Problemas insuperáveis do surgimento do código genético em um mundo RNA

Insuperable Problems Of The Genetic Code Initially Emerging In An RNA World

Peter Wills, Charles Carter

doi: https://doi.org/10.1101/140657

This article is a preprint and has not been peer-reviewed [what does this mean?].

Source/Fonte: Friendly Atheist

Abstract

Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide-RNA world.

Copyright 

The copyright holder for this preprint is the author/funder. All rights reserved. No reuse allowed without permission.

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Dez regras simples para a estruturação de artigos científicos

Ten simple rules for structuring papers

Konrad P Kording,  Brett Mensh

doi: https://doi.org/10.1101/088278

This article is a preprint and has not been peer-reviewed [what does this mean?].

Source/Fonte

Abstract

Good scientific writing is essential to career development and to the progress of science. A well-structured manuscript allows readers and reviewers to get excited about the subject matter, to understand and verify the paper's contributions, and to integrate these contributions into a broader context. However, many scientists struggle with producing high-quality manuscripts and typically get little training in paper writing. Focusing on how readers consume information, we present a set of 10 simple rules to help you get across the main idea of your paper. These rules are designed to make your paper more influential and the process of writing more efficient and pleasurable.

Copyright

The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC 4.0 International license.

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Manuscript 101: um exercício de escrita baseado em dados

Manuscript 101: A Data-Driven Writing Exercise For Beginning Scientists

Michael A. Halbisen, Amy Ralston

doi: https://doi.org/10.1101/139204

This article is a preprint and has not been peer-reviewed [what does this mean?].

Abstract Info/History Metrics Supplementary material Preview PDF

Source/Fonte: The Balance

Abstract

Learning to write a scientific manuscript is one of the most important and rewarding scientific training experiences, yet most young scientists only embark on this experience relatively late in graduate school, after gathering sufficient data in the lab. Yet, familiarity with the process of writing a scientific manuscript and receiving peer reviews, often leads to a more focused and driven experimental approach. To jump-start this training, we developed a protocol for teaching manuscript writing and reviewing in the classroom, appropriate for new graduate or upper-level undergraduate students of developmental biology. First, students are provided one of four cartoon data sets, which are focused on genetic models of animal development. Students are instructed to use their creativity to convert evidence into argument, and then to integrate their interpretations into a manuscript, including an illustrated, mechanistic model figure. After student manuscripts are submitted, manuscripts are redacted and distributed to classmates for peer review. Here, we present our cartoon datasets, homework instructions, and grading rubrics as a new resource for the scientific community. We also describe methods for developing new datasets so that instructors can adapt this activity to other disciplines. Our data-driven manuscript writing exercise, as well as the formative and summative assessments resulting from the peer review, enables students to learn fundamental concepts in developmental genetics. In addition, students practice essential skills of scientific communication, including arguing from evidence, developing and testing models, the unique conventions of scientific writing, and the joys of scientific story telling.

Copyright 

The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC 4.0 International license.

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Os méritos científicos da teoria do Design Inteligente

Correção: este blogger é apenas mestre em História da Ciência pela PUC-São Paulo, e não Dr. como aparece no vídeo.

Pesquisadores descobrem contraceptivos perfeitos na medicina tradicional chinesa

Regulation of the sperm calcium channel CatSper by endogenous steroids and plant triterpenoids

Nadja Mannowetz a, Melissa R. Miller a, and Polina V. Lishko a,1

aDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720

Edited by David E. Clapham, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, and approved April 20, 2017 (received for review January 10, 2017)

Source/Fonte: WebMD

Significance

The calcium channel of sperm—CatSper—is vital for male fertility. CatSper is activated by the hormone progesterone, but its pharmacological profile is not well studied. By exploring steroid selectivity of CatSper activation, we found one additional agonist—pregnenolone sulfate—and the two plant-derived inhibitors pristimerin and lupeol. By averting sperm hyperactivation, both inhibitors can prevent fertilization, thus acting as contraceptive agents. Additionally, by exploring CatSper regulation by endogenous steroids, we explain why CatSper is silent within the male reproductive tract and is only activated in close proximity to the egg. Interestingly, both testosterone and hydrocortisone antagonize the action of progesterone at physiological concentrations, which may explain why elevated levels of these steroids in the female organism affect fertility.

Abstract

The calcium channel of sperm (CatSper) is essential for sperm hyperactivated motility and fertility. The steroid hormone progesterone activates CatSper of human sperm via binding to the serine hydrolase ABHD2. However, steroid specificity of ABHD2 has not been evaluated. Here, we explored whether steroid hormones to which human spermatozoa are exposed in the male and female genital tract influence CatSper activation via modulation of ABHD2. The results show that testosterone, estrogen, and hydrocortisone did not alter basal CatSper currents, whereas the neurosteroid pregnenolone sulfate exerted similar effects as progesterone, likely binding to the same site. However, physiological concentrations of testosterone and hydrocortisone inhibited CatSper activation by progesterone. Additionally, testosterone antagonized the effect of pregnenolone sulfate. We have also explored whether steroid-like molecules, such as the plant triterpenoids pristimerin and lupeol, affect sperm fertility. Interestingly, both compounds competed with progesterone and pregnenolone sulfate and significantly reduced CatSper activation by either steroid. Furthermore, pristimerin and lupeol considerably diminished hyperactivation of capacitated spermatozoa. These results indicate that (i) pregnenolone sulfate together with progesterone are the main steroids that activate CatSper and (ii) pristimerin and lupeol can act as contraceptive compounds by averting sperm hyperactivation, thus preventing fertilization.

CatSper steroids lupeol triterpenoids pristimerin

Footnotes

1To whom correspondence should be addressed. Email: lishko{at}berkeley.edu.

Author contributions: N.M. and P.V.L. designed research; N.M., M.R.M., and P.V.L. performed research; N.M. contributed new reagents/analytic tools; M.R.M. helped with pilot experiments; P.V.L. led the research study; N.M. and P.V.L. analyzed data; and N.M. and P.V.L. wrote the paper.

Conflict of interest statement: P.V.L. and N.M. are inventors on a patent application filed by University of California, Berkeley related to the work presented in this paper.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1700367114/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

Mordehai Milgrom, o físico do Instituto de Ciência Weizmann, nega a existência da matéria escura

The Physicist Who Denies Dark Matter

Maybe Newtonian physics doesn’t need dark matter to work.

BY ODED CARMELI

MAY 18, 2017

He is one of those dark matter people,” Mordehai Milgrom said about a colleague stopping by his office at the Weizmann Institute of Science. Milgrom introduced us, telling me that his friend is searching for evidence of dark matter in a project taking place just down the hall.

“There are no ‘dark matter people’ and ‘MOND people,’ ” his colleague retorted.

“I am ‘MOND people,’” Milgrom proudly proclaimed, referring to Modified Newtonian Dynamics, his theory that fixes Newtonian physics instead of postulating the existence of dark matter and dark energy—two things that, according to the standard model of cosmology, constitute 95.1 percent of the total mass-energy content of the universe.

This friendly incident is indicative of (“Moti”) Milgrom’s calmly quixotic character. There is something almost misleading about the 70-year-old physicist wearing shorts in the hot Israeli summer, whose soft voice breaks whenever he gets excited. Nothing about his pleasant demeanor reveals that this man claims to be the third person to correct Newtonian physics: First Max Planck (with quantum theory), then Einstein (with relativity), now Milgrom.

This year marks Milgrom’s 50th year at the Weizmann. I visited him there to learn more about how it feels to be a science maverick, what he appreciates about Thomas Kuhn’s The Structure of Scientific Revolutions, and why he thinks dark matter and dark energy don’t exist.

What inspired you to dedicate your life to the motion of stars?

I remember very vividly the way physics struck me. I was 16 and I thought: Here is a way to understand how things work, far beyond the understanding of my peers. It wasn’t a long-term plan. It was a daily attraction. I simply loved physics, the same way other people love art or sports. I never dreamed of one day making a major discovery, like correcting Newton.

I had a terrific physics teacher at school, but when you study textbook material, you’re studying done deals. You still don’t see the effort that goes into making breakthrough science, when things are unclear and advances are made intuitively and often go wrong. They don’t teach you that at school. They teach you that science always goes forward: You have a body of knowledge, and then someone discovers something and expands that body of knowledge. But it doesn’t really work that way. The progress of science is never linear.

How did you get involved with the problem of dark matter?

Toward the end of my Ph.D., the physics department here wanted to expand. So they asked three top Ph.D. students working on particle physics to choose a new field. We chose astrophysics, and the Weizmann Institute pulled some strings with institutions abroad so they would accept us as postdocs. And so I went to Cornell to fill my gaps in astrophysics.

After a few years in high energy astrophysics, working on the physics of X-ray radiation in space, I decided to move to yet another field: The dynamics of galaxies. It was a few years after the first detailed measurements of the speed of stars orbiting spiral galaxies came in. And, well, there was a problem with the measurements.

To understand this problem, one needs to wrap one’s head around some celestial rotations. Our planet orbits the sun, which, in turn, orbits the center of the Milky Way galaxy. Inside solar systems, the gravitational pull from the mass of the sun and the speed of the planets are in balance. By Newton’s laws, this is why Mercury, the innermost planet in our solar system, orbits the sun at over 100,000 miles per hour, while the outermost plant, Neptune, is crawling at just over 10,000 miles per hour.

Now, you might assume that the same logic would apply to galaxies: The farther away the star is from the galaxy’s center, the slower it revolves around it; however, while at smaller radiuses the measurements were as predicted by Newtonian physics, farther stars proved to move much faster than predicted from the gravitational pull of the mass we see in these galaxies. The observed gap got a lot wider when, in the late 1970s, radio telescopes were able to detect and measure the cold gas clouds at the outskirts of galaxies. These clouds orbit the galactic center five times farther than the stars, and thus the anomaly grew to become a major scientific puzzle.

One way to solve this puzzle is to simply add more matter. If there is too little visible mass at the center of galaxies to account for the speed of stars and gas, perhaps there is more matter than meets the eye, matter that we cannot see, dark matter.

...

READ MORE HERE: Nautilus

"Pequenos relógios" cristalizam a compreensão das colisões de meteoritos

Atomic-scale age resolution of planetary events

L. F. White, J. R. Darling, D. E. Moser, D. A. Reinhard, T. J. Prosa, D. Bullen, D. Olson, D. J. Larson, D. Lawrence & I. Martin

Nature Communications 8, Article number: 15597 (2017)

doi:10.1038/ncomms15597

Download Citation

Geochemistry Meteoritics

Received: 20 September 2016 Accepted: 12 April 2017

Published online: 26 May 2017

The Barringer meteorite impact crater in Arizona, USA. 

Abstract

Resolving the timing of crustal processes and meteorite impact events is central to understanding the formation, evolution and habitability of planetary bodies. However, identifying multi-stage events from complex planetary materials is highly challenging at the length scales of current isotopic techniques. Here we show that accurate U-Pb isotopic analysis of nanoscale domains of baddeleyite can be achieved by atom probe tomography. Within individual crystals of highly shocked baddeleyite from the Sudbury impact structure, three discrete nanostructural domains have been isolated yielding average 206Pb/238U ages of 2,436±94 Ma (protolith crystallization) from homogenous-Fe domains, 1,852±45 Ma (impact) from clustered-Fe domains and 1,412±56 Ma (tectonic metamorphism) from planar and subgrain boundary structures. Baddeleyite is a common phase in terrestrial, Martian, Lunar and asteroidal materials, meaning this atomic-scale approach holds great potential in establishing a more accurate chronology of the formation and evolution of planetary crusts.

Acknowledgements

We gratefully acknowledge the support of CAMECA in conducting APT analyses. This project was supported by Royal Society Research Grant RG160237, the Elspeth Matthews Fund of the Geological Society of London and a University of Portsmouth RDF Grant to J.R.D., and Canadian NSERC Discovery Grants to D.M. We thank I. Barker for his expert assistance with SEM analyses, Vale and Xstrata for assistance with fieldwork and two anonymous reviewers whose insights helped to improve this manuscript.

Author information

Affiliations

School of Earth and Environmental Sciences, University of Portsmouth, Burnaby Building, Burnaby Road, Portsmouth PO1 3QL, UK

L. F. White, J. R. Darling & D. Bullen

Department of Earth Sciences, University of Western Ontario, London, Canada N6A 5B7

D. E. Moser

CAMECA, Madison, Wisconsin 53711, USA

D. A. Reinhard, T. J. Prosa, D. Olson, D. J. Larson, D. Lawrence & I. Martin

Contributions

All authors contributed to this work. D.E.M. and J.R.D. designed the initial project. All authors conducted portions of either, or both, the fundamental SEM and APT data collection and processing. L.F.W., D.A.R., D.E.M. and J.R.D. reduced and interpreted the APT data. L.F.W. reduced the SEM data. L.F.W. wrote the main paper and all authors discussed the results and commented on the manuscript at all stages.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to L. F. White.

FREE PDF GRATIS: Nature Communications Sup. Info. Reviewers File Excel File 

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Quando rápido é melhor: fundamentos e mecanismos de enovelamento de proteínas de acessos ultrarrápidos

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches

Victor Muñoz, Michele Cerminara

Biochemical Journal Aug 30, 2016, 473 (17) 2545-2559; 

DOI: 10.1042/BCJ20160107

Abstract

Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico. All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats.

FREE PDF GRATIS: Biochemical Journal

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NOTA DESTE BLOGGER:

Notem na figura de enovelamento de proteínas o formato da Estrela de Davi.

Rápido enovelamento e lento desenovelamento de uma proteína pré-cambriana ressurgida.

PNAS,  vol. 114 no. 21 

Adela M. Candel,  E4122–E4123. 

doi: 10.1073/pnas.1703227114
Fast folding and slow unfolding of a resurrected Precambrian protein

Adela M. Candel a, M. Luisa Romero-Romero a,1, Gloria Gamiz-Arco a, Beatriz Ibarra-Molero a, and Jose M. Sanchez-Ruiz a,2

Author Affiliations

a Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada 18071, Spain

Source/Fonte: MD Simulation of Protein Folding

Tzul et al. (1) report different unfolding rates and similar folding rates for a number of thioredoxins. The authors interpret this result as evidence of the principle of minimal frustration. Their study includes several resurrected Precambrian thioredoxins that we have previously prepared and characterized (2⇓⇓–5).

We agree that the principle of minimal frustration is essential to understand protein evolution. However, approximate folding-rate invariance is easily explained without invoking this principle. Thioredoxin kinetic stability relies on a transition state that is substantially unstructured (5, 6). Therefore, mutations that changed unfolding rates to tune kinetic stability during evolution likely had much less effect on folding rates, as implied by the well-known principles of ϕ-value analysis (7).

Moreover, our experimental results are not consistent with folding-rate invariance being a general feature of thioredoxins. Fig. 1 shows folding–unfolding rates for the modern Escherichia coli thioredoxin and a resurrected Precambrian thioredoxin. The unfolding of the ancestral protein is ∼three orders-of-magnitude slower than the unfolding of the modern protein, indicating enhanced kinetic stability. However, in clear …

[Full Text of this Article]

↵2To whom correspondence should be addressed. Email: sanchezr@ugr.es.

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo do PNAS e mais 33.000 publicações científicas.

A forma geral da regra de Hamilton não faz predições e nem pode ser testada empiricamente!

The general form of Hamilton’s rule makes no predictions and cannot be tested empirically

Martin A. Nowak a,b,c, Alex McAvoy a, Benjamin Allen a,d, and Edward O. Wilson e,1

Author Affiliations

aProgram for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138;

bDepartment of Mathematics, Harvard University, Cambridge, MA 02138;

cDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;

dDepartment of Mathematics, Emmanuel College, Boston, MA 02115;

eMuseum of Comparative Zoology, Harvard University, Cambridge, MA 02138

Contributed by Edward O. Wilson, April 13, 2017 (sent for review February 2, 2017; reviewed by Michael Doebeli and Jan Rychtar)

Source/Fonte

Significance

Hamilton’s rule is a well-known concept in evolutionary biology. It is usually perceived as a statement that makes predictions about natural selection in situations where interactions occur between genetic relatives. Here, we examine what has been called the “exact and general” formulation of Hamilton’s rule. We show that in this formulation, which is widely endorsed by proponents of inclusive fitness theory, Hamilton’s rule does not make any prediction and cannot be tested empirically. This formulation of Hamilton’s rule is not a consequence of natural selection and not even a statement specifically about biology. We give simple and transparent expressions for the quantities of benefit, cost, and relatedness that appear in Hamilton’s rule, which reveal that these quantities depend on the data that are to be predicted.

Abstract

Hamilton’s rule asserts that a trait is favored by natural selection if the benefit to others, [Math Processing Error]B, multiplied by relatedness, [Math Processing Error]R, exceeds the cost to self, [Math Processing Error]C. Specifically, Hamilton’s rule states that the change in average trait value in a population is proportional to [Math Processing Error]BR−C. This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton’s rule provides valuable intuition, there is disagreement even among experts as to how the quantities [Math Processing Error]B, [Math Processing Error]R, and [Math Processing Error]C should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton’s rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton’s rule does not make predictions and cannot be tested empirically. It turns out that the parameters [Math Processing Error]B and [Math Processing Error]C depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called “exact and general” by its proponents, Hamilton’s rule can “predict” only the data that have already been given.

evolution cooperation kin selection sociobiology

Footnotes

1To whom correspondence should be addressed. Email: ewilson@oeb.harvard.edu.

Author contributions: M.A.N., A.M., B.A., and E.O.W. designed research, performed research, analyzed data, and wrote the paper.

Reviewers: M.D., University of British Columbia; and J.R., The University of North Carolina at Greensboro.

The authors declare no conflict of interest.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

O custo energético na "construção" de um vírus

Energetic cost of building a virus

Gita Mahmoudabadia, Ron Milob, and Rob Phillipsa,c,1

Author Affiliations

aDepartment of Bioengineering, California Institute of Technology, Pasadena, CA 91125;

bDepartment of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;

cDepartment of Applied Physics, California Institute of Technology, Pasadena, CA 91125

Edited by Ned S. Wingreen, Princeton University, Princeton, NJ, and accepted by Editorial Board Member Curtis G. Callan Jr. April 19, 2017 (received for review January 30, 2017)"

Source/Fonte:

Human hepegivirus 1 has parts of both hepatitis C virus (above) and human pegivirus.

David Marchal/Science Source

Significance

Viruses rely entirely on their host as an energy source. Despite numerous experimental studies that demonstrate the capability of viruses to rewire and undermine their host’s metabolism, we still largely lack a quantitative understanding of an infection’s energetics. However, the energetics of a viral infection is at the center of broader evolutionary and physical questions in virology. By enumerating the energetic costs of different viral processes, we open the door to quantitative predictions about viral evolution. For example, we predict that, for the majority of viruses, translation will serve as the dominant cost of building a virus, and that selection, rather than drift, will govern the fate of new genetic elements within viral genomes.

Abstract

Viruses are incapable of autonomous energy production. Although many experimental studies make it clear that viruses are parasitic entities that hijack the molecular resources of the host, a detailed estimate for the energetic cost of viral synthesis is largely lacking. To quantify the energetic cost of viruses to their hosts, we enumerated the costs associated with two very distinct but representative DNA and RNA viruses, namely, T4 and influenza. We found that, for these viruses, translation of viral proteins is the most energetically expensive process. Interestingly, the costs of building a T4 phage and a single influenza virus are nearly the same. Due to influenza’s higher burst size, however, the overall cost of a T4 phage infection is only 2–3% of the cost of an influenza infection. The costs of these infections relative to their host’s estimated energy budget during the infection reveal that a T4 infection consumes about a third of its host’s energy budget, whereas an influenza infection consumes only ≈ 1%. Building on our estimates for T4, we show how the energetic costs of double-stranded DNA phages scale with the capsid size, revealing that the dominant cost of building a virus can switch from translation to genome replication above a critical size. Last, using our predictions for the energetic cost of viruses, we provide estimates for the strengths of selection and genetic drift acting on newly incorporated genetic elements in viral genomes, under conditions of energy limitation.

viral energetics viral evolution T4 influenza cellular energetics

Footnotes

1To whom correspondence should be addressed. Email: phillips@pboc.caltech.edu.

Author contributions: G.M., R.M., and R.P. designed research, performed research, analyzed data, and wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission. N.S.W. is a guest editor invited by the Editorial Board.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1701670114/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

A modelagem integrativa da evolução do gene e do genoma enraíza a árvore da vida da Archaea.

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Tom A. Williams a,b,1, Gergely J. Szöllősi c,2, Anja Spang d,2, Peter G. Foster e, Sarah E. Heaps b,f, Bastien Boussau g, Thijs J. G. Ettema d, and T. Martin Embley b

Author Affiliations

aSchool of Earth Sciences, University of Bristol, Bristol BS8 1TQ, United Kingdom;

bInstitute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;

cMTA-ELTE Lendület Evolutionary Genomics Research Group, 1117 Budapest, Hungary;

dDepartment of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden;

eDepartment of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom;

fSchool of Mathematics & Statistics, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom;

gUniv Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, F-69622 Villeurbanne, France

Edited by W. Ford Doolittle, Dalhousie University, Halifax, Canada, and approved April 24, 2017 (received for review November 7, 2016)

Significance

The Archaea represent a primary domain of cellular life, play major roles in modern-day biogeochemical cycles, and are central to debates about the origin of eukaryotic cells. However, understanding their origins and evolutionary history is challenging because of the immense time spans involved. Here we apply a new approach that harnesses the information in patterns of gene family evolution to find the root of the archaeal tree and to resolve the metabolism of the earliest archaeal cells. Our approach robustly distinguishes between published rooting hypotheses, suggests that the first Archaea were anaerobes that may have fixed carbon via the Wood–Ljungdahl pathway, and quantifies the cumulative impact of horizontal transfer on archaeal genome evolution.

Abstract

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.

evolution phylogenetics Archaea

Footnotes

1To whom correspondence should be addressed. Email: tom.a.williams@bristol.ac.uk.

2G.J.S. and A.S. contributed equally to this work.

Author contributions: T.A.W., T.J.G.E., and T.M.E. designed research; T.A.W., G.J.S., A.S., P.G.F., S.E.H., and B.B. performed research; G.J.S. and B.B. contributed new reagents/analytic tools; T.A.W., G.J.S., A.S., P.G.F., S.E.H., and B.B. analyzed data; and T.A.W., A.S., T.J.G.E., and T.M.E. 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.1618463114/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

As compensações da mutação genética conduzem à evolução paralela

Environment determines evolutionary trajectory in a constrained phenotypic space

David T Fraebel Harry Mickalide Diane Schnitkey Jason Merritt Thomas E Kuhlman Seppe Kuehn 

University of Illinois at Urbana-Champaign, United States

DOI: http://dx.doi.org/10.7554/eLife.24669

Published March 27, 2017

Cite as eLife 2017;6:e24669

Source/Fonte: The Economist

Abstract

Constraints on phenotypic variation limit the capacity of organisms to adapt to the multiple selection pressures encountered in natural environments. To better understand evolutionary dynamics in this context, we select Escherichia coli for faster migration through a porous environment, a process which depends on both motility and growth. We find that a trade-off between swimming speed and growth rate constrains the evolution of faster migration. Evolving faster migration in rich medium results in slow growth and fast swimming, while evolution in minimal medium results in fast growth and slow swimming. In each condition parallel genomic evolution drives adaptation through different mutations. We show that the trade-off is mediated by antagonistic pleiotropy through mutations that affect negative regulation. A model of the evolutionary process shows that the genetic capacity of an organism to vary traits can qualitatively depend on its environment, which in turn alters its evolutionary trajectory.

DOI: http://dx.doi.org/10.7554/eLife.24669.001

eLife digest

In nature organisms face many challenges, and species adapt to their environment by changing heritable traits over the course of many generations. How organisms adapt is often limited by trade-offs, in which improving one trait can only come at the expense of another.

In the laboratory, scientists use well-controlled environments to study how populations adapt to specific challenges without interference from their natural habitat. Most experiments, however, only look at simple challenges and do not take into account that organisms in the wild face many pressures at the same time. Fraebel et al. wanted to know what happens when an organism’s performance depends on two traits that are restricted by a trade-off. The experiments used populations of the bacterium Escherichia coli, which can go through hundreds of generations in a week, providing ample opportunity to study mutations and their impact on heritable traits.

Through a combination of mathematical modeling and experiments, Fraebel et al. found that the environment is crucial for determining how bacteria adapt when their swimming speed and population growth rate are restricted by a trade-off. When nutrients are plentiful, E. coli populations evolve to spread faster by swimming more quickly despite growing more slowly. Yet, if nutrients are scarcer, the bacteria evolve to spread faster by growing more quickly despite swimming more slowly. In each scenario, the experiments identified single mutations that changed both swimming speed and growth rate by modifying regulatory activity in the cell.

A better understanding of how an organism’s genetic architecture, its environment and trade-offs are connected may help identify the traits that are most easily changed by mutations. The ultimate goal would be to be able to predict evolutionary responses to complex selection pressures.

DOI: http://dx.doi.org/10.7554/eLife.24669.002

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A profunda ignorância dos cientistas sobre a origem dos sexos

Sex chromosome evolution: historical insights and future perspectives

Jessica K. Abbott, Anna K. Nordén, Bengt Hansson

Published 3 May 2017.DOI: 10.1098/rspb.2016.2806

Source/Fonte

Abstract

Many separate-sexed organisms have sex chromosomes controlling sex determination. Sex chromosomes often have reduced recombination, specialized (frequently sex-specific) gene content, dosage compensation and heteromorphic size. Research on sex determination and sex chromosome evolution has increased over the past decade and is today a very active field. However, some areas within the field have not received as much attention as others. We therefore believe that a historic overview of key findings and empirical discoveries will put current thinking into context and help us better understand where to go next. Here, we present a timeline of important conceptual and analytical models, as well as empirical studies that have advanced the field and changed our understanding of the evolution of sex chromosomes. Finally, we highlight gaps in our knowledge so far and propose some specific areas within the field that we recommend a greater focus on in the future, including the role of ecology in sex chromosome evolution and new multilocus models of sex chromosome divergence.

Authors' contributions

A.K.N., B.H. and J.K.A. all contributed to developing the ideas presented here and wrote the manuscript together. A.K.N. created figure 1 and J.K.A. created table 1.

Competing interests

We declare we have no competing interests.

Funding

This work has been supported by ERC-StG-2015-678148 (to J.K.A.) and VR-2014-5222 (to B.H.).

Acknowledgements

The authors thank two anonymous reviewers for constructive feedback on an earlier version of the manuscript.

Received January 12, 2017.

Accepted April 4, 2017.

© 2017 The Authors.

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Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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Cientistas editam estocasticamente as sinapses das planárias que dirigem a forma do corpo

Long-Term, Stochastic Editing of Regenerative Anatomy via Targeting Endogenous Bioelectric Gradients

Fallon Durant, Junji Morokuma, Christopher Fields, Katherine Williams, Dany Spencer Adams, Michael Levin

Open Access

DOI: http://dx.doi.org/10.1016/j.bpj.2017.04.011 

Article Info

Publication History

Editor: Stanislav Shvartsman.

Accepted: April 14, 2017 Received: January 20, 2017

User License

Creative Commons Attribution – NonCommercial – No Derivs (CC BY-NC-ND 4.0)

Source/Fonte: Biophysical Journal

Abstract

We show that regenerating planarians’ normal anterior-posterior pattern can be permanently rewritten by a brief perturbation of endogenous bioelectrical networks. Temporary modulation of regenerative bioelectric dynamics in amputated trunk fragments of planaria stochastically results in a constant ratio of regenerates with two heads to regenerates with normal morphology. Remarkably, this is shown to be due not to partial penetrance of treatment, but a profound yet hidden alteration to the animals’ patterning circuitry. Subsequent amputations of the morphologically normal regenerates in water result in the same ratio of double-headed to normal morphology, revealing a cryptic phenotype that is not apparent unless the animals are cut. These animals do not differ from wild-type worms in histology, expression of key polarity genes, or neoblast distribution. Instead, the altered regenerative bodyplan is stored in seemingly normal planaria via global patterns of cellular resting potential. This gradient is functionally instructive, and represents a multistable, epigenetic anatomical switch: experimental reversals of bioelectric state reset subsequent regenerative morphology back to wild-type. Hence, bioelectric properties can stably override genome-default target morphology, and provide a tractable control point for investigating cryptic phenotypes and the stochasticity of large-scale epigenetic controls.

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Primeira evidência empírica de androgênese ocorrendo naturalmente em vertebrados!

First empirical evidence of naturally occurring androgenesis in vertebrates

Miguel Morgado-Santos, Sara Carona, Luís Vicente, Maria João Collares-Pereira

Published 24 May 2017.DOI: 10.1098/rsos.170200

Abstract

Androgenesis among vertebrates is considered a rare phenomenon, with some cases reported so far, but linked to experiments involving gamete manipulation (artificial androgenesis). Herein, we report the first empirical evidence of the natural occurrence of spontaneous androgenesis in a vertebrate, the Squalius alburnoides allopolyploid complex. A genetically screened random sample of a natural population was allowed to reproduce in an isolated pond without any human interference, and the viable offspring obtained was later analysed for paternity. Both nuclear and mitochondrial markers showed that the only allodiploid fish found among all the allotriploid offspring was androgenetically produced by an allodiploid male. This specimen had no female nuclear genomic input, and the sequence of the mitochondrial fragment examined differed from that of the male progenitor, matching one of the parental females available in the pond, probably the mother. The possible role of androgenesis in the reproductive dynamics of this highly successful vertebrate complex is discussed.

Authors' contributions

Conception and design: M.M.-S., L.V. and M.J.C.-P. Acquisition of data: M.M.-S. and S.C. Analysis and interpretation of data: M.M.-S., S.C. and M.J.C.-P. Drafting the article: M.M.-S. Revising the article critically: S.C. and M.J.C.-P. Final approval of the version to be published: M.M.-S., S.C., L.V. and M.J.C.-P.

Competing interests

We have no competing interests.

Funding

This work was supported by Portuguese National Funds, through Fundação para a Ciência e a Tecnologia (FCT) (project nos UID/BIA/00329/2013, PEstOE/BIA/UI0329/2014; grant no. SFRH/BD/65154/2009).

Acknowledgements

We thank I. Cowx for language revision and comments to an earlier version, M. A. Aboim for help with microsatellite genotyping, and the anonymous reviewers for their insightful recommendations. We also thank the ICNF for authorizing fish sampling and use in experimental trials.

Footnotes

Electronic supplementary material is available online at https://dx.doi.org/10.6084/m9.figshare.c.3780131.

Received March 3, 2017.

Accepted April 27, 2017.

© 2017 The Authors.

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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