Uma visão radical da evolução das organelas

segunda-feira, maio 04, 2020

Alternating terminal electron‐acceptors at the basis of symbiogenesis: How oxygen ignited eukaryotic evolution

Dave Speijer

First published:05 January 2017 https://doi.org/10.1002/bies.201600174



Abstract

What kind of symbiosis between archaeon and bacterium gave rise to their eventual merger at the origin of the eukaryotes? I hypothesize that conditions favouring bacterial uptake were based on exchange of intermediate carbohydrate metabolites required by recurring changes in availability and use of the two different terminal electron chain acceptors, the bacterial one being oxygen. Oxygen won, and definitive loss of the archaeal membrane potential allowed permanent establishment of the bacterial partner as the proto‐mitochondrion, further metabolic integration and highly efficient ATP production. This represents initial symbiogenesis, when crucial eukaryotic traits arose in response to the archaeon‐bacterium merger. The attendant generation of internal reactive oxygen species (ROS) gave rise to a myriad of further eukaryotic adaptations, such as extreme mitochondrial genome reduction, nuclei, peroxisomes and meiotic sex. Eukaryotic origins could have started with shuffling intermediate metabolites as is still essential today.

FREE PDF GRATIS: BioEssays

Inferindo entropia a partir da estrutura

Inferring entropy from structure

Gil Ariel
Department of Mathematics, Bar-Ilan University, 52000 Ramat Gan, Israel

Haim Diamant
Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, 69978 Tel Aviv, Israel



Abstract

The thermodynamic definition of entropy can be extended to nonequilibrium systems based on its relation to information. To apply this definition in practice requires access to the physical system’s microstates, which may be prohibitively inefficient to sample or difficult to obtain experimentally. It is beneficial, therefore, to relate the entropy to other integrated properties which are accessible out of equilibrium. We focus on the structure factor, which describes the spatial correlations of density fluctuations and can be directly measured by scattering. The information gained by a given structure factor regarding an otherwise unknown system provides an upper bound for the system’s entropy. We prove that the maximum-entropy model corresponds to an equilibrium system with an effective pair-interaction. Approximate closed-form relations for the effective pair-potential and entropy in terms of the structure factor are obtained. The relations are used to estimate the entropy of an exactly solvable model and numerical examples of systems out of equilibrium, and the results are compared with other entropy-estimation methods. The focus is on low-dimensional examples, where our method, as well as a recently proposed compression-based one, can be tested against a rigorous direct-sampling technique. The entropy inferred from the structure factor is found to be consistent with the other methods, superior for larger system sizes, and accurate in identifying global transitions. Our approach allows for extensions of the theory to more complex systems and to higher-order correlations.

FREE PDF GRATIS: arXiv 

Mais uma hipótese sobre a origem da vida: de três funções privilegiadas a quatro pilares

sábado, maio 02, 2020

Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars

by Stuart Bartlett 1,2,* and Michael L. Wong 3,4
 
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA

Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan

Department of Astronomy and Astrobiology Program, University of Washington, Seattle, WA 98195, USA

NASA Nexus for Exoplanet System Science’s Virtual Planetary Laboratory, University of Washington, Seattle, WA 98195, USA

Author to whom correspondence should be addressed.


Received: 23 March 2020 / Revised: 12 April 2020 / Accepted: 13 April 2020 / Published: 16 April 2020

(This article belongs to the Special Issue Frontiers of Astrobiology)



Abstract

Motivated by the need to paint a more general picture of what life is—and could be—with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research. Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning. Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. This new classification system allows the astrobiological community to more clearly define the questions that propel their research—e.g., whether they are developing a historical narrative to explain the origin of life (on Earth), or a universal narrative for the emergence of lyfe, or whether they are seeking signs of life specifically, or lyfe at large across the universe. While the concept of “life as we don’t know it” is not new, the four pillars of lyfe offer a novel perspective on the living state that is indifferent to the particular components that might produce it. 

Keywords: definition of life; origin of life; astrobiology; mechanotroph

FREE PDF GRATIS: Life

Esclarecendo a respeito da palavra F(unção) em genômica.

quinta-feira, abril 30, 2020

Getting clear about the F-word in genomics

Stefan Linquist ,W. Ford Doolittle, Alexander F. Palazzo



Although biology is generally awash with adaptationist “just-so” stories, the situation in molecular biology and genomics is particularly bad. Various types of non-coding DNA are routinely interpreted as functional without adequate consideration of non-adaptationist alternative hypotheses [1]. Part of the problem is surely due to a failure in these disciplines to appreciate theoretical developments in population genetics, which outline the conditions under which genetic elements are selected [2]. However, as a number of authors have noted, the problem is also partly due to a confusion about the various possible meanings of “function” in biology [3–5]. Our central thesis is that there exists an overlooked dichotomy in the way that researchers see natural selection to be related to function. Traits or genetic elements that are merely under purifying selection have what we call maintenance functions whereas those that have historically been under directional selection have origin functions. We argue that ignoring this distinction encourages a form of pan-adaptationism, where highly plausible non-adaptive explanations for the origins of certain genetic elements or traits are themselves ignored. Thus, our recommendation is for researchers to always clarify which sense of “function” they mean (origin or maintenance) when talking or writing about selected effects.

Citation: Linquist S, Doolittle WF, Palazzo AF (2020) Getting clear about the F-word in genomics. PLoS Genet 16(4): e1008702. https://doi.org/10.1371/journal.pgen.1008702

Editor: Jonathan Flint, University of California Los Angeles, UNITED STATES

Published: April 1, 2020

Copyright: © 2020 Linquist et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: Financial support for this research was provided by the Social Sciences and Humanities Research Council of Canada (https://www.sshrc-crsh.gc.ca/, grant #430335) to Stefan Linquist and by the Natural Sciences and Engineering Research Council of Canada (nserc-crsng.gc.ca, grant # GLDSU44989) to W. Ford Doolittle. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

FREE PDF GRATIS: PLoS Genetics

Design de movimentos coletivos de interruptores, rotores e motores moleculares sintéticos

segunda-feira, abril 20, 2020

Design of Collective Motions from Synthetic Molecular Switches, Rotors, and Motors

Damien Dattler Gad Fuks Joakim Heiser Emilie Moulin Alexis Perrot Xuyang Yao Nicolas Giuseppone*

Cite this: Chem. Rev. 2020, 120, 1, 310-433

Publication Date:December 23, 2019


Copyright © 2019 American Chemical Society


Abstract

Precise control over molecular movement is of fundamental and practical importance in physics, biology, and chemistry. At nanoscale, the peculiar functioning principles and the synthesis of individual molecular actuators and machines has been the subject of intense investigations and debates over the past 60 years. In this review, we focus on the design of collective motions that are achieved by integrating, in space and time, several or many of these individual mechanical units together. In particular, we provide an in-depth look at the intermolecular couplings used to physically connect a number of artificial mechanically active molecular units such as photochromic molecular switches, nanomachines based on mechanical bonds, molecular rotors, and light-powered rotary motors. We highlight the various functioning principles that can lead to their collective motion at various length scales. We also emphasize how their synchronized, or desynchronized, mechanical behavior can lead to emerging functional properties and to their implementation into new active devices and materials.

FREE PDF GRATIS: Chemical Reviews 129 MBs!!!

Actina: a percepção do nível atômico das proteínas promove compreensão fundamental da vida humana: mero acaso, fortuita necessidade ou design inteligente?

sexta-feira, abril 17, 2020

Mechanism of actin N-terminal acetylation

Grzegorz Rebowski1,*, Malgorzata Boczkowska1,*, Adrian Drazic2, Rasmus Ree2, Marianne Goris3, Thomas Arnesen2,3,4 and Roberto Dominguez1,†

1Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

2Department of Biomedicine, University of Bergen, Bergen, Norway.

3Department of Biological Sciences, University of Bergen, Bergen, Norway.

4Department of Surgery, Haukeland University Hospital, Bergen, Norway.

↵†Corresponding author. Email: droberto@pennmedicine.upenn.edu

↵* These authors contributed equally to this work.

Science Advances 08 Apr 2020:

Vol. 6, no. 15, eaay8793

DOI: 10.1126/sciadv.aay8793

Fig. 3 Structural basis of NAA80 binding to actin-profilin.

Abstract

About 80% of human proteins are amino-terminally acetylated (Nt-acetylated) by one of seven Nt-acetyltransferases (NATs). Actin, the most abundant protein in the cytoplasm, has its own dedicated NAT, NAA80, which acts posttranslationally and affects cytoskeleton assembly and cell motility. Here, we show that NAA80 does not associate with filamentous actin in cells, and its natural substrate is the monomeric actin-profilin complex, consistent with Nt-acetylation preceding polymerization. NAA80 Nt-acetylates actin-profilin much more efficiently than actin alone, suggesting that profilin acts as a chaperone for actin Nt-acetylation. We determined crystal structures of the NAA80-actin-profilin ternary complex, representing different actin isoforms and different states of the catalytic reaction and revealing the first structure of NAT-substrate complex at atomic resolution. The structural, biochemical, and cellular analysis of mutants shows how NAA80 has evolved to specifically recognize actin among all cellular proteins while targeting all six actin isoforms, which differ the most at the amino terminus.

FREE PDF GRATIS: Science Advances Sup. Info.

Darwin, as árvores evolutivas não podem revelar taxas de especiação e extinção

Nature

Article

Published: 15 April 2020

Extant timetrees are consistent with a myriad of diversification histories

Stilianos Louca & Matthew W. Pennell 

Nature (2020)


Figure 1 | Assessing evolutionary histories. Louca and Pennell1 raise questions about a standard approach to estimating past rates of species formation (speciation) and extinction that uses data from a lineage-through-time plot. The number of species in the present depends on how speciation and extinction rates varied over time in the past. 

Abstract

Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics1. However, there has been considerable debate surrounding the reliability of these inferences2,3,4,5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth–death model, which underlies most existing methods of estimation. We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These ‘congruent’ scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence. We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions.

Data availability

No new data were generated for this manuscript. All phylogenetic datasets used as examples have previously been published previously, and are cited where appropriate.

Code availability

Computational methods used for this article—including functions for simulating birth–death models, for constructing models within a given congruence class, for calculating the likelihood of a congruence class and for directly fitting congruence classes (either in terms of λp or in terms of rp and ρλo) to extant timetrees—are implemented in the R package castor v.1.5.5, which is available from The Comprehensive R Archive Network at https://cran.r-project.org/package=castor.

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Bertrand Russell 'falou e disse': o argumento de design não tem defeito lógico formal

segunda-feira, abril 13, 2020

Argumento de design: “Este argumento não tem defeito lógico formal; suas premissas são empíricas e sua conclusão professa ser alcançada de acordo com os cânones usuais da inferência empírica. A questão de se deve ser aceito ou não, portanto, não se refere a questões metafísicas gerais, mas a considerações comparativamente detalhadas ”(B. Russell, History of Western Philosophy [Nova York: Simon & Schuster, 1945], p. 589) .

 
Design argument: “This argument has no formal logical defect; its premises are empirical, and its conclusion professes to be reached in accordance with the usual canons of empirical inference. The question whether it is to be accepted or not turns, therefore, not on general metaphysical questions, but on comparatively detailed considerations” (B. Russell, History of Western Philosophy [New York: Simon & Schuster, 1945], p. 589).

Pegadas gigantes de dinossauros são encontradas no teto de uma caverna!!!

sábado, abril 11, 2020

Middle Jurassic tracks of sauropod dinosaurs in a deep karst cave in France

Jean-David Moreau, Vincent Trincal, Emmanuel Fara, Louis Baret, Alain Jacquet, Claude Barbini

Article: e1728286 | Received 29 Oct 2018, Accepted 13 Dec 2019, Published online: 25 Mar 2020



A scientist on a caving trip happened to spot dinosaur tracks in the ceiling of Castelbouc Cave in France. Credit: Jean-David Moreau et al./J. Vertebr. Paleontol.

ABSTRACT

Although the deep galleries of natural underground cavities are difficult to access and are sometimes dangerous, they have the potential to preserve trace fossils. Here, we report on the first occurrence of sauropod dinosaur tracks inside a karstic cave. Three trackways are preserved on the roof of the Castelbouc cave 500 m under the surface of the Causse Méjean plateau, southern France. The tracks are Bathonian in age (ca. 168–166 Ma), a crucial but still poorly known time interval in sauropod evolution. The three trackways yield sauropod tracks that are up to 1.25 m long and are therefore amongst the largest known dinosaur footprints worldwide. The trackmakers are hypothesized to be titanosauriforms. Some of the tracks are extremely well preserved and show impressions of digits, digital pads, and claws. We erect the new ichnogenus and ichnospecies Occitanopodus gandi, igen. et isp. nov. In order to characterize depositional environments, we conducted sedimentological, petrographic, and mineralogical analyses. The tracks from Castelbouc attest the presence of sauropods in proximal littoral environments during the Middle Jurassic. This discovery demonstrates the great potential of prospecting in deep karst caves that can occasionally offer larger and better-preserved surfaces than outdoor outcrops.

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SARS-CoV-2 (COVID-19) pelos números

quinta-feira, abril 02, 2020

SARS-CoV-2 (COVID-19) by the numbers

Yinon M Bar-On, Avi Flamholz, Rob Phillips, Ron Milo Is a corresponding author

The Weizmann Institute for Science, Israel; University of California, Berkeley, United States; California Institute of Technology, United States

FEATURE ARTICLE Mar 31, 2020


Abstract

The current SARS-CoV-2 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this snapshot, our aim is to provide a one-stop, curated graphical source for the key numbers that help us understand the virus driving our current global crisis. The discussion is framed around two broad themes: 1) the biology of the virus itself and 2) the characteristics of the infection of a single human host. Our one-page summary provides the key numbers pertaining to SARS-CoV-2, based mostly on peer-reviewed literature. The numbers reported in summary format are substantiated by the annotated references below. Readers are urged to remember that much uncertainty remains and knowledge of this pandemic and the virus driving it is rapidly evolving. In the paragraphs below we provide 'back of the envelope' calculations that exemplify the insights that can be gained from knowing some key numbers and using quantitative logic. These calculations serve to improve our intuition through sanity checks, but do not replace detailed epidemiological analysis.

FREE PDF GRATIS: eLIFE

Inglês científico como língua estrangeira

terça-feira, março 31, 2020

Scientific English as a Foreign Language

Nancy A. Burnham and Frederick L. Hutson

Department of Physics
Worcester Polytechnic Institute
100 Institute Road, Worcester, MA 01609-2280 USA

October 29, 2007


Abstract

These lessons in Scientific English were written for the benefit of our colleagues 
at the Ecole Polytechic Fédérale de Lausanne in Switzerland, where we were researchers from 1994-1999. As native English speakers, we were beseiged by nonnative speakers asking for help with their manuscripts, as many as five requests per week.

Each language group is susceptible to predictable mistakes in English; these lessons were written for our colleagues: French- and German-speaking scientists with a solid foundation in English. They appear in no particular order, having been prompted by typical mistakes that we observed from week to week.

Most lessons are followed by a quiz and a humorous quotation. In their original format, the lessons were emailed with blank spaces in the quizzes so that the subscribers — the list grew from a dozen to seven hundred — could test their knowledge before checking their answers at a website. In 2003, the web pages were migrated to http://users.wpi.edu/~nab/sci_eng/. And in 2007, Scott Cogan (Université de Franche-Comté, Besançon, France) kindly transformed them into a LaTeX file, to which we added a table of contents and this abstract.

Although we are now busy with physics education and research in the United States, Fred still occasionally corrects manuscripts and dissertations. You may contact him at flh@wpi.edu.

O princípio antrópico: mero acaso, fortuita necessidade ou design inteligente?

Has the universe developed for the express purpose of being observed and understood by intelligent beings, or is it just a lucky break for the intelligent beings that they exist at all?

The Anthropic Principle was proposed in Poland in 1973, during a special two-week series of synopsia commemorating Copernicus’s 500th birthday. It was proposed by Brandon Carter, who, on Copernicus’s birthday, had the audacity to proclaim that humanity did indeed hold a special place in the Universe, an assertion that is the exact opposite of Copernicus’s now universally accepted theory.

Carter was not, however, claiming that the Universe was our own personal playground, made specifically with humanity in mind. The version of the Anthropic Principle that he proposed that day, which is now referred to as the Weak Anthropic Principle (WAP) stated only that by our very existence as carbon-based intelligent creatures, we impose a sort of selection effect on the Universe. For example, in a Universe where just one of the fundamental constants that govern nature was changed - say, the strength of gravity - we wouldn’t be here to wonder why gravity is the strength it is. The following is the official definition of the WAP:

“Weak Anthropic Principle (WAP): the observed values of all physical and cosmological quantities are not equally probable but they take on the values restricted by the requirement that there exist sites where carbon-based life can evolve and by the requirement that the Universe be old enough for it to have already done so.” (The Anthropic Cosmological Principle by John Barrow and Frank Tipler, p. 16)

Later, Carter also proposed the Strong Anthropic Principle (SAP), which states that the Universe had to bring humanity into being. This version is much more teleological, if not theological, and is of a highly speculative nature. Nonetheless, Carter had scientific reasons to propose it. The definition of the SAP) is as follows:

“Strong Anthropic Principle (SAP): the Universe must have those properties which allow life to develop within it at some stage in it’s history.” (The Anthropic Cosmological Principle, p. 21)

In addition to the WAP and SAP, there are the Participatory and Final Anthropic Principles. The Participatory Anthropic Principle states not only that the Universe had to develop humanity (or some other intelligent, information-gathering life form) but that we are necessary to it’s existence, as it takes an intelligent observer to collapse the Universe’s waves and probabilities from superposition into relatively concrete reality. The Final Anthropic Principle states that once the Universe has brought intelligence into being, it will never die out. These two are also very speculative.

The Selection effect of the WAP              



            
Links and references                         

Send comments or questions to:
JRedmane@aolNOSPAM.com
(redmove the NOSPAM from the address before sending)

Splicing do RNA pelo Spliceossoma: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, março 26, 2020

RNA Splicing by the Spliceosome

Annual Review of Biochemistry

Vol. 89:- (Volume publication date June 2020)
Review in Advance first posted online on December 3, 2019. (Changes may still occur before final publication.)


Max E. Wilkinson,* Clément Charenton,* and Kiyoshi Nagai*

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; email: mwilkin@mrc-lmb.cam.ac.uk, ccharent@mrc-lmb.cam.ac.uk

*All authors contributed equally to this article. M.E. Wilkinson and C. Charenton would like to dedicate this review to the memory of Kiyoshi Nagai (1949–2019)

Source/Fonte: Chemistry World

Abstract

The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5′ splice site (5′SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5′SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5′SS, producing a free 5′ exon. Removal of the BP adenosine from the active site allows the 3′SS to bind, so that the 5′ exon attacks the 3′SS to produce mature mRNA and an excised lariat intron.

Expected final online publication date for the Annual Review of Biochemistry, Volume 89 is June 22, 2020. Please see


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Annual Review of Biochemistry Sup Info

Modelo computacional de célula humana revela nova visão sobre o processamento de informação genética: mero acaso, fortuita necessidade ou design inteligente?

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Zhaleh Ghaemi , Joseph R. Peterson, Martin Gruebele, Zaida Luthey-Schulten



Abstract

Spatial organization is a characteristic of all cells, achieved in eukaryotic cells by utilizing both membrane-bound and membrane-less organelles. One of the key processes in eukaryotes is RNA splicing, which readies mRNA for translation. This complex and highly dynamical chemical process involves assembly and disassembly of many molecules in multiple cellular compartments and their transport among compartments. Our goal is to model the effect of spatial organization of membrane-less organelles (specifically nuclear speckles) and of organelle heterogeneity on splicing particle biogenesis in mammalian cells. Based on multiple sources of complementary experimental data, we constructed a spatial model of a HeLa cell to capture intracellular crowding effects. We then developed chemical reaction networks to describe the formation of RNA splicing machinery complexes and splicing processes within nuclear speckles (specific type of non-membrane-bound organelles). We incorporated these networks into our spatially-resolved human cell model and performed stochastic simulations for up to 15 minutes of biological time, the longest thus far for a eukaryotic cell. We find that an increase (decrease) in the number of nuclear pore complexes increases (decreases) the number of assembled splicing particles; and that compartmentalization is critical for the yield of correctly-assembled particles. We also show that a slight increase of splicing particle localization into nuclear speckles leads to a disproportionate enhancement of mRNA splicing and a reduction in the noise of generated mRNA. Our model also predicts that the distance between genes and speckles has a considerable effect on the mRNA production rate, with genes located closer to speckles producing mRNA at higher levels, emphasizing the importance of genome organization around speckles. The HeLa cell model, including organelles and sub-compartments, provides a flexible foundation to study other cellular processes that are strongly modulated by spatiotemporal heterogeneity.

Author summary

The spliceosome is one of the most complex cellular machineries. It cuts and splices the RNA code in eukaryotic cells by dynamically assembling and disassembling. The components of spliceosome are formed in both the nucleus and the cytoplasm within the cell and primarily localized in nuclear membrane-less organelles. Therefore, a computational model of spliceosomal function must contain a spatial model of the entire cell. However, building such a model is a challenging task, mainly due to the lack of homogeneous experimental data and a suitable computational framework. Here, we overcome these challenges and present a spatially-resolved HeLa cell model, with nuclear, subnuclear, and extensive cytoplasmic structures. The three-dimensional model is supplemented by reaction-diffusion processes to shed light on the function of the spliceosome.

Citation: Ghaemi Z, Peterson JR, Gruebele M, Luthey-Schulten Z (2020) An in-silico human cell model reveals the influence of spatial organization on RNA splicing. PLoS Comput Biol 16(3): e1007717. 

Editor: Attila Csikász-Nagy, King’s College London, UNITED KINGDOM

Received: August 14, 2019; Accepted: February 6, 2020; Published: March 25, 2020

Copyright: © 2020 Ghaemi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files. Additionally, the code we developed can be downloaded from Github through: https://eukaryoticcellbuilder.github.io/HeLa_Builder/.

Funding: This work was supported by the NSF grants MCB-1244570 on the Evolution of Translation:From Molecules to Cells to Z.G. and Z.L-S. and NSF Center for the Physics of Living Cells grant PHY-1430124 to M.G. and Z.L-S.,the NSF Graduate Fellowship [grant DGE-1144245] to J.R.P., and the NIH P41-GM104601 to Z.L-S. Z.L-S held the Murchison-Mallory Chair and M.G. held the James R. Eiszner Chair while this work was carried out. Supercomputer time was provided by XStream-XSEDE [grant TG-MCA03S027]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

FREE PDF GRATIS: PLoS Computational Biology

O Coronavírus-19 não foi intencionalmente planejado.

domingo, março 22, 2020

The proximal origin of SARS-CoV-2
Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes & Robert F. Garry 
Nature Medicine (2020)

To the Editor — Since the first reports of novel pneumonia (COVID-19) in Wuhan, Hubei province, China1,2, there has been considerable discussion on the origin of the causative virus, SARS-CoV-23 (also referred to as HCoV-19)4. Infections with SARS-CoV-2 are now widespread, and as of 11 March 2020, 121,564 cases have been confirmed in more than 110 countries, with 4,373 deaths5.
Source/Fonte: Nature Medicine
SARS-CoV-2 is the seventh coronavirus known to infect humans; SARS-CoV, MERS-CoV and SARS-CoV-2 can cause severe disease, whereas HKU1, NL63, OC43 and 229E are associated with mild symptoms6. Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data. We offer a perspective on the notable features of the SARS-CoV-2 genome and discuss scenarios by which they could have arisen. Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.

Notable features of the SARS-CoV-2 genome

Our comparison of alpha- and betacoronaviruses identifies two notable genomic features of SARS-CoV-2: (i) on the basis of structural studies7,8,9 and biochemical experiments1,9,10, SARS-CoV-2 appears to be optimized for binding to the human receptor ACE2; and (ii) the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site at the S1–S2 boundary through the insertion of 12 nucleotides8, which additionally led to the predicted acquisition of three O-linked glycans around the site.
...
FREE PDF GRATIS: Nature Medicine

Uma previsão científica de pandemia por Coronavírus na China ignorada

sexta-feira, março 20, 2020

Bat Coronaviruses in China

Yi Fan 1,2, Kai Zhao 1,2, Zheng-Li Shi 1,2 andPeng Zhou 1,2,*

CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China

University of Chinese Academy of Sciences, Beijing 100049, China

Author to whom correspondence should be addressed.

Viruses 2019, 11(3), 210; https://doi.org/10.3390/v11030210

Received: 29 January 2019 / Revised: 26 February 2019 / Accepted: 26 February 2019 / Published: 2 March 2019


Abstract

During the past two decades, three zoonotic coronaviruses have been identified as the cause of large-scale disease outbreaks–Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Swine Acute Diarrhea Syndrome (SADS). SARS and MERS emerged in 2003 and 2012, respectively, and caused a worldwide pandemic that claimed thousands of human lives, while SADS struck the swine industry in 2017. They have common characteristics, such as they are all highly pathogenic to humans or livestock, their agents originated from bats, and two of them originated in China. Thus, it is highly likely that future SARS- or MERS-like coronavirus outbreaks will originate from bats, and there is an increased probability that this will occur in China. Therefore, the investigation of bat coronaviruses becomes an urgent issue for the detection of early warning signs, which in turn minimizes the impact of such future outbreaks in China. The purpose of the review is to summarize the current knowledge on viral diversity, reservoir hosts, and the geographical distributions of bat coronaviruses in China, and eventually we aim to predict virus hotspots and their cross-species transmission potential. 

Keywords: coronavirus; bat; epidemiology; cross-species; zoonosis

FREE PDF GRATIS: Viruses

Avi Loeb, Universidade Harvard, 'falou e disse': A falseabilidade deve ser marca registrada de qualquer teoria científica.



A falseabilidade deve ser uma marca registrada de qualquer teoria científica.


O fator X na vida - Segredos da célula com Michael Behe - Episódio 5

quinta-feira, março 12, 2020

Mais outra hipótese sobre a origem da vida: emergência espontânea de moléculas auto-replicantes contendo nucleobases e aminoácidos

terça-feira, março 10, 2020

Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids

Bin Liu Charalampos G. Pappas Jim Ottelé Gaël Schaeffer Christoph Jurissek Priscilla F. Pieters Meniz Altay Ivana Marić Marc C. A. Stuart Sijbren Otto*

Cite this: J. Am. Chem. Soc. 2020, 142, 9, 4184-4192

Publication Date:February 5, 2020


Copyright © 2020 American Chemical Society



Abstract

The conditions that led to the formation of the first organisms and the ways that life originates from a lifeless chemical soup are poorly understood. The recent hypothesis of “RNA-peptide coevolution” suggests that the current close relationship between amino acids and nucleobases may well have extended to the origin of life. We now show how the interplay between these compound classes can give rise to new self-replicating molecules using a dynamic combinatorial approach. We report two strategies for the fabrication of chimeric amino acid/nucleobase self-replicating macrocycles capable of exponential growth. The first one relies on mixing nucleobase- and peptide-based building blocks, where the ligation of these two gives rise to highly specific chimeric ring structures. The second one starts from peptide nucleic acid (PNA) building blocks in which nucleobases are already linked to amino acids from the start. While previously reported nucleic acid-based self-replicating systems rely on presynthesis of (short) oligonucleotide sequences, self-replication in the present systems start from units containing only a single nucleobase. Self-replication is accompanied by self-assembly, spontaneously giving rise to an ordered one-dimensional arrangement of nucleobase nanostructures.

FREE PDF GRATIS: J Am Chem Soc  Sup. Info.

Mais uma hipótese sobre a origem da vida em um universo inflacionário

segunda-feira, março 09, 2020

Scientific Reports

Emergence of life in an inflationary universe

Tomonori Totani 

Scientific Reports volume 10, Article number: 1671

The center of the Milky Way galaxy, as visualized by the Spitzer Space Telescope’s infrared cameras.

Abstract

Abiotic emergence of ordered information stored in the form of RNA is an important unresolved problem concerning the origin of life. A polymer longer than 40–100 nucleotides is necessary to expect a self-replicating activity, but the formation of such a long polymer having a correct nucleotide sequence by random reactions seems statistically unlikely. However, our universe, created by a single inflation event, likely includes more than 10100 Sun-like stars. If life can emerge at least once in such a large volume, it is not in contradiction with our observations of life on Earth, even if the expected number of abiogenesis events is negligibly small within the observable universe that contains only 1022 stars. Here, a quantitative relation is derived between the minimum RNA length lmin required to be the first biological polymer, and the universe size necessary to expect the formation of such a long and active RNA by randomly adding monomers. It is then shown that an active RNA can indeed be produced somewhere in an inflationary universe, giving a solution to the abiotic polymerization problem. On the other hand, lmin must be shorter than ~20 nucleotides for the abiogenesis probability close to unity on a terrestrial planet, but a self-replicating activity is not expected for such a short RNA. Therefore, if extraterrestrial organisms of a different origin from those on Earth are discovered in the future, it would imply an unknown mechanism at work to polymerize nucleotides much faster than random statistical processes.
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FREE PDF GRATIS: Scientific Reports