As células "calculam" as proporções para controlar a expressão de genes: mero acaso, fortuita necessidade ou design inteligente?

Sensing relative signal in the Tgf-β/Smad pathway

Christopher L. Frick a,1, Clare Yarka a, Harry Nunns a, and Lea Goentoro a,1 

Author Affiliations

a Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125

Edited by Arup K. Chakraborty, Massachusetts Institute of Technology, Cambridge, MA, and approved February 3, 2017 (received for review July 12, 2016)

Significance

It is not fully understood how cells process information in the face of noise. We posed this question in the transforming growth factor-β (Tgf-β) pathway, a major intercellular signaling pathway in animal cells. We found evidence that rather than sensing the signaling state of the Tgf-β pathway, cells sense the signaling state relative to background. Finding that signaling dynamics are interpreted in a relative manner may have implications for how we understand the pathway’s context-dependent outcomes and roles in diseases. Our work reinforces an emerging principle that individual cells process signal in a relative manner.

Abstract

How signaling pathways function reliably despite cellular variation remains a question in many systems. In the transforming growth factor-β (Tgf-β) pathway, exposure to ligand stimulates nuclear localization of Smad proteins, which then regulate target gene expression. Examining Smad3 dynamics in live reporter cells, we found evidence for fold-change detection. Although the level of nuclear Smad3 varied across cells, the fold change in the level of nuclear Smad3 was a more precise outcome of ligand stimulation. The precision of the fold-change response was observed throughout the signaling duration and across Tgf-β doses, and significantly increased the information transduction capacity of the pathway. Using single-molecule FISH, we further observed that expression of Smad3 target genes (ctgf, snai1, and wnt9a) correlated more strongly with the fold change, rather than the level, of nuclear Smad3. These findings suggest that some target genes sense Smad3 level relative to background, as a strategy for coping with cellular noise.

signal transduction fold-change detection Tgf-β Smad information

Footnotes

1 To whom correspondence may be addressed. Email: goentoro@caltech.edu or cfrick@caltech.edu.

Author contributions: C.L.F. and L.G. designed research; C.L.F. and C.Y. performed research; H.N. contributed new reagents/analytic tools; C.L.F. and C.Y. analyzed data; and C.L.F. and L.G. wrote the paper.

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.1611428114/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Reinaldo Lopes, Folha de São Paulo, joga pedra na Geni, oops, na TDI

Universidade Mackenzie de SP abre centro que questiona a evolução.

Fernanda Perrin - Folhapress

Um texto mequetrefe, enviesado e em descompasso com a verdade sobre a TDI, de Reinaldo José Lopes, para a Folha de São Paulo, um jornalista científico com uma agenda a defender: o naturalismo filosófico.

Neddy vai se debruçar sobre o panfleto nitidamente ideológico e responder à falta de objetividade jornalística - reportar sobre o evento. 

Ah, ele precisa aprender pelo menos uma coisa bem basilar - consenso não é uma coisa boa em ciência. Consenso é coisa de político, e nós sabemos no que tem dado isso. A ciência só avança porque há os que contradizem os paradigmas!

Acoplamento químico-mecânico perfeito de FoF1-ATP sintase: mero acaso, fortuita necessidade ou design inteligente?

Perfect chemomechanical coupling of FoF1-ATP synthase

Naoki Soga a,1, Kazuya Kimura a, Kazuhiko Kinosita, Jr. a, Masasuke Yoshida b, and Toshiharu Suzuki a,b,1,2  

Author Affiliations

a Department of Physics, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan;

b Department of Molecular Bioscience, Kyoto Sangyo University, Kyoto 603-8555, Japan

Edited by Pierre A. Joliot, Institut de Biologie Physico-Chimique, Paris, France, and approved April 4, 2017 (received for review January 20, 2017)

Source/Fonte: “ATP Synthase: The Power Plant of the Cell.”

Significance

Peter D. Mitchell, a Nobel awardee in 1978, proposed that FoF1-ATP synthase converts energy between electrochemical potential of H+ across biological membrane (Δμ∼H+Δμ∼H+), which is established by respiratory chain complexes, and chemical potential of adenine nucleotide [ΔG(ATP)]. However, the efficiency of the energy conversion has been a matter of debate for over 50 years. In this study, with a highly reproducible analytical system using FoF1-ATP synthase from thermophilic Bacillus, apparently perfect energy conversion was observed. Mitchell’s prediction thus has quantitative evidence.

Abstract

FoF1-ATP synthase (FoF1) couples H+ flow in Fo domain and ATP synthesis/hydrolysis in F1 domain through rotation of the central rotor shaft, and the H+/ATP ratio is crucial to understand the coupling mechanism and energy yield in cells. Although H+/ATP ratio of the perfectly coupling enzyme can be predicted from the copy number of catalytic β subunits and that of H+ binding c subunits as c/β, the actual H+/ATP ratio can vary depending on coupling efficiency. Here, we report actual H+/ATP ratio of thermophilic Bacillus FoF1, whose c/β is 10/3. Proteoliposomes reconstituted with the FoF1 were energized with ΔpH and Δψ by the acid−base transition and by valinomycin-mediated diffusion potential of K+ under various [ATP]/([ADP]⋅[Pi]) conditions, and the initial rate of ATP synthesis/hydrolysis was measured. Analyses of thermodynamically equilibrated states, where net ATP synthesis/hydrolysis is zero, show linear correlation between the chemical potential of ATP synthesis/hydrolysis and the proton motive force, giving the slope of the linear function, that is, H+/ATP ratio, 3.3 ± 0.1. This value agrees well with the c/β ratio. Thus, chemomechanical coupling between Fo and F1 is perfect.

FoF1-ATP synthase chemiosmotic coupling theory ATPase proton motive force electrochemical potential

Footnotes

1 Present address: Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan.

2 To whom correspondence should be addressed. Email: toshisuz@appchem.t.u-tokyo.ac.jp.

Author contributions: N.S., K. Kinosita, M.Y., and T.S. designed research; N.S. and K. Kimura performed research; N.S. and T.S. analyzed data; and N.S., M.Y., and T.S. wrote the paper.

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.1700801114/-/DCSupplemental.

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NOTA DESTE BLOGGER:

Os autores usaram a palavra "perfect" treze vezes no artigo, o que é incomum em artigos científicos, mas esses japoneses ousaram seguir a evidência aonde ela os estava levando: complexidade absurda que o mero acaso e a fortuita necessidade não conseguem explicar. Restou o que? Design Inteligente!!!

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Sinais mais antigos de vida na Terra preservados em fontes termais de cerca de 3.5 bilhões de anos: ponto para Darwin?

Earliest signs of life on land preserved in ca. 3.5 Ga hot spring deposits

Tara Djokic, Martin J. Van Kranendonk, Kathleen A. Campbell, Malcolm R. Walter & Colin R. Ward

Nature Communications 8, Article number: 15263 (2017)

doi: 10.1038/ncomms15263 

Download Citation

Microbiology Chemical origin of life Palaeontology Precambrian geology

Received: 18 July 2016 Accepted: 15 March 2017

Published online: 09 May 2017

Abstract

The ca. 3.48 Ga Dresser Formation, Pilbara Craton, Western Australia, is well known for hosting some of Earth’s earliest convincing evidence of life (stromatolites, fractionated sulfur/carbon isotopes, microfossils) within a dynamic, low-eruptive volcanic caldera affected by voluminous hydrothermal fluid circulation. However, missing from the caldera model were surface manifestations of the volcanic-hydrothermal system (hot springs, geysers) and their unequivocal link with life. Here we present new discoveries of hot spring deposits including geyserite, sinter terracettes and mineralized remnants of hot spring pools/vents, all of which preserve a suite of microbial biosignatures indicative of the earliest life on land. These include stromatolites, newly observed microbial palisade fabric and gas bubbles preserved in inferred mineralized, exopolymeric substance. These findings extend the known geological record of inhabited terrestrial hot springs on Earth by ∼3 billion years and offer an analogue in the search for potential fossil life in ancient Martian hot springs.

Acknowledgements

Many thanks to: J. Reinter for discussion and assistance with Raman spectroscopic data; C. Marjo for assistance with Raman spectroscopic data; K. Privat for assistance with SEM-EDS data and the electron microscope unit, UNSW. Research support provided by the Australian Centre for Astrobiology and School of Biological, Earth and Environmental Sciences at the University of New South Wales, the Sloan Foundation and the ARC Centre for excellence Core to Crust Fluid Systems. Phanerozoic hot spring comparative studies were supported by funding to K.A.C. from the New Zealand government (RSNZ Marsden Fund and Ministry of Business, Innovation and Employment) and the National Geographic Society. Gigapan image generated by Ken Williford and the abcLab, Jet Propulsion Laboratory, California Institute of Technology. Kind hospitality in the field was provided by Faye and Geoff Myers, and Haoma Mining.

Author information

Affiliations

Australian Centre for Astrobiology, PANGEA Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales 2052, Australia

Tara Djokic, Martin J. Van Kranendonk & Malcolm R. Walter

Australian Research Council Centre of Excellence for Core to Crust Fluid Systems (CCFS), Macquarie University, New South Wales 2109, Australia

Tara Djokic & Martin J. Van Kranendonk

Big Questions Institute, University of New South Wales Australia, Kensington, New South Wales, 2052 Australia

Martin J. Van Kranendonk

School of Environment, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand

Kathleen A. Campbell

School of Biological, Earth and Environmental Sciences, University of New South Wales Australia, Kensington, New South Wales 2052, Australia

Colin R. Ward

Contributions

The methodology was conceived and designed by T.D. and M.J.V.K. Geological mapping was carried out by T.D. and M.J.V.K. Petrographic analyses were carried out by T.D., M.J.V.K., K.A.C. and M.R.W. SEM-EDS data were acquired and interpreted by T.D. and M.J.V.K. XRD analysis spectra were acquired by C.R.W. All authors contributed to discussion, interpretation and writing.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Tara Djokic.

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A arma secreta do DNA contra nós e emaranhados: mero acaso, fortuita necessidade ou design inteligente?

DNA's secret weapon against knots and tangles

A simple process seems to explain how massive genomes stay organized. But no one can agree on what powers it.

Elie Dolgin

19 April 2017

Leonid Mirny swivels in his office chair and grabs the power cord for his laptop. He practically bounces in his seat as he threads the cable through his fingers, creating a doughnut-sized loop. “It's a dynamic process of motors constantly extruding loops!” says Mirny, a biophysicist here at the Massachusetts Institute of Technology in Cambridge.

Mirny's excitement isn't about keeping computer accessories orderly. Rather, he's talking about a central organizing principle of the genome — how roughly 2 metres of DNA can be squeezed into nearly every cell of the human body without getting tangled up like last year's Christmas lights.

Source/Fonte: Mirny Lab

He argues that DNA is constantly being slipped through ring-like motor proteins to make loops. This process, called loop extrusion, helps to keep local regions of DNA together, disentangling them from other parts of the genome and even giving shape and structure to the chromosomes.

Scientists have bandied about similar hypotheses for decades, but Mirny's model, and a similar one championed by Erez Lieberman Aiden, a geneticist at Baylor College of Medicine in Houston, Texas, add a new level of molecular detail at a time of explosive growth for research into the 3D structure of the genome. The models neatly explain the data flowing from high-profile projects on how different parts of the genome interact physically — which is why they've garnered so much attention.

But these simple explanations are not without controversy. Although it has become increasingly clear that genome looping regulates gene expression, possibly contributing to cell development and diseases such as cancer, the predictions of the models go beyond what anyone has ever seen experimentally.

For one thing, the identity of the molecular machine that forms the loops remains a mystery. If the leading protein candidate acted like a motor, as Mirny proposes, it would guzzle energy faster than it has ever been seen to do. “As a physicist friend of mine tells me, 'This is kind of the Higgs boson of your field',” says Mirny; it explains one of the deepest mysteries of genome biology, but could take years to prove.

And although Mirny's model is extremely similar to Lieberman Aiden's — and the differences esoteric — sorting out which is right is more than a matter of tying up loose ends. If Mirny is correct, “it's a complete revolution in DNA enzymology”, says Kim Nasmyth, a leading chromosome researcher at the University of Oxford, UK. What's actually powering the loop formation, he adds, “has got to be the biggest problem in genome biology right now”.

...

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Darwin, são princípios de design que regem o acoplamento químico-mecânico de cinesina

Design principles governing chemomechanical coupling of kinesin

Tomonari Sumi

Scientific Reports 7, Article number: 1163 (2017)

doi: 10.1038/s41598-017-01328-9  

Download Citation

Biophysical chemistry Motor protein function Motor protein regulation

Received: 13 October 2016 Accepted: 28 March 2017 Published online: 25 April 2017

Source/Fonte - “ATP Synthase: The Power Plant of the Cell.”

Abstract

A systematic chemomechanical network model for the molecular motor kinesin is presented in this report. The network model is based on the nucleotide-dependent binding affinity of the heads to an microtubule (MT) and the asymmetries and similarities between the chemical transitions caused by the intramolecular strain between the front and rear heads. The network model allows for multiple chemomechanical cycles and takes into account all possible mechanical transitions between states in which one head is strongly bound and the other head is weakly bound to an MT. The results obtained from the model show the ATP-concentration dependence of the dominant forward stepping cycle and support a gated rear head mechanism in which the forward step is controlled by ATP hydrolysis and the resulting ADP-bound state of the rear head when the ATP level is saturated. When the ATP level is saturated, the energy from ATP hydrolysis is used to concentrate the chemical transition flux to a force-generating state that can produce the power stroke. In contrast, when the ATP level is low, the hydrolysis energy is consumed to avoid states in which the leading head is weakly bound to an MT and to inhibit frequent backward steps upon loading.

Acknowledgements

This work was supported by the Grants-in-Aid for Scientific Research (KAKENHI) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. I would like to thank Prof. Stefan Klumpp in Georg-August-Universität Göttingen for extensive discussion about the chemomechanical network modeling and an extension of the steady state balance condition. I would also like to thank Prof. Michio Tomishige in Tokyo University for useful discussions. I also thank Enago (www.enago.jp) for the English language review.

Author information

Affiliations

Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan

Tomonari Sumi

Department of Chemistry, Faculty of Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama, 700-8530, Japan

Tomonari Sumi

Competing Interests

The authors declare that they have no competing interests.

Corresponding author

Correspondence to Tomonari Sumi.

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O Homo naledi não tem 2-3 milhões de anos de idade - é apenas um jovem de 236 a 335 mil anos de idade!

The age of Homo naledi and associated sediments in the Rising Star Cave, South Africa

Paul HGM Dirks Eric M Roberts Hannah Hilbert-Wolf Jan D Kramers John Hawks Anthony Dosseto Mathieu Duval Marina Elliott Mary Evans Rainer Grün John Hellstrom Andy IR Herries Renaud Joannes-Boyau Tebogo V Makhubela Christa J Placzek Jessie Robbins Carl Spandler Jelle Wiersma Jon Woodhead Lee R Berger

James Cook University, Australia; University of the Witwatersrand, South Africa; University of Johannesburg, South Africa; University of Wisconsin-Madison, United States; University of Wollongong, Australia; Environmental Futures Research Institute, Griffith University, Australia; Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Spain; The Australian National University, Australia; The University of Melbourne, Australia; La Trobe University, Australia; Southern Cross University, Australia

DOI: http://dx.doi.org/10.7554/eLife.24231

Published May 9, 2017

Cite as eLife 2017;6:e24231

Source/Fonte: University of Wisconsin S. V. Medaris

Abstract

New ages for flowstone, sediments and fossil bones from the Dinaledi Chamber are presented. We combined optically stimulated luminescence dating of sediments with U-Th and palaeomagnetic analyses of flowstones to establish that all sediments containing Homo naledi fossils can be allocated to a single stratigraphic entity (sub-unit 3b), interpreted to be deposited between 236 ka and 414 ka. This result has been confirmed independently by dating three H. naledi teeth with combined U-series and electron spin resonance (US-ESR) dating. Two dating scenarios for the fossils were tested by varying the assumed levels of 222Rn loss in the encasing sediments: a maximum age scenario provides an average age for the two least altered fossil teeth of 253 +82/–70 ka, whilst a minimum age scenario yields an average age of 200 +70/–61 ka. We consider the maximum age scenario to more closely reflect conditions in the cave, and therefore, the true age of the fossils. By combining the US-ESR maximum age estimate obtained from the teeth, with the U-Th age for the oldest flowstone overlying Homo naledi fossils, we have constrained the depositional age of Homo naledi to a period between 236 ka and 335 ka. These age results demonstrate that a morphologically primitive hominin, Homo naledi, survived into the later parts of the Pleistocene in Africa, and indicate a much younger age for the Homo naledi fossils than have previously been hypothesized based on their morphology.

DOI: http://dx.doi.org/10.7554/eLife.24231.001

eLife digest

Species of ancient humans and the extinct relatives of our ancestors are typically described from a limited number of fossils. However, this was not the case with Homo naledi. More than 1500 fossils representing at least 15 individuals of this species were unearthed from the Rising Star cave system in South Africa between 2013 and 2014. Found deep underground in the Dinaledi Chamber, the H. naledi fossils are the largest collection of a single species of an ancient human-relative discovered in Africa.

After the discovery was reported, a number of questions still remained. Not least among these questions was: how old were the fossils? The material was undated, and predictions ranged from anywhere between 2 million years old and 100,000 years old. H. naledi shared several traits with the most primitive of our ancient relatives, including its small brain. As a result, many scientists guessed that H. naledi was an old species in our family tree, and possibly one of the earliest species to evolve in the genus Homo.

Now, Dirks et al. – who include many of the researchers who were involved in the discovery of H. naledi – report that the fossils are most likely between 236,000 and 335,000 years old. These dates are based on measuring the concentration of radioactive elements, and the damage caused by these elements (which accumulates over time), in three fossilized teeth, plus surrounding rock and sediments from the cave chamber. Importantly, the most crucial tests were carried out at independent laboratories around the world, and the scientists conducted the tests without knowing the results of the other laboratories. Dirks et al. took these extra steps to make sure that the results obtained were reproducible and unbiased.

The estimated dates are much more recent than many had predicted, and mean that H. naledi was alive at the same time as the earliest members of our own species – which most likely evolved between 300,000 and 200,000 years ago. These new findings demonstrate why it can be unwise to try to predict the age of a fossil based only on its appearance, and emphasize the importance of dating specimens via independent tests. Finally in two related reports, Berger et al. suggest how a primitive-looking species like H. naledi survived more recently than many would have predicted, while Hawks et al. describe the discovery of more H. naledi fossils from a separate chamber in the same cave system.

DOI: http://dx.doi.org/10.7554/eLife.24231.002

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Darwin, macacos nos mordam: transferência horizontal maciça de elementos transponíveis em insetos

Massive horizontal transfer of transposable elements in insects

Jean Peccouda,1, Vincent Loiseaua, Richard Cordauxa, and Clément Gilberta,1

 

Author Affiliations

Edited by Nancy L. Craig, Johns Hopkins University School of Medicine, Baltimore, MD, and approved March 20, 2017 (received for review December 22, 2016)

Significance

Eukaryotes normally receive their genetic material from their parents but may occasionally, like prokaryotes do, acquire DNA from unrelated organisms through horizontal transfer (HT). In animals and plants, HT mostly concerns transposable elements (TEs), probably because these pieces of DNA can move within genomes. Assessing the impact of HTs on eukaryote evolution and the factors shaping the dynamics of these HTs requires large-scale systematic studies. We have analyzed the genomes from 195 insect species and found that no fewer than 2,248 events of HT of TEs occurred during the last 10 My, particularly between insects that were closely related and geographically close. These results suggest that HT of TEs plays a major role in insect genome evolution.

Abstract

Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24% (2.08% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.

horizontal transfer transposable elements insects genome evolution biogeography

Footnotes

1To whom correspondence may be addressed. Email: clement.gilbert30@gmail.com or jean.peccoud@univ-poitiers.fr.

Author contributions: J.P., R.C., and C.G. designed research; J.P., V.L., and C.G. performed research; J.P. and V.L. analyzed data; and J.P., R.C., and C.G. wrote the paper.

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.1621178114/-/DCSupplemental.

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Pobre Darwin, mais complexidade: nematocistos balísticos em dinoflagelados representam um novo extremo em complexidade de organelas!

Microbial arms race: Ballistic “nematocysts” in dinoflagellates represent a new extreme in organelle complexity

Gregory S. Gavelis1,2,*,†, Kevin C. Wakeman3,4, Urban Tillmann5, Christina Ripken6, Satoshi Mitarai6, Maria Herranz1, Suat Özbek7, Thomas Holstein7, Patrick J. Keeling1 and Brian S. Leander1,2

+ See all authors and affiliations

Science Advances 31 Mar 2017:

Vol. 3, no. 3, e1602552

DOI: 10.1126/sciadv.1602552

Abstract

We examine the origin of harpoon-like secretory organelles (nematocysts) in dinoflagellate protists. These ballistic organelles have been hypothesized to be homologous to similarly complex structures in animals (cnidarians); but we show, using structural, functional, and phylogenomic data, that nematocysts evolved independently in both lineages. We also recorded the first high-resolution videos of nematocyst discharge in dinoflagellates. Unexpectedly, our data suggest that different types of dinoflagellate nematocysts use two fundamentally different types of ballistic mechanisms: one type relies on a single pressurized capsule for propulsion, whereas the other type launches 11 to 15 projectiles from an arrangement similar to a Gatling gun. Despite their radical structural differences, these nematocysts share a single origin within dinoflagellates and both potentially use a contraction-based mechanism to generate ballistic force. The diversity of traits in dinoflagellate nematocysts demonstrates a stepwise route by which simple secretory structures diversified to yield elaborate subcellular weaponry.

Keywords Convergent evolution cnidocyst extrusome secretory secretion minicollagen mucocyst trichocyst red queen

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Darwin, mais complexidade especificada: o DNA é um código triplo de triplos!!!

Case for the genetic code as a triplet of triplets

Fabienne F. V. Chevance a and Kelly T. Hughes a,1 

Author Affiliations

Edited by John R. Roth, University of California, Davis, CA, and approved March 21, 2017 (received for review September 5, 2016)

Source/Fonte

Significance

The genetic code for life is a triplet base code. It is known that adjacent codons can influence translation of a given codon and that codon pair biases occur throughout nature. We show that mRNA translation at a given codon can be affected by the two previous codons. Data presented here support a model in which the evolutionary selection pressure on a single codon is over five successive codons, including synonymous codons. This work provides a foundation for the interpretation of how single DNA base changes might affect translation over multiple codons and should be considered in the characterization of the effects of DNA base changes on human disease.

Abstract

The efficiency of codon translation in vivo is controlled by many factors, including codon context. At a site early in the Salmonella flgM gene, the effects on translation of replacing codons Thr6 and Pro8 of flgM with synonymous alternates produced a 600-fold range in FlgM activity. Synonymous changes at Thr6 and Leu9 resulted in a twofold range in FlgM activity. The level of FlgM activity produced by any codon arrangement was directly proportional to the degree of in vivo ribosome stalling at synonymous codons. Synonymous codon suppressors that corrected the effect of a translation-defective synonymous flgM allele were restricted to two codons flanking the translation-defective codon. The various codon arrangements had no apparent effects on flgM mRNA stability or predicted mRNA secondary structures. Our data suggest that efficient mRNA translation is determined by a triplet-of-triplet genetic code. That is, the efficiency of translating a particular codon is influenced by the nature of the immediately adjacent flanking codons. A model explains these codon-context effects by suggesting that codon recognition by elongation factor-bound aminoacyl-tRNA is initiated by hydrogen bond interactions between the first two nucleotides of the codon and anticodon and then is stabilized by base-stacking energy over three successive codons.

translation genetic code context effects on translation tRNA synonymous codon effects

Footnotes

1To whom correspondence should be addressed. Email: hughes@biology.utah.edu.

Author contributions: F.F.V.C. and K.T.H. designed research, performed research, and wrote the paper.

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.1614896114/-/DCSupplemental.

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Assédios sexuais e estupros na Academia - no Brasil não tem disso não! Será???

Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault

Kathryn B. H. Clancy , Robin G. Nelson, Julienne N. Rutherford, Katie Hinde

Published: July 16, 2014 https://doi.org/10.1371/journal.pone.0102172

Source/Fonte: Equality Archive

Abstract

Little is known about the climate of the scientific fieldwork setting as it relates to gendered experiences, sexual harassment, and sexual assault. We conducted an internet-based survey of field scientists (N = 666) to characterize these experiences. Codes of conduct and sexual harassment policies were not regularly encountered by respondents, while harassment and assault were commonly experienced by respondents during trainee career stages. Women trainees were the primary targets; their perpetrators were predominantly senior to them professionally within the research team. Male trainees were more often targeted by their peers at the research site. Few respondents were aware of mechanisms to report incidents; most who did report were unsatisfied with the outcome. These findings suggest that policies emphasizing safety, inclusivity, and collegiality have the potential to improve field experiences of a diversity of researchers, especially during early career stages. These include better awareness of mechanisms for direct and oblique reporting of harassment and assault and, the implementation of productive response mechanisms when such behaviors are reported. Principal investigators are particularly well positioned to influence workplace culture at their field sites.

Citation: Clancy KBH, Nelson RG, Rutherford JN, Hinde K (2014) Survey of Academic Field Experiences (SAFE): Trainees Report Harassment and Assault. PLoS ONE 9(7): e102172. https://doi.org/10.1371/journal.pone.0102172

Editor: Coren Lee Apicella, University of Pennsylvania, United States of America

Received: April 2, 2014; Accepted: June 14, 2014; Published: July 16, 2014

Copyright: © 2014 Clancy 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: The authors confirm that, for approved reasons, some access restrictions apply to the data underlying the findings. The data used in this project stem from a survey about people's experiences with sexual harassment and sexual assault. The sensitive nature of these data – and the fact that, because so many field sciences are small, combinations of discipline/country of origin/gender/sexuality/ethnicity can make a person uniquely identifying – mean that the Authors will not be sharing this data publicly. The limited, de-identified data may be available by contacting the corresponding author at kclancy@illinois.edu.

Funding: Financial support was provided by start-up funds from the University of Illinois, Urbana-Champaign Department of Anthropology and Institute for Genomic Biology (KC), Academic Senate funds from the University of California, Riverside, and start-up funds from Skidmore College (RN), K12HD055892 (National Institutes of Health Building Interdisciplinary Research Careers in Women's Health Program (JR)), and start-up funds from Harvard University (KH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

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Universidade Presbiteriana Mackenzie lança novo centro sobre o Design Inteligente

Universidade Mackenzie do Brasil vai lançar novo centro sobre Design Inteligente

Evolution News | @DiscoveryCSC

2 de maio de 2017, 11:28 AM

Esta semana, uma das mais prestigiadas universidades privadas do Brasil vai lançar um centro acadêmico sobre Design Inteligente em conjunto com o Discovery Institute.

Nesta sexta-feira e sábado vindouros, 5-6 de maio, a Universidade Presbiteriana Mackenzie em São Paulo vai inaugurar o Discovery Institute-Mackenzie, um centro de pesquisa interdisciplinar da universidade que promoverá pesquisa científica dentro do design inteligente na natureza, bem como explorar a relação entre a ciência e a cultura, incluindo a relação entre a ciência e a fé.

“Isto é um marco histórico no debate sobre as origens, e testifica para a crescente influência no mundo inteiro tanto do design inteligente e o Discovery Institute,” disse Steve Buri, presidente do Discovery Institute.

Buri assistirá as festividades de inauguração para o novo centro juntamente com o professor de Bioquímica da Universidade Lehigh (e membro sênior do CSC) Michael Behe; o biólogo molecular e diretor do Biologic Institute, Douglas Axe; o físico e coordenador de pesquisa do CSC, Brian Miller. Uma recepção e encontro sexta-feira à noite serão seguidos de uma conferência sobre o Design Inteligente durante o sábado com apresentações de Behe, Axe, e Miller, além de cientistas brasileiros.

Discovery Institute-Mackenzie é um projeto conjunto da Universidade Mackenzie e da Sociedade Brasileira do Design Inteligente, que é dirigido pelo químico pesquisador Dr. Marcos Eberlin. Um membro da Academia Brasileira de Ciências, o Dr. Eberlin é um dos cientistas mais renomados no Brasil. Autor de mais de 700 artigos científicos, ele dirige pesquisas no Laboratório Thomson de Espectrometria de Massas que ele fundou na Universidade de Campinas, onde ele tem sido professor de Química no Instituto de Química. Durante sua carreira, ele tem supervisionado pessoalmente cerca de cientistas doutorandos e pós-doutorandos na área de química.

“Tem havido um crescimento fenomenal no design inteligente entre os jovens cientistas no Brasil”, disse Eberlin. “Com o lançamento do Discovery Institute-Mackenzie, o Brasil está preparado para fazer uma contribuição significante para o debate do design inteligente, não apenas no Brasil, mas ao redor do mundo”.

John West, Diretor Associado do CSC destacou que o Discovery Institute-Mackenzie é o resultado de vários anos de discussões com a liderança e corpo docente da Universidade Mackenzie, culminando em um acordo oficial de cooperação assinado ano passado.

Com mais de 40.000 alunos universitários e de pós-graduação, o Mackenzie é uma das mais velhas e mais respeitadas universidades no Brasil. Foi a primeira instituição educacional no Brasil a ser coeducacional, e desde o começo acolhe estudantes de todas as classes sociais, raças, e formações religiosas. O Mackenzie até ajudou introduzir o futebol no Brasil.

Discovery Institute-Mackenzie irá financiar pesquisa científica e acadêmica, realizar conferências, produzir programas de televisão e vídeos, publicar livros, e criar materiais educacionais.

“A Universidade Mackenzie fornece uma plataforma estratégica para alcançar mais de 200 milhões de pessoas no Brasil”, disse West. “Mas, mais do que isso, ela pode fornecer um modelo para outras instituições acadêmicas ao redor do mundo sobre como uma perspectiva de design inteligente pode encorajar pesquisa científica de primeira classe, bem como modelar uma relação construtiva entre a ciência e a cultura.”

Foto: Visão aérea de parte do campus da Universidade Presbiteriana Mackenzie de São Paulo, de charlesblack (trabalho próprio) [CC BY-SA 1.0], via Wikimedia Commons.

Popper, o Profeta: reinterpretações inteligentes escondem o Dogma Central do falsificacionismo?

”Não é amplamente conhecido que Popper deu uma palestra importante na Royal Society em 1986 intitulada “A new interpretation of Darwinism” (Uma nova interpretação do Darwinismo). Ela foi dada na presença com os laureado com o Prêmio Nobel, Sir Peter Medawar, Max Perutz e outras figuras, e ela deve ter chocado sua audiência. Ele propusera uma interpretação completamente radical do neodarwinismo, rejeitando essencialmente a Síntese Moderna ao propor que os organismos mesmos são a fonte dos processos criativos de evolução, e não as mutações aleatórias no DNA. Ele disse que o Darwinismo (mas eu tenho certeza que ele quis dizer neodarwinismo) não era tão errado quanto era seriamente incompleto. Ele viu que a transcrição reversa, que é o process que permite que segmentos do DNA sejam transportados de uma região do genoma através de um RNA intermediário, enfraquece imensamente o Dogma Central. Em particular, ela enfraquece o dogma em justificar a teoria do neodarwinismo desde ela muda o genomo da ideia de ler somente do neodarwinismo para o genoma ler-escrever.

Portanto, ele era profundamente desconfiado das manobras e redefinições sofisticadas para proteger da falsificação o dogma. Na sua visão de ciência de “conjecturas e refutações” é melhor reconhecer quando uma versão forte de uma teoria já foi refutada. A versão forte neodarwinista do Dogma Central fora refutada. Mas ele foi além do que isso. Ele viu que a transcrição reversa poderia ser uma das rotas através da qual os processos lamarckistas e reorganização completa dos genomas poderiam ocorrer. Novamente, o filósofo nele queria ver isso reconhecido, não escondido por detrás de uma rede de reinterpretações inteligentes.”

Denis Noble

“Dance to the Tune of Life - Biological Relativity”

página 199

”It is not widely known that Popper gave an important lecture to the Royal Society in 1986 entitled “A new interpretation of Darwinism”. It was given on the presence of Nobel laureates Sir Peter Medawar, Max Perutz and other figures, and it must have shocked his audience. He proposed a completely radical interpretation of Neo-Darwinism, essentially rejecting the Modern Synthesis by proposing that organisms themselves are the source of the creative processes of evolution, not random mutations in DNA. He said that Darwinism (but I am sure he meant Neo-Darwinism) was not so much wrong as seriously incomplete. He saw that reverse transcription, which is the process that allows DNA segments to be transported from one region of the genome to another via an RNA intermediate, greatly weakens the Central Dogma. In particular, it weakens the dogma in justifying Neo-Darwinism theory since it changes the genome from the read-only idea of Neo-Darwinism to a read-write genome.

He was therefore deeply suspicious of sophisticated manoeuvrings and redefinitions to protect the dogma from falsification. In his “conjectures and refutations” view of science it is better to acknowledge when a strong version of a theory has been refuted. The strong Neo-Darwinist interpretation of the Central Dogma was refuted. But he went further than this. He saw that reverse transcription could be one of the routes through which Lamarckian processes and wholesale reorganisation of genomes could occur. Again, the philosopher in him wanted to see this recognised, not hidden behind a web of clever re-interpretations.”

Denis Noble

“Dance to the Tune of Life - Biological Relativity”

page 199

A complexidade na natureza é muito, mas muito fácil de surgir - será mesmo???

Rich complex behaviour of self-assembled nanoparticles far from equilibrium

Serim Ilday, Ghaith Makey, Gursoy B. Akguc, Özgün Yavuz, Onur Tokel, Ihor Pavlov, Oguz Gülseren & F. Ömer Ilday

Nature Communications 8, Article number: 14942 (2017)

doi: 10.1038/ncomms14942 

Download Citation

Nonlinear phenomenaSelf-assembly

Received: 04 October 2016 Accepted: 13 February 2017

Published online: 26 April 2017

Source/Fonte: Research Perspectives

Abstract

A profoundly fundamental question at the interface between physics and biology remains open: what are the minimum requirements for emergence of complex behaviour from nonliving systems? Here, we address this question and report complex behaviour of tens to thousands of colloidal nanoparticles in a system designed to be as plain as possible: the system is driven far from equilibrium by ultrafast laser pulses that create spatiotemporal temperature gradients, inducing Marangoni flow that drags particles towards aggregation; strong Brownian motion, used as source of fluctuations, opposes aggregation. Nonlinear feedback mechanisms naturally arise between flow, aggregate and Brownian motion, allowing fast external control with minimal intervention. Consequently, complex behaviour, analogous to those seen in living organisms, emerges, whereby aggregates can self-sustain, self-regulate, self-replicate, self-heal and can be transferred from one location to another, all within seconds. Aggregates can comprise only one pattern or bifurcated patterns can coexist, compete, endure or perish.

Acknowledgements

This work was supported partially by the European Research Council (ERC) Consolidator Grant ERC-617521 NLL and TÜBITAK under project 115F110.

Author information

Affiliations

Department of Physics, Bilkent University, Ankara 06800, Turkey

Serim Ilday, Ghaith Makey, Gursoy B. Akguc, Onur Tokel, Ihor Pavlov, Oguz Gülseren & F. Ömer Ilday

Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey

Özgün Yavuz & F. Ömer Ilday

Contributions

S.I. designed the research and interpreted the results with help from F.Ö.I, O.G. and O.T. Experiments were performed by S.I., with help from G.M., Ö.Y. and I.P. Analytical model was developed by F.Ö.I. Numerical simulations were performed by G.B.A., S.I. and O.G. Image processing analyses were conducted by G.M.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Serim Ilday.

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