Os dímeros da ATP sintase mitocondrial induzem a curvatura da membrana e se auto-montam em fileiras: mero acaso, fortuita necessidade ou design inteligente?

segunda-feira, fevereiro 18, 2019

Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows

Thorsten B. Blum, Alexander Hahn, Thomas Meier, Karen M. Davies, and Werner Kühlbrandt

PNAS published ahead of print February 13, 2019


Edited by David J. DeRosier, Brandeis University, Waltham, MA, and approved January 3, 2019 (received for review September 25, 2018)


Proteoliposomes of reconstituted Y. lipolytica ATP synthase dimers. (A and C) ATP synthase dimers (yellow) form rows that bend the lipid bilayer (light blue). Insets shows cross-sections (white lines), indicating that dimer rows bend the lipid bilayer by ∼90° (dashed red lines). (B) Flat membrane regions are devoid of ATP synthase. (D) Parallel rows of bidirectionally inserted dimers bend the bilayer into a corrugated sheet. (Scale bars, 100 nm.)

Significance

The ATP synthase in the inner membrane of mitochondria generates most of the ATP that enables higher organisms to live. The inner membrane forms deep invaginations called cristae. Mitochondrial ATP synthases are dimeric complexes of two identical monomers. It is known that the ATP synthase dimers form rows along the tightly curved cristae ridges. Computer simulations suggest that the dimer rows bend the membrane locally, but this has not been shown experimentally. In this study, we use electron cryotomography to provide experimental proof that ATP synthase dimers assemble spontaneously into rows upon membrane reconstitution, and that these rows bend the membrane. The assembly of ATP synthase dimers into rows is most likely the first step in the formation of mitochondrial cristae.

Abstract

Mitochondrial ATP synthases form dimers, which assemble into long ribbons at the rims of the inner membrane cristae. We reconstituted detergent-purified mitochondrial ATP synthase dimers from the green algae Polytomella sp. and the yeast Yarrowia lipolytica into liposomes and examined them by electron cryotomography. Tomographic volumes revealed that ATP synthase dimers from both species self-assemble into rows and bend the lipid bilayer locally. The dimer rows and the induced degree of membrane curvature closely resemble those in the inner membrane cristae. Monomers of mitochondrial ATP synthase reconstituted into liposomes do not bend membrane visibly and do not form rows. No specific lipids or proteins other than ATP synthase dimers are required for row formation and membrane remodelling. Long rows of ATP synthase dimers are a conserved feature of mitochondrial inner membranes. They are required for cristae formation and a main factor in mitochondrial morphogenesis.

mitochondria ATP synthase membrane curvature electron cryotomography subtomogram averaging

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Como as proteínas se tornam incorporadas em uma membrana celular: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, fevereiro 14, 2019

Insertion and folding pathways of single membrane proteins guided by translocases and insertases

Tetiana Serdiuk1, Anja Steudle2, Stefania A. Mari1, Selen Manioglu1, H. Ronald Kaback3,4,5, Andreas Kuhn2 and Daniel J. Müller1,*

See all authors and affiliations

Science Advances 30 Jan 2019: Vol. 5, no. 1, eaau6824



Source/Fonte: Spark Notes

Abstract

Biogenesis in prokaryotes and eukaryotes requires the insertion of α-helical proteins into cellular membranes for which they use universally conserved cellular machineries. In bacterial inner membranes, insertion is facilitated by YidC insertase and SecYEG translocon working individually or cooperatively. How insertase and translocon fold a polypeptide into the native protein in the membrane is largely unknown. We apply single-molecule force spectroscopy assays to investigate the insertion and folding process of single lactose permease (LacY) precursors assisted by YidC and SecYEG. Both YidC and SecYEG initiate folding of the completely unfolded polypeptide by inserting a single structural segment. YidC then inserts the remaining segments in random order, whereas SecYEG inserts them sequentially. Each type of insertion process proceeds until LacY folding is complete. When YidC and SecYEG cooperate, the folding pathway of the membrane protein is dominated by the translocase. We propose that both of the fundamentally different pathways along which YidC and SecYEG insert and fold a polypeptide are essential components of membrane protein biogenesis.

Acknowledgments: 

We thank R. Newton for discussing the manuscript, R. E. Dalbey for providing plasmid pT7-7 encoding YidC with a His10-tag at the C terminus, D. Balasubramaniam and J. Sugihara for providing some of the LacY and YidC samples used, D. Fotiadis for providing plasmid encoding the PreScission protease, the BioEM Lab of the University of Basel for providing TEM access and assistance, and N. Beerenwinkel for encouraging and constructive comments. Funding: This work was supported by the ETH-Zürich (to D.J.M.), the Swiss National Science Foundation (grant 205320_160199 to D.J.M.), and the National Center of Competence in Research “NCCR Molecular Systems Engineering” (to D.J.M.). Author contributions: T.S., D.J.M., A.K., and H.R.K. designed the experiments. A.K. and A.S. designed the SecY-YidC fusion construct. A.S. cloned, expressed, purified, and reconstituted the SecYEG and SecYEG-YidC fusion construct. T.S. performed the SMFS experiments. S.A.M. recorded AFM and TEM images. S.M. recorded Western blots. All authors analyzed experimental data and wrote the paper. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.

Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

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Proteínas análogas à linguagem natural: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, fevereiro 13, 2019

Grammar of protein domain architectures

Lijia Yu, Deepak Kumar Tanwar, Emanuel Diego S. Penha, Yuri I. Wolf, Eugene V. Koonin, and Malay Kumar Basu

PNAS published ahead of print February 7, 2019


Edited by Clyde A. Hutchison III, J. Craig Venter Institute, La Jolla, CA, and approved January 4, 2019 (received for review August 27, 2018).


Phylogenetic tree built from cross-entropy values. Domain bigram models were generated from 37 selected eukaryotic clades (Dataset S2) from the main branches of Eukaryota. The cross-entropies of bigram models were calculated in an all-vs.-all comparison. The entropy values were then normalized to create a distance matrix (see Methods for details), and the tree was constructed using the neighbor-joining method. The major groups are colored as shown in the legend.

Significance

Genomes appear similar to natural language texts, and protein domains can be treated as analogs of words. To investigate the linguistic properties of genomes further, we calculated the complexity of the “protein languages” in all major branches of life and identified a nearly universal value of information gain associated with the transition from a random domain arrangement to the current protein domain architecture. An exploration of the evolutionary relationship of the protein languages identified the domain combinations that discriminate between the major branches of cellular life. We conclude that there exists a “quasi-universal grammar” of protein domains and that the nearly constant information gain we identified corresponds to the minimal complexity required to maintain a functional cell.

Abstract

From an abstract, informational perspective, protein domains appear analogous to words in natural languages in which the rules of word association are dictated by linguistic rules, or grammar. Such rules exist for protein domains as well, because only a small fraction of all possible domain combinations is viable in evolution. We employ a popular linguistic technique, n-gram analysis, to probe the “proteome grammar”—that is, the rules of association of domains that generate various domain architectures of proteins. Comparison of the complexity measures of “protein languages” in major branches of life shows that the relative entropy difference (information gain) between the observed domain architectures and random domain combinations is highly conserved in evolution and is close to being a universal constant, at ∼1.2 bits. Substantial deviations from this constant are observed in only two major groups of organisms: a subset of Archaea that appears to be cells simplified to the limit, and animals that display extreme complexity. We also identify the n-grams that represent signatures of the major branches of cellular life. The results of this analysis bolster the analogy between genomes and natural language and show that a “quasi-universal grammar” underlies the evolution of domain architectures in all divisions of cellular life. The nearly universal value of information gain by the domain architectures could reflect the minimum complexity of signal processing that is required to maintain a functioning cell.

n-grambigramprotein domainlanguagedomain architecture

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Uma proposta para o futuro da publicação científica nas ciências da vida

A proposal for the future of scientific publishing in the life sciences

Bodo M. Stern , Erin K. O’Shea 

Published: February 12, 2019 https://doi.org/10.1371/journal.pbio.3000116

Source/Fonte: Internet

Abstract

Science advances through rich, scholarly discussion. More than ever before, digital tools allow us to take that dialogue online. To chart a new future for open publishing, we must consider alternatives to the core features of the legacy print publishing system, such as an access paywall and editorial selection before publication. Although journals have their strengths, the traditional approach of selecting articles before publication (“curate first, publish second”) forces a focus on “getting into the right journals,” which can delay dissemination of scientific work, create opportunity costs for pushing science forward, and promote undesirable behaviors among scientists and the institutions that evaluate them. We believe that a “publish first, curate second” approach with the following features would be a strong alternative: authors decide when and what to publish; peer review reports are published, either anonymously or with attribution; and curation occurs after publication, incorporating community feedback and expert judgment to select articles for target audiences and to evaluate whether scientific work has stood the test of time. These proposed changes could optimize publishing practices for the digital age, emphasizing transparency, peer-mediated improvement, and post-publication appraisal of scientific articles.

Citation: Stern BM, O’Shea EK (2019) A proposal for the future of scientific publishing in the life sciences. PLoS Biol 17(2): e3000116. https://doi.org/10.1371/journal.pbio.3000116

Published: February 12, 2019

Copyright: © 2019 Stern, O’Shea. 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.

FREE PDF GRATIS: PLoS Biology
Funding: The authors received no specific funding for this work.




Competing interests: We have read the journal's policy and the authors of this manuscript have the following competing interest: Both authors are employees of the Howard Hughes Medical Institute.




Abbreviations: CV, curriculum vitae; DOI, digital object identifier; HHMI, Howard Hughes Medical Institute; JIF, journal impact factor; ORCID, open researcher and contributor ID




Provenance: Not commissioned; externally peer-reviewed.

Darwin, olha só o presente: mais de 1.000 cientistas com Ph. D. são céticos da capacidade da seleção natural como mecanismo evolucionário!

terça-feira, fevereiro 12, 2019


Darwin, celebrando o seu dia, eis aqui uma lista de dissidentes científicos que, colocando em risco suas carreiras acadêmicas, questionam a capacidade da seleção natural como mecanismo responsável pelas novidades evolucionárias.  

Nova tradução de A Caixa Preta de Darwin: o desafio da bioquímica à teoria da evolução

A Caixa Preta de Darwin: o desafio da bioquímica à teoria da evolução

Ciências

Michael J. Behe

R$ 70,00

Disponível a partir de 28/02/2019

Em 1996, A caixa preta de Darwin lançou ao mundo a Teoria do Design Inteligente: o argumento de que a natureza exibe evidências de design que vão muito além do acaso darwinista. O livro catalisou um debate bastante acalorado sobre a evolução, que continua cada vez mais a se intensificar nos Estados Unidos e no mundo, incluindo o Brasil. Em um amplo espectro científico, a obra se estabeleceu como o texto básico e fundamental do design inteligente (DI), o argumento que precisa ser considerado para determinar se a evolução, segundo propôs Darwin, é mesmo suficiente para explicar a vida da forma que hoje a conhecemos. No posfácio da edição comemorativa do 10º aniversário do livro, Behe explica como a complexidade descoberta por microbiologistas cresceu drasticamente desde a publicação de seu livro e como essa complexidade irredutível tem sido um desafio contínuo ao darwinismo, que, sistematicamente, tem falhado em explicá-la. No posfácio comemorativo desta edição de 2019, Behe reforça o poder crescente de seus argumentos – tão atuais e devastadores em 2019 quanto eram em 1996 – e comemora o crescimento do DI no Brasil e no mundo. A caixa preta de Darwin é histórico, indispensável e ainda mais importante hoje do que era em 1996!

Detalhes

ISBN: 978-85-8293-824-9
Ano: 2019
Nº Paginas: 432
Edição: 1
Dimensões: 16 x 23 cm
Peso: 0,600 g
Categoria: Ciências

Dr. Vladimir Voeikov 'falou e disse': o neodarwinismo é ideologia e filosofia que impede o avanço da ciência

"A ideologia e filosofia do neodarwinismo que é vendida pelos seus adeptos como uma fundação teórico-científica da biologia impede seriamente o desenvolvimento da ciência e esconde dos seus estudantes os problemas reais da área."

"The ideology and philosophy of neo-Darwinism which is sold by its adepts as a scientific theoretical foundation of biology seriously hampers the development of science and hides from students the field’s real problems."

Dr. Vladimir L. Voeikov, Professor de Bioorgânica, Universidade Estadual de Moscou; membro da Academia Russa de Ciências Naturais/Professor of Bioorganic, Moscow State University; member of the Russian Academy of Natural Sciences.

A “Máquina de Estabilização dos Oceanos” pode representar um fator primordial subjacente ao efeito do “aquecimento global na mudança climática”

segunda-feira, fevereiro 11, 2019

ACS Vol.9 No.1, January 2019

The “Ocean Stabilization Machine” May Represent a Primary Factor Underlying the Effect of “Global Warming on Climate Change”

DOI: 10.4236/acs.2019.91009

Author(s) Yanjun Mao1, Jiqing Tan2*, Bomin Chen3, Huiyi Fan2 Affiliation(s)

1Climate Center, Zhejiang Meteorologic Bureau, Hangzhou, China.

2Earth Science School, Zhejiang University, Hangzhou, China.

3Shanghai Climate Center, Shanghai, China.

Image result for global warming effects on the ocean
Source/Fonte: TreeHugger

ABSTRACT

Contemporary references to global warming pertain to the dramatic increase in monthly global land surface temperature (GLST) anomalies since 1976. In this paper, we argue that recent global warming is primarily a result of natural causes; we have established three steps that support this viewpoint. The first is to identify periodic functions that perfectly match all of the monthly anomaly data for GLST; the second is to identify monthly sea surface temperature (SST) anomalies that are located within different ocean basin domains and highly correlated with the monthly GLST anomalies; and the third is to determine whether the dramatically increasing (or dramatically decreasing) K-line diagram signals that coincide with GLST anomalies occurred in El Niño years (or La Niña years). We have identified 15,295 periodic functions that perfectly fit the monthly GLST anomalies from 1880 to 2013 and show that the monthly SST anomalies in six domains in different oceans are highly correlated with the monthly GLST anomalies. In addition, most of the annual dramatically increasing GLST anomalies occur in El Niño years; and most of the annual dramatically decreasing GLST anomalies occur in La Niña years. These findings indicate that the “ocean stabilization machine” might represent a primary factor underlying the effect of “global warming on climate change”.

KEYWORDS

Global Warming, Monthly Global Land Surface Temperature (GLST) Anomalies, Monthly SST Anomalies, Ocean Stabilization Machine, K-Line Diagram Signals

Vida sem design intencional???

Life without design

Constructor theory is a new vision of physics, but it helps to answer a very old question: why is life possible at all?

Automotive Industry mural by Marvin Beerbohm, 1940. Detroit Public Library. Photo by Smithsonian Institution/Corbis

Chiara Marletto is a postdoctoral research associate and junior research fellow at Wolfson College at the University of Oxford.

2,400 words

Edited by Ed Lake

Living things have puzzled and challenged us since the dawn of our species. Even in the light of our modern scientific understanding, they seem remarkable. A merlin falcon hunting its prey, a hummingbird suspended in the air beside a flower, the self-reproduction of a bacterial cell: all are instances of stunning control and precision. How could anything so complex have originated from inert matter?

For millennia, some of the most brilliant thinkers have attempted to answer this question. Most of them concluded that living things must have been produced by an intentional design process. They were wrong, of course: the theory of evolution by variation and natural selection – Charles Darwin’s momentous leap – shows how those stupendously intricate mechanisms can come about without one. Yet the task of showing how life itself can arise without design is surprisingly vexed.

The very problem Darwin’s theory addresses is ultimately rooted in physics: living things have certain properties that seem to set them apart from other aggregations of inert matter. They have many different subparts – instantiating biological adaptations – all coordinating to some function. That’s the key property: they closely resemble objects that have literally been designed, such as factories and robots. For example, the ciliary muscles and the lens in the eye coordinate exquisitely to permit vision, just like the optical components of a sophisticated camera. In modern biology, this is called the appearance of design – a property described by Socrates and given canonical expression in 1802 by William Paley in his ‘watchmaker’ argument for the existence of God.

More generally, living things, again just like factories and robots, have the ability to perform physical transformations with a very high degree of precision, and to do so repeatedly and reliably. A goat’s jaws and heart just keep on chewing and beating for its whole lifetime. If you got the goat to graze your lawn, it would mow it to high accuracy and be just as capable of doing the same when presented with another lawn. It just keeps going: the goat is, among other things, a lawnmowing machine.

Unlike factories, all living things rely on a rather peculiar contrivance: the living cell. Cells can self-reproduce, manufacturing new instances of themselves in a process involving, at its heart, the faithful replication of the genetic information contained in the cell’s DNA. We find this capacity nowhere in the rest of nature. Even among human technologies, there are only dim foreshadowings of it, such as 3D printers that print some of their own spare parts.

Why should such features of living things constitute a problem for physics? Crucially, what can and cannot be made to happen in the physical world is determined by physical laws. For example, a perpetual motion machine cannot be constructed, no matter what resources are devoted to the task, as it is forbidden by those laws. Conversely, given the presence of life in our universe, physics must be such as to allow for it.

But our laws of physics provide only certain elementary objects, such as simple chemicals, in great numbers. These objects do not, in themselves, have the ability to repeatedly cause highly accurate transformations. Neither do they seem adapted to do anything in particular. If they do cause transformations, it is neither very accurately nor reliably: they wear out and make errors, their resources get depleted, and so on. In other words, the laws of physics contain no built-in facility for accurate transformations; nor, in particular, for biological adaptations that can bring such transformations about. They are no-design, in this special sense. Thus the problem with living things, expressed within physics, is that they are highly adapted to effect all sorts of transformations to high accuracy, whereas the laws of physics aren’t.

Given that life isn’t the output of an intentional design process, but evolved, how could living things have evolved given these design-free laws of physics? Darwin’s theory addresses this problem, explaining that variation and natural selection bring about the appearance of design. But this in itself doesn’t close the explanatory gap, as we can see especially clearly in the modern version of Darwin’s theory – neo-Darwinism. At its heart are the replicators, or genes – bits of DNA that are transmitted, by replication, to the next generation. Moreover, for replication to be as accurate as it is in living things, accurate self-reproduction of the cell is also required. In short, the theory presupposes the possibility of certain accurate physical transformations, and these are just what no-design laws of physics fail to provide in their starter kit.

Here’s where the puzzle arises. Biological replication and self‑reproduction are in fact such stupendously well‑orchestrated physical transformations that one must explain how they are possible under the simple, no‑design laws of physics such as ours. This additional explanation, which was not included in the theory of evolution, is essential for that theory to properly explain how living things arise without intentional design – to close the explanatory gap.

...

READ MORE HERE: Aeon

Scinapse - Pesquise, nunca busque novamente!

domingo, fevereiro 10, 2019


Scinapse: Do research, never re-search/Pesquise, nunca busque novamente

Micróbios incomuns contêm pistas para o início da vida

sábado, fevereiro 09, 2019

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere

Stephanie A. Carr, Sean P. Jungbluth, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Tanja Woyke, Michael S. Rappé & Beth N. Orcutt

The ISME Journal (2019)

Fig. 1



Abstract

The exploration of Earth’s terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage’s evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.

Acknowledgements
The authors thank the AT18-07 cruise party for their assistance including Andrew Fisher as chief scientist; Samuel Hulme, Geoff Wheat, and the late James Cowen for assistance with fluid sampling; Keir Becker for observatory expertise; and Tina Lin, Oliver Hseih, and the late Katrina Edwards for sample handling. We thank the staff of the Single Cell Genomics Center at Bigelow Laboratory for Ocean Sciences for expert handling, sorting, amplification, and sequencing of single cells, the Joint Genome Institute for metagenomic sequencing, Daniel Rogers for mcrA standards, and Bo Barker Jørgensen at Aarhus University for supporting Orcutt’s participation in the cruise. The 2011 cruise was supported by NSF grants MCB-0604014 (lead J. Cowen), OCE-0726887 (lead K. Becker), and OCE-1031808 (lead A. Fisher). SAC was supported by postdoctoral fellowships from the Center for Dark Energy Biosphere Investigations (C-DEBI; NSF award OCE-0939564) and the NSF (OCE-1521614). The efforts of SPJ and MSR were supported by NSF grants MCB-0604014 and OCE-1260723. BNO acknowledges support from C-DEBI, the NASA Astrobiology Institute (NNA13AA92A), and NSF (OCE-1233226). This work was also supported by the grants DEB-1441717 (NSF), OCE-1335810 (NSF) and CSP2013-987 (DOE JGI) to RS. The work conducted by the US Department of Energy Joint Genome Institute (JGI), a US Department of Energy Office of Science User Facility, is supported under contract no. DE-AC02-05CH11231. This is C-DEBI contribution number 451, HIMB contribution number 1747, and SOEST contribution number 10573.

Author information
Affiliations

Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
Stephanie A. Carr, Ramunas Stepanauskas & Beth N. Orcutt
Hartwick College, Oneonta, NY, USA

Stephanie A. Carr
Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA

Sean P. Jungbluth
Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA

Sean P. Jungbluth, Emiley A. Eloe-Fadrosh & Tanja Woyke
Hawaii Institute of Marine Biology, University of Hawaii at Manoa, PO BOX 1346, Kaneohe, HI, 96744, USA

Sean P. Jungbluth & Michael S. Rappé

Conflict of interest
The authors declare that they have no conflict of interest.

Corresponding authors
Correspondence to Michael S. Rappé or Beth N. Orcutt.

Pesquisa sugere que a vida era abundante na Terra 3,5 bilhões de anos atrás

Role of APS reductase in biogeochemical sulfur isotope fractionation

Min Sub Sim, Hideaki Ogata, Wolfgang Lubitz, Jess F. Adkins, Alex L. Sessions, Victoria J. Orphan & Shawn E. McGlynn 

Nature Communications volume 10, Article number: 44 (2019)

Fig. 1

The pathway of dissimilatory sulfate reduction with the molecular structures of sulfur-containing metabolites and the enzymes catalyzing their transformation. Adenosine phosphosulfate reductase, the enzyme of interest in this study, breaks the first S–O bond in the sulfate group, which involves the transfer of two electrons

Abstract

Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20‰, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.

Acknowledgments

This work was supported by the Research Resettlement Fund for the new faculty of Seoul National University to M.S.S., the NASA Research Opportunities in Space and Earth Sciences grant award number NNX14AO48G to S.E.M. and V.J.O., JSPS KAKENHI Grant Number 10751084 to S.E.M., and the Gordon and Betty Moore Foundation Grant GBMF 3306 to V.J.O. and A.L.S. This research was a part of the project titled ‘Understanding the deepsea biosphere on seafloor hydrothermal vents in the Indian Ridge (20170411)’, funded by the Ministry of Oceans and Fisheries, Korea. We are grateful for insightful and helpful conversations with Boswell A. Wing, David T. Johnston, David A. Fike, and Itay Halevy. We are especially grateful to Tatsuhiko Yagi and Yoshiki Higuchi for helping with initiating collaboration.

Author information

Affiliations

School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, South Korea
Min Sub Sim
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA

Min Sub Sim, Jess F. Adkins, Alex L. Sessions, Victoria J. Orphan & Shawn E. McGlynn
Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany

Hideaki Ogata & Wolfgang Lubitz
Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan

Hideaki Ogata
Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, 152-8550, Japan
Shawn E. McGlynn

Contributions

M.S.S. and S.E.M. devised the study. H.O. and W.L. purified APS reductase, and M.S.S. executed enzymatic assay and sulfur isotope measurements. M.S.S. and S.E.M. wrote the first draft of the manuscript, and J.F.A., A.L.S., and V.J.O. contributed to interpretation and writing.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Min Sub Sim or Shawn E. McGlynn.

Cientistas estudam a organização da vida em uma escala planetária

sexta-feira, fevereiro 08, 2019

Universal scaling across biochemical networks on Earth

Hyunju Kim1,2,*, Harrison B. Smith2,*, Cole Mathis1,3, Jason Raymond2 and Sara I. Walker1,2,4,5,†

1Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA.

2School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA.

3Department of Physics, Arizona State University, Tempe, AZ, USA.

4ASU-SFI Center for Biosocial Complex Systems, Tempe, AZ, USA.

5Blue Marble Space Institute of Science, Seattle, WA, USA.

↵†Corresponding author. Email: sara.i.walker@asu.edu

↵* These authors contributed equally to this work.

Science Advances 16 Jan 2019:

Vol. 5, no. 1, eaau0149


Source/Fonte: Internet

Abstract

The application of network science to biology has advanced our understanding of the metabolism of individual organisms and the organization of ecosystems but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, we constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes and 8658 cataloged biochemical reactions. We uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical reaction networks to random reaction networks reveals that the observed biological scaling is not a product of chemistry alone but instead emerges due to the particular structure of selected reactions commonly participating in living processes. We show that the topology of biochemical networks for the three domains of life is quantitatively distinguishable, with >80% accuracy in predicting evolutionary domain based on biochemical network size and average topology. Together, our results point to a deeper level of organization in biochemical networks than what has been understood so far.

FREE PDF GRATIS: Science Advances

Cromossomos Y masculinos não são 'terras genéticas desertas'

quinta-feira, fevereiro 07, 2019

Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome

Ching-Ho Chang and Amanda M. Larracuente

GENETICS January 1, 2019 vol. 211 no. 1 333-348; https://doi.org/10.1534/genetics.118.301765


Abstract

Heterochromatic regions of the genome are repeat-rich and poor in protein coding genes, and are therefore underrepresented in even the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family, crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.

DROSOPHILA MELANOGASTER GENOME Y CHROMOSOME LONG-READ ASSEMBLY GENE DUPLICATIONS GENE CONVERSION CRYSTAL-STELLATE GENETICS OF SEX

FREE PDF GRATIS: Genetics

Uma publicação científica darwinista convoca artigos sobre teleologia e educação da evolução

sábado, fevereiro 02, 2019

Call for Papers: Teleology and Evolution Education

New Content Item

Evolution: Education and Outreach invites original contributions exploring all aspects of teleological reasoning and teleological language pertinent to the teaching and learning of evolution. The scope of papers to be included in this special issue will range from theoretical reflections on the role that teleology should play in evolution education to empirical studies addressing teleology-related aspects of teaching and learning evolution. Submitted papers may, for example, address: the assessment of students’ teleological reasoning and teleological misconceptions about evolution; teaching strategies and learning environments focusing on teleology; or teachers’ teleology-related instructional practices and professional development. The literature on teleology is diverse; we welcome a range of positions from a variety of disciplines (e.g., cognitive psychology, learning sciences, biology education, philosophy of science).
Questions about contributions may be directed to Prof. Marcus Hammann, Guest Editor of the special issue, or to Editor-in-Chief Ross Nehm. Submissions are now open, with an anticipated publication date of December 2019.
Evolution: Education and Outreach is now celebrating its 10th anniversary, and has recently attained SCOPUS indexing.
Submitted papers will be reviewed in a timely manner and published directly after acceptance (i.e. without waiting for the accomplishment of all other contributions). Thanks to the Evolution: Education and Outreach open access policy, the articles published in this thematic series will have a wide, global audience.

Submission instructions
Before submitting your manuscript, please ensure you have carefully read the submission guidelines for Evolution: Education and Outreach. The complete manuscript should be submitted through the journal submission system. To ensure that you submit to the correct thematic series please select the appropriate section in the drop-down menu upon submission. In addition, indicate within your cover letter that you wish your manuscript to be considered as part of the thematic series on series title. All submissions will undergo rigorous peer review, and accepted articles will be published within the journal as a collection.
Submissions will also benefit from the usual advantages of open access publication:
Rapid publication: Online submission, electronic peer review and production make the process of publishing your article simple and efficient
High visibility and international readership in your field: Open access publication ensures high visibility and maximum exposure for your work - anyone with online access can read your article
No space constraints: Publishing online means unlimited space for figures, extensive data and video footage.
Authors retain copyright, licensing the article under a Creative Commons license: articles can be freely redistributed and reused as long as the article is correctly attributed.
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NOTA DESTE BLOGGER:
Mas Darwin não tinha eliminado de uma vez por todas a teleologia na biologia evolucionária???
Eu queria ver a cara de meus amigos professores universitários de Biologia e de História da Ciência que disseram que eu tinha embarcado numa canoa furada da teoria do Design Inteligente por propor a teleologia nas coisas biológicas. Eu queria ver a cara da Galera dos meninos e meninas de Darwin pelas suas provocações e deboches: a ciência está nos vindicando - a teleologia é real na natureza e pode ser detectada!!!

Boas e más notícias sobre as usinas de dessalinização

Water 2019, 11(2), 208; https://doi.org/10.3390/w11020208

Biological and Physical Effects of Brine Discharge from the Carlsbad Desalination Plant and Implications for Future Desalination Plant Constructions

Karen Lykkebo Petersen 1,2,* , Nadine Heck 3,4, Borja G. Reguero 3,4OrcID, Donald Potts 3,5OrcID, Armen Hovagimian 6OrcID and Adina Paytan 3

Department of Earth and Planetary Sciences, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA

Department of Ecology, Environment and Plant Science, Stockholm University, Svante Arrhenius väg 20A, 114 18 Stockholm, Sweden

Institute of Marine Sciences, University of California, Santa Cruz, 1156 High St., Santa Cruz, CA 95064, USA

The Nature Conservancy, 115 McAllister Way, Santa Cruz, CA, 95060, USA

Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA

Cowell College, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA

Author to whom correspondence should be addressed.

Received: 9 December 2018 / Revised: 18 January 2019 / Accepted: 22 January 2019 / Published: 25 January 2019

(This article belongs to the Special Issue Ecological Status Assessment of Transitional Waters)

The Ashkelon desalination facility, one of the largest in the world, is one of five plants along the Mediterranean Sea providing Israelis with 65 percent of their drinking water. 
Source/Fonte: Times of Israel

Abstract

Seawater reverse osmosis (SWRO) desalination is increasingly used as a technology for addressing shortages of freshwater supply and desalination plants are in operation or being planned world-wide and specifically in California, USA. However, the effects of continuous discharge of high-salinity brine into coastal environments are ill-constrained and in California are an issue of public debate. We collected in situ measurements of water chemistry and biological indicators in coastal waters (up to ~2 km from shore) before and after the newly constructed Carlsbad Desalination Plant (Carlsbad, CA, USA) began operations. A bottom water salinity anomaly indicates that the spatial footprint of the brine discharge plume extended about 600 m offshore with salinity up to 2.7 units above ambient (33.2). This exceeds the maximum salinity permitted for this location based on the California Ocean Plan (2015 Amendment to Water Quality Control Plan). However, no significant changes in the assessed biological indicators (benthic macrofauna, BOPA-index, brittle-star survival and growth) were observed at the discharge site. A model of mean ocean wave potential was used as an indicator of coastal mixing at Carlsbad Beach and at other locations in southern and central CA where desalination facilities are proposed. Our results indicated that to minimize environmental impacts discharge should target waters where a long history of anthropogenic activity has already compromised the natural setting. To ensure adequate mixing of the discharge brine desalination plants should be constructed at high-energy sites with sandy substrates, and discharge through diffusor systems.

Keywords: SWRO desalination; brine discharge; osmotic stress; coastal monitoring; impacted coastal systems

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

FREE PDF GRATIS: Water Sup. Info.

Metabolismo essencial para uma célula mínima

sexta-feira, fevereiro 01, 2019

Essential metabolism for a minimal cell

Marian Breuer, Tyler M Earnest, Chuck Merryman, Kim S Wise, Lijie Sun, Michaela R Lynott, Clyde A Hutchison, Hamilton O Smith, John D Lapek David J Gonzalez, Valérie de Crécy-Lagard, Drago Haas, Andrew D Hanson, Piyush Labhsetwar, John I Glass, Zaida Luthey-Schulten 

University of Illinois at Urbana-Champaign, United States; J Craig Venter Institute, United States; University of California, San Diego, United States; University of Florida, United States

RESEARCH ARTICLE Jan 18, 2019

Source/Fonte: Scientific Reports

Abstract

JCVI-syn3A, a robust minimal cell with a 543 kbp genome and 493 genes, provides a versatile platform to study the basics of life. Using the vast amount of experimental information available on its precursor, Mycoplasma mycoides capri, we assembled a near-complete metabolic network with 98% of enzymatic reactions supported by annotation or experiment. The model agrees well with genome-scale in vivo transposon mutagenesis experiments, showing a Matthews correlation coefficient of 0.59. The genes in the reconstruction have a high in vivo essentiality or quasi-essentiality of 92% (68% essential), compared to 79% in silico essentiality. This coherent model of the minimal metabolism in JCVI-syn3A at the same time also points toward specific open questions regarding the minimal genome of JCVI-syn3A, which still contains many genes of generic or completely unclear function. In particular, the model, its comparison to in vivo essentiality and proteomics data yield specific hypotheses on gene functions and metabolic capabilities; and provide suggestions for several further gene removals. In this way, the model and its accompanying data guide future investigations of the minimal cell. Finally, the identification of 30 essential genes with unclear function will motivate the search for new biological mechanisms beyond metabolism.

FREE PDF GRATIS: eLIFE

Chegou a hora de uma defesa filosófica robusta da verdade científica

quarta-feira, janeiro 30, 2019

Getting it right

Truth is neither absolute nor timeless. But the pursuit of truth remains at the heart of the scientific endeavour


‘...the strength of the thread does not reside in the fact that some one fibre runs through its whole length, but in the overlapping of many fibres’ – Ludwig Wittgenstein.


Think of the number of scenarios in which truth matters in science. We care to know whether increased CO2 emission levels cause climate change, and how fast. We care to know whether smoking tobacco increases the risk of lung cancer. We care to know whether poor diet exposes children to the risk of developing obesity, or whether forecasts of economic growth are correct. Truth in science is not esoteric dilly-dallying. It shapes climate science, medicine, public health, the economy and many other worldly endeavours. 

That truth matters to science is hardly news. For a long time, people have looked to science for truths about the world. The Scientific Revolution was nothing if not the triumph of Galileo’s scientific truth – hard-won through his telescopic observations – over centuries of dogma about the geocentric system. With its system of epicycles and deferents, Ptolemaic astronomy was at once sophisticated and false. It served to, at best, ‘save the appearances’ about how planets seemed to move in the sky. It did not tell the truth about planetary motion until the discovery of the Copernican explanation. Or consider the Chemical Revolution at the end of the 18th century. We no longer, after all, believe in phlogiston – the fictional imponderable fluid that Georg Ernst Stahl, Joseph Priestley and other natural philosophers at the time believed to be at work in combustion and calcination phenomena. Antoine Lavoisier’s scientific truth about oxygen prevailed over false beliefs about phlogiston.

The main actors of these scientific revolutions often fostered this way of thinking about science as an enquiry leading to the inevitable triumph of truth over past errors. Two centuries after Galileo’s successful defence of the heliocentric system, this idea of the course of scientific truth continued to inspire philosophers. In his Cours de philosophie positive (1830-42), Auguste Comte saw the evolution of human knowledge in three main stages: ‘the Theological, or fictitious; the Metaphysical, or abstract; and the Scientific, or positive’. In the ‘positive’, the third and last stage, ‘an explanation of facts is simply the establishment of a connection between single phenomena and some general facts, the number of which continually diminishes with the progress of science’.

Comte’s positivism was soon decontextualised from its political and social context (after all, Comte started his career working for the social theorist Henri de Saint-Simon, and positivism was inspired by the Industrial Revolution). By the end of the 19th century (and in its early 20th-century reappearance, which I do not have the space to discuss here), the word ‘positivism’ had become – to the ears of many – synonymous with an unfailing optimism in the power of science and technology, and their steady progress toward truth.

In some scientific quarters, this Comtean notion of how science evolves and progresses remains common currency. But philosophers of science, over the past half-century, have turned against the representation of science as a ceaseless forward march toward truth. It is just not how science works, how it moves through history. It flies in the face of the wonderful and subtle historical nuances of how scientific revolutions have in fact occurred. It does not accommodate how some of the greatest scientific minds held dearly to some false beliefs. It wilfully ignores the many voices, disagreements and controversies through which scientific knowledge has often advanced and progressed over time. Simple faith in the ‘Whiggish’ narrative of science naively presumes that progress is marked by some cumulative acquisition of ‘more true beliefs’.

However, many (and legitimate in their own right) criticisms against this naive view of science have committed a similar mistake. They have offered a portrait of science purged of any commitment to truth. They see truth as an inconvenient and disposable feature of science. Fraught as the ideal and pursuit of truth is with tendencies to petty doctrinairism, it is nonetheless a mistake to try to purge it. The fallacy of positivist philosophy was to think of science as coming in stages of some sort, or following a particular path, or historical cycles. The anti-truth trend in the philosophy of science has often ended up repeating this same misstep. It is important to move beyond the sterile dichotomy between the old (quasi-positivist) view of truth in science and the rival anti-truth trend of recent decades.
...

READ MORE HERE: Aeon

Extra! Extra! Extra! O núcleo interno da Terra é relativamente jovem!

terça-feira, janeiro 29, 2019

Young inner core inferred from Ediacaran ultra-low geomagnetic field intensity

Richard K. Bono, John A. Tarduno, Francis Nimmo & Rory D. Cottrell 

Nature Geoscience volume 12, pages143–147 (2019) 

Source/Fonte: NASA

Abstract

An enduring mystery about Earth has been the age of its solid inner core. Plausible yet contrasting core thermal conductivity values lead to inner core growth initiation ages that span 2 billion years, from ~0.5 to >2.5 billion years ago. Palaeomagnetic data provide a direct probe of past core conditions, but heretofore field strength data were lacking for the youngest predicted inner core onset ages. Here we present palaeointensity data from the Ediacaran (~565 million years old) Sept-Îles intrusive suite measured on single plagioclase and clinopyroxene crystals that hosted single-domain magnetic inclusions. These data indicate a time-averaged dipole moment of ~0.7 × 1022 A m2, the lowest value yet reported for the geodynamo from extant rocks and more than ten times smaller than the strength of the present-day field. Palaeomagnetic directional studies of these crystals define two polarities with an unusually high angular dispersion (S = ~26°) at a low latitude. Together with 14 other directional data sets that suggest a hyper-reversal frequency, these extraordinary low field strengths suggest an anomalous field behaviour, consistent with predictions of geodynamo simulations, high thermal conductivities and an Ediacaran onset age of inner core growth.

Acknowledgements

We thank G. Kloc for the sample preparation, B. L. McIntyre and R. Wiegandt for the electron microscope analyses and T. Zhou for magnetic hysteresis measurements. This work was supported by the National Science Foundation (grant nos EAR1520681 and EAR1656348 to J.A.T.).

Author information
Author notes

Richard K. Bono
Present address: Geomagnetism Laboratory, University of Liverpool, Liverpool, UK

Affiliations

Department of Earth & Environmental Sciences, University of Rochester, Rochester, NY, USA
Richard K. Bono, John A. Tarduno & Rory D. Cottrell
Department of Physics & Astronomy, University of Rochester, Rochester, NY, USA
John A. Tarduno
Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA, USA
Francis Nimmo

Contributions

J.A.T. and R.K.B. conducted the field studies. R.K.B. conducted the palaeomagnetic measurements on the feldspars and R.D.C. measured clinopyroxenes; both data sets were analysed by R.K.B., R.D.C. and J.A.T. Electron microscope analyses were conducted by J.A.T. Core thermal conductivity models were provided by F.N. All the authors participated in the writing of the manuscript. J.A.T. conceived and supervised the study. We thank J. Feinberg for helpful comments.

Competing interests
The authors declare no competing interests.

Corresponding author
Correspondence to John A. Tarduno.

FREE TO READ ONLINE/LEITURA GRATIS ONLINE: Nature Geoscience

Material estelar pode ser um bloco construtor na origem da vida

sábado, janeiro 26, 2019

First detection of the pre-biotic molecule glycolonitrile (HOCH2CN) in the interstellar medium

S Zeng D Quénard I Jiménez-Serra J Martín-Pintado V M Rivilla L Testi R Martín-Doménech

Monthly Notices of the Royal Astronomical Society: Letters, Volume 484, Issue 1, 21 March 2019, Pages L43–L48, https://doi.org/10.1093/mnrasl/slz002

Published: 14 January 2019 

Article history Received: 06 September 2018 Revision Received: 07 January 2019 

Accepted: 07 January 2019

Image of the Rho Ophiuchi star formation region with IRAS16293-2422 B circled.
Credit: ESO/Digitized Sky Survey 2. Acknowledgement: Davide De Martin

ABSTRACT

Theories of a pre-RNA world suggest that glycolonitrile (HOCH2CN) is a key species in the process of ribonucleotide assembly, which is considered as a molecular precursor of nucleic acids. In this Letter, we report the first detection of this pre-biotic molecule in the interstellar medium by using ALMA data obtained at frequencies between 86.5 GHz and 266.5 GHz toward the Solar-type protostar IRAS16293–2422 B. A total of 15 unblended transitions of HOCH2CN were identified. Our analysis indicates the presence of a cold (Tex = 24 ± 8 K) and a warm (Tex = 158 ± 38 K) component meaning that this molecule is present in both the inner hot corino and the outer cold envelope of IRAS16293 B. The relative abundance with respect to H2 is (6.5 ± 0.6) × 10−11 and ≥(6 ± 2) × 10−10 for the warm and cold components, respectively. Our chemical modelling seems to underproduce the observed abundance for both the warm and cold component under various values of the cosmic ray ionization rate (ζ). Key gas phase routes for the formation of this molecule might be missing in our chemical network.

Keywords  line: identification, Instrumentation: interferometers, ISM: molecules, ISM: individual: IRAS16293-2422 B