. 

Editor: John P. Hart, New York State Museum, UNITED STATES

Received: September 9, 2016; Accepted: December 16, 2016; Published: January 6, 2017

Copyright: © 2017 Bourgeon 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 file.

Funding: Support was provided by Fonds de Recherche Québécois Société et Culture (2015-SE-179537), grant received by AB.

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

FREE PDF GRATIS: PLoS One

O neoproterozóico (entre 1 bilhão e 541 milhões de anos atrás)

The Neoproterozoic

Nicholas J. ButterfieldemailPress enter key to Email the author

Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ, UK

Open Archive

DOI: http://dx.doi.org/10.1016/j.cub.2015.07.021


Summary

The Neoproterozoic era was arguably the most revolutionary in Earth history. Extending from 1000 to 541 million years ago, it stands at the intersection of the two great tracts of evolutionary time: on the one side, some three billion years of pervasively microbial ‘Precambrian’ life, and on the other the modern ‘Phanerozoic’ biosphere with its extraordinary diversity of large multicellular organisms. The disturbance doesn’t stop here, however: over this same stretch of time the planet itself was in the throes of change. Tectonically, it saw major super-continental reconfigurations, climatically its deepest ever glacial freeze, and geochemically some of the most anomalous perturbations on record. What lies behind this dramatic convergence of biological and geological phenomena, and how exactly did it give rise to the curiously complex world that we now inhabit?


© 2015 Elsevier Ltd. Published by Elsevier Inc.

FREE PDF GRATIS: Current Biology

Darwin, o tempo não se correlaciona com o modo evolucionário encontrado no registro fóssil

domingo, janeiro 15, 2017

Tempo does not correlate with mode in the fossil record

Kjetil Lysne Voje

First published: 9 November 2016 Full publication history


Volume 70, Issue 12, December 2016, Pages 2678–2689


Abstract

The dominating view of evolution based on the fossil record is that established species remain more or less unaltered during their existence. Substantial evolution is on the other hand routinely reported for contemporary populations, and most quantitative traits show high potential for evolution. These contrasting observations on long- and short-time scales are often referred to as the paradox of stasis, which rests on the fundamental assumption that periods of morphological stasis in the fossil record represent minimal evolutionary change. Investigating 450 fossil time series, I demonstrate that the nonaccumulating morphological fluctuations during stasis travel similar distances in morphospace compared to lineages showing directional change. Hence, lineages showing stasis are commonly undergoing considerable amounts of evolution, but this evolution does not accumulate to produce large net evolutionary changes over time. Rates of evolutionary change across modes in the fossil record may be more homogenous than previously assumed and advocated, supporting the claim that substantial evolution is not exclusively or causally linked to the process of speciation. Instead of exemplifying minimal evolution, stasis likely represents information on the dynamics of the adaptive landscape on macroevolutionary time scales, including the persistence of adaptive zones and ecological niches over millions of years.

+++++

Subscription or payment needed/Requer assinatura ou pagamento: Evolution

+++++

Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente o artigo da Evolution e de mais 30.000 publicações científicas.

Gorduras simples e aminoácidos para explicar a origem da vida

sábado, janeiro 14, 2017

Fatty acids' double role in the prebiotic formation of a hydrophobic dipeptide

Sara Murillo-Sánchez, a Damien Beaufils, b Juan Manuel González Mañas, c Robert Pascal *b and Kepa Ruiz-Mirazo *ad 

Show Affiliations

Chem. Sci., 2016,7, 3406-3413


Received 11 Dec 2015, Accepted 09 Feb 2016

First published online 09 Feb 2016 This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.

Image of the supramolecular structures formed by fatty acids in an aqueous environment taken using the cryo electron microscopy technique-TEM.
Credit: Adela Rendón, in collaboration with CIC-BioGUNE

Abstract

In search of a connection between prebiotic peptide chemistry and lipid compartments, the reaction of a 5(4H)-oxazolone with leucinamide was extensively explored under buffered aqueous conditions, where diverse amphiphiles and surfactants could form supramolecular assemblies. Significant increases in yield and changes in stereoselectivity were observed when fatty acids exceeded their critical aggregation concentration, self-assembling into vesicles in particular. This effect does not take place below the fatty acid solubility limit, or when other anionic amphiphiles/surfactants are used. Data from fluorimetric and Langmuir trough assays, complementary to the main HPLC results reported here, demonstrate that the dipeptide product co-localizes with fatty acid bilayers and monolayers. Additional experiments in organic solvents suggest that acid–base catalysis operates at the water–aggregate interface, linked to the continuous proton exchange dynamics that fatty acids undergo at pH values around their effective pKa. These simple amphiphiles could therefore play a dual role as enhancers of peptide chemistry under prebiotic conditions, providing soft and hydrophobic organic domains through self-assembly and actively inducing catalysis at their interface with the aqueous environment. Our results support a systems chemistry approach to life's origin.

FREE PDF GRATIS: Chemical Science Sup. Info.