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

Getting clear about the F-word in genomics

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

Published: April 1, 2020 https://doi.org/10.1371/journal.pgen.1008702

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.

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

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

https://doi.org/10.1021/acs.chemrev.9b00288

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.

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

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.

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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

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!!!

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

https://doi.org/10.1080/02724634.2019.172828

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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Journal of Vertebrate Paleontology

SARS-CoV-2 (COVID-19) pelos números

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

Source/Fonte

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.

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