Banco de Dados de Biologia – Uma Lista de Códigos Biológicos

sexta-feira, dezembro 02, 2022

 

National Human Genome Research Institute

FREE PDF GRATIS: Codebiology.org

Analisando disparidade e taxas de evolução morfológica com métodos comparativos baseados em modelos filogenéticos

quinta-feira, dezembro 01, 2022

Analyzing Disparity and Rates of Morphological Evolution with Model-Based Phylogenetic Comparative Methods

Thomas F Hansen, Geir H Bolstad, Masahito Tsuboi

Systematic Biology, Volume 71, Issue 5, September 2022, Pages 1054–1072, https://doi.org/10.1093/sysbio/syab079

Published: 02 December 2021


Relative overall rates of morphological evolution in early tetrapodomorphs.

Nature Ecology & Evolution volume 5, pages1403–1414 (2021)

Abstract

Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species, we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.

[Baldwin effect; beak shape; behavioral drive; bird; brain size; disparity; phylogenetic comparative method; rate of evolution.]

FREE PDF GRATIS: Systematic Biology

Transdução de sinal mitocondrial: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, novembro 16, 2022

Mitochondrial signal transduction

Martin Picard, Orian S. Shirihai

Open Access DOI: https://doi.org/10.1016/j.cmet.2022.10.00



Summary

The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.

Keywords signal transduction evolution mitochondrial networks steroid hormones receptors amplification membrane potential communication mito-nuclear signaling tissuespecific mitotypes stress  responses metabokines mitokines energyhealth

FREE PDF GRATIS: Cell Metabolism

Renovando a taxonomia de Lineu: uma proposta para reestruturar os níveis mais altos do Sistema Natural.

segunda-feira, novembro 14, 2022

Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System

Peter T. S. van der Gulik, Wouter D. Hoff, David Speijer

First published: 10 November 2022 https://doi.org/10.1111/brv.12920



ABSTRACT

During the last century enormous progress has been made in the understanding of biological diversity, involving a dramatic shift from macroscopic to microscopic organisms. The question now arises as to whether the Natural System introduced by Carl Linnaeus, which has served as the central system for organizing biological diversity, can accommodate the great expansion of diversity that has been discovered. Important discoveries regarding biological diversity have not been fully integrated into a formal, coherent taxonomic system. In addition, because of taxonomic challenges and conflicts, various proposals have been made to abandon key aspects of the Linnaean system. We review the current status of taxonomy of the living world, focussing on groups at the taxonomic level of phylum and above. We summarize the main arguments against and in favour of abandoning aspects of the Linnaean system. Based on these considerations, we conclude that retaining the Linnaean Natural System provides important advantages. We propose a relatively small number of amendments for extending this system, particularly to include the named rank of world (Latin alternative mundis) formally to include non-cellular entities (viruses), and the named rank of empire (Latin alternative imperium) to accommodate the depth of diversity in (unicellular) eukaryotes that has been uncovered. We argue that in the case of both the eukaryotic domain and the viruses the cladistic approach intrinsically fails. However, the resulting semi-cladistic system provides a productive way forward that can help resolve taxonomic challenges. The amendments proposed allow us to: (i) retain named taxonomic levels and the three-domain system, (ii) improve understanding of the main eukaryotic lineages, and (iii) incorporate viruses into the Natural System. Of note, the proposal described herein is intended to serve as the starting point for a broad scientific discussion regarding the modernization of the Linnaean system.

FREE PDF GRATIS: Biological Reviews

Erik Svensson (Universidade de Lund) 'falou e disse': o estudo da evolução está fraturando – e isso pode ser uma coisa boa!

sábado, novembro 12, 2022

The study of evolution is fracturing – and that may be a good thing

Published: November 9, 2022 4.24pm GMT

Author: Erik Svensson

Professor (Evolutionary Ecology Unit, Department of Biology), Lund University

Disclosure statement:

Erik Svensson receives funding from from the Swedish Research Council (VR; grant no. 2020-03123).

How will life on Earth and the ecosystems that support it adapt to climate change? Which species will go extinct – or evolve into something new? How will microbes develop further resistance to antibiotics?

These kinds of questions, which are of fundamental importance to our way of life, are all a focus for researchers who study evolution and will prove increasingly important as the planet heats up.

But finding the answers isn’t the only challenge facing evolutionary biology. Charles Darwin’s theories might be over 150 years old but major questions about how evolution works are far from settled.

Evolutionary biology is now undergoing one of the most intense debates it has had for more than a generation. And how this debate plays out could have a significant impact on the future of this scientific field.

Some biologists and philosophers claim that evolutionary biology needs reform, arguing that traditional explanations for how organisms change through time that scientists have assumed since the 1930s are holding back the assimilation of novel findings

Contemporary evolutionary biology, a vocal minority argue, is incomplete. The dominant and traditional view of the field is too preoccupied with how the genes in a population change over time. This neglects, these critics argue, how individual organisms shape their environments and adjust themselves during their lifetimes to survive and reproduce.

Some go so far as to say that evolutionary theory itself is in crisis and must be replaced with something new.

Not all biologists are convinced. Some argue that repeated calls for reform are mistaken and can actually hinder progress.

...

READ MORE HERE: The Conversation

Universo 'assimétrico' pode significar revisão do modelo cosmológico padrão.

domingo, novembro 06, 2022

A Challenge to the Standard Cosmological Model

Nathan J. Secrest 1, Sebastian von Hausegger 2, Mohamed Rameez 3, Roya Mohayaee 2,4, and Subir Sarkar 2

Published 2022 September 28 • © 2022. The Author(s). Published by the American Astronomical Society.

The Astrophysical Journal Letters, Volume 937, Number 2



Abstract

We present the first joint analysis of catalogs of radio galaxies and quasars to determine whether their sky distribution is consistent with the standard ΛCDM model of cosmology. This model is based on the cosmological principle, which asserts that the universe is statistically isotropic and homogeneous on large scales, so the observed dipole anisotropy in the cosmic microwave background (CMB) must be attributed to our local peculiar motion. We test the null hypothesis that there is a dipole anisotropy in the sky distribution of radio galaxies and quasars consistent with the motion inferred from the CMB, as is expected for cosmologically distant sources. Our two samples, constructed respectively from the NRAO VLA Sky Survey and the Wide-field Infrared Survey Explorer, are systematically independent and have no shared objects. Using a completely general statistic that accounts for correlation between the found dipole amplitude and its directional offset from the CMB dipole, the null hypothesis is independently rejected by the radio galaxy and quasar samples with p-values of 8.9 × 10−3 and 1.2 × 10−5, respectively, corresponding to 2.6σ and 4.4σ significance. The joint significance, using sample-size-weighted Z-scores, is 5.1σ. We show that the radio galaxy and quasar dipoles are consistent with each other and find no evidence for any frequency dependence of the amplitude. The consistency of the two dipoles improves if we boost to the CMB frame assuming its dipole to be fully kinematic, suggesting that cosmologically distant radio galaxies and quasars may have an intrinsic anisotropy in this frame.

FREE PDF GRATIS: The Astrophysical Journal Letters

Livro Open Access - A History of Scientific Journals: Publishing at the Royal Society, 1665-2015

terça-feira, outubro 11, 2022

New open access book: A History of Scientific Journals: Publishing at the Royal Society, 1665-2015 (UCL Press)


Modern scientific research has changed so much since Isaac Newton’s day: it is more professional, collaborative and international, with more complicated equipment and a more diverse community of researchers. Yet the use of scientific journals to report, share and store results is a thread that runs through the history of science from Newton’s day to ours. Scientific journals are now central to academic research and careers. Their editorial and peer-review processes act as a check on new claims and findings, and researchers build their careers on the list of journal articles they have published. The journal that reported Newton’s optical experiments still exists. First published in 1665, and now fully digital, the Philosophical Transactions has carried papers by Charles Darwin, Dorothy Hodgkin and Stephen Hawking. It is now one of eleven journals published by the Royal Society of London.

Unrivalled insights from the Royal Society’s comprehensive archives have enabled the authors to investigate more than 350 years of scientific journal publishing. The editorial management, business practices and financial difficulties of the Philosophical Transactions and its sibling Proceedings reveal the meaning and purpose of journals in a changing scientific community. At a time when we are surrounded by calls to reform the academic publishing system, it has never been more urgent that we understand its history.

Free download/Download gratis: https://bit.ly/3SMcHOl

Darwin, nós temos um problema: o requisito de celularidade para ocorrer a abiogênese

sábado, outubro 01, 2022

Computational and Structural Biotechnology Journal

Volume 19, 2021, Pages 2202-2212

The requirement of cellularity for abiogenesis

AdrianoCaliari a JianXu b Tetsuya Yomo b

a School of Software Engineering, East China Normal University, Shanghai 200062, PR China

b Laboratory of Biology and Information Science, Biomedical Synthetic Biology Research Center, School of Life Sciences, East China Normal University, Shanghai 200062, PR China

Received 17 February 2021, Revised 10 April 2021, Accepted 13 April 2021, Available online 17 April 2021, Version of Record 24 April 2021.

https://doi.org/10.1016/j.csbj.2021.04.030 


Abstract

The history of modern biochemistry started with the cellular theory of life. By putting aside the holistic protoplasmic theory, scientists of the XX century were able to advance the functional classification of cellular components significantly. The cell became the unit of the living. Current theories on the abiogenesis of life must account for a moment in evolution (chemical or biological) when this was not the case. Investigating the role of compartments and membranes along chemical and biotic evolution can lead a more generalised idea of living organisms that is fundamental to advance our efforts in astrobiology, origin of life and artificial life studies. Furthermore, it may provide insights in unexplained evolutionary features such as the lipid divide between Archaea and Eubacteria. By surveying our current understanding of the involvement of compartments in abiogenesis and evolution, the idea of cells as atomistic units of a general theory of biology will be discussed. The aim is not to undermine the validity of the cellular theory of life, but rather to elucidate possible biases with regards to cellularity and the origin of life. An open discussion in these regards could show the inherent limitations of non-cellular compartmentalization that may lead to the necessity of cellular structures to support complex life.

FREE PDF GRATIS: Computational and Structural Biotechnology Journal

Darwin, nós temos um problema: expondo os pontos fracos evolutivos do genoma humano

sexta-feira, setembro 23, 2022

Extreme purifying selection against point mutations in the human genome

Noah Dukler, Mehreen R. Mughal, Ritika Ramani, Yi-Fei Huang & Adam Siepel 

Nature Communications volume 13, Article number: 4312 (2022)


Abstract

Large-scale genome sequencing has enabled the measurement of strong purifying selection in protein-coding genes. Here we describe a new method, called ExtRaINSIGHT, for measuring such selection in noncoding as well as coding regions of the human genome. ExtRaINSIGHT estimates the prevalence of “ultraselection” by the fractional depletion of rare single-nucleotide variants, after controlling for variation in mutation rates. Applying ExtRaINSIGHT to 71,702 whole genome sequences from gnomAD v3, we find abundant ultraselection in evolutionarily ancient miRNAs and neuronal protein-coding genes, as well as at splice sites. By contrast, we find much less ultraselection in other noncoding RNAs and transcription factor binding sites, and only modest levels in ultraconserved elements. We estimate that ~0.4–0.7% of the human genome is ultraselected, implying ~ 0.26–0.51 strongly deleterious mutations per generation. Overall, our study sheds new light on the genome-wide distribution of fitness effects by combining deep sequencing data and classical theory from population genetics.

RNA, o epicentro de informação genética

terça-feira, setembro 20, 2022

RNA, the Epicenter of Genetic Information

By John Mattick, Paulo Amaral

Copyright Year 2023 ISBN 9780367567781

Published September 20, 2022 by CRC Press

422 Pages 78 Color & 23 B/W Illustrations

Available on Taylor & Francis eBooks



Book Description

The origin story and emergence of molecular biology is muddled. The early triumphs in bacterial genetics and the complexity of animal and plant genomes complicate an intricate history. This book documents the many advances, as well as the prejudices and founder fallacies. It highlights the premature relegation of RNA to simply an intermediate between gene and protein, the underestimation of the amount of information required to program the development of multicellular organisms, and the dawning realization that RNA is the cornerstone of cell biology, development, brain function and probably evolution itself. Key personalities, their hubris as well as prescient predictions are richly illustrated with quotes, archival material, photographs, diagrams and references to bring the people, ideas and discoveries to life, from the conceptual cradles of molecular biology to the current revolution in the understanding of genetic information.

Key Features

- Documents the confused early history of DNA, RNA and proteins - a transformative history of molecular biology like no other.

- Integrates the influences of biochemistry and genetics on the landscape of molecular biology.

- Chronicles the important discoveries, preconceptions and misconceptions that retarded or misdirected progress.

- Highlights major pioneers and contributors to molecular biology, with a focus on RNA and noncoding DNA.

- Summarizes the mounting evidence for the central roles of non-protein-coding RNA in cell and developmental biology.

- Provides a thought-provoking retrospective and forward-looking perspective for advanced students and professional researchers.

The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license.

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Nomenklatura científica, nós temos um problema: diminuindo a Navalha de Ockham!

terça-feira, setembro 13, 2022

Cutting Down Ockham's Razor

William of Ockham famously argued that the simplest explanation is likely the best one. The idea is appealing, widely believed, and deeply misleading.

By Jim Al-Khalili

 Save your razors for shaving hairs Image/Imagem

We hear all the time that the simplest explanations are usually the right ones. This truth-testing idea—known as Ockham’s razor, after the English medieval philosopher William of Ockham—has been embraced by no less authorities than Isaac Newton and Albert Einstein. Today scientists invoke Ockham’s razor on topics ranging from Covid’s origins to cosmic dark matter, while folks debating a subject on social media regularly invoke it as their final arbiter. After all, why complicate something more than you need to? Isn’t it better to shave ideas down to their essential truths?

Ockham’s razor sounds logical and definitive, which is exactly what makes it dangerous. Not only is the assumption of simplicity often false, but following it blindly can lead to serious misunderstandings, both in science and in everyday life.

A well-known historical validation of the principle of simplicity in science was in the overthrow of the geocentric model of the universe. The ancient Greeks codified a cosmology in which Earth was motionless while the sun, moon, planets, and stars all moved around it in perfect circular paths. That model held sway for nearly 2,000 years, despite becoming increasingly cumbersome as it was modified to account for the observed movements of planets like Mars, which was seen to slow down, speed up, and sometimes even double back on itself.

The Greeks attempted to account for this “retrograde” motion of Mars by assuming that it followed a secondary, smaller circular path, called an epicycle, that was bolted onto its primary circular motion around Earth. Later, improved observations of Mars and the other planets required further tinkering with the geocentric model, such as adding epicycles on top of epicycles and shifting Earth slightly away from the center of all the other bodies’ orbits.

Then, in the 16th century, Nicolaus Copernicus swept away this makeshift model and replaced it with his much simpler heliocentric picture in which the sun, not Earth, is at the center of the universe. In this view, the complicated motions of Mars as seen from Earth could be explained as a consequence of the two planets orbiting the sun at different distances and speeds. Both the Earth-centered and sun-centered models worked, in the sense that they predicted the motions of heavenly bodies reasonably well, but we now know that only one of them is correct: the Copernican model, the one without all the clumsy extras. This, we are told, is Ockham’s razor in action.

But the above account is wrong. Although Copernicus correctly replaced Earth with the sun at the center of the known cosmos, he still believed the planetary orbits to be perfect circles rather than their actual ellipses. As a result, he still needed the epicycles and other unwieldy patch-ups of the old geocentric model to get this heliocentric system to work. Although we now know that Earth does indeed go around the sun, we also know that the true dynamics of our solar system are far more convoluted than anything the ancient Greeks could have imagined. In place of epicycles, we have an ever-shifting system of ellipses whose shapes can never be calculated with perfect precision. It is Ockham’s razor in reverse.

An equally famous example in the history of science is Darwin’s theory of evolution through natural selection. It provides a unifying explanation for the tremendous variety of life we find on Earth, all of which evolved over billions of years from a single origin. Darwin’s theory is based on a few simple assumptions: 1) that individuals within a population of any species vary; 2) that these variations pass down through the generations; 3) that more individuals are born in each generation than can survive; 4) that those with characteristics better adapted to suit their environment are more likely to survive and reproduce. That’s it.

However, wrapped up in these modest assumptions are the mind-bogglingly complex fields of evolutionary biology and genetics, which are among the most challenging areas in all of science. If we are to truly apply Ockham’s razor to life on Earth, then surely the nonscientific theory of creationism—that all life was brought forth as it is today by a supernatural maker—is far simpler than Darwinian evolution.

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Read more/Leia mais: Open Mind Magazine

Revisitando a extinção do mundo RNA

sexta-feira, agosto 26, 2022

Revisiting the Extinction of the RNA World

Anthony C. Forster*

Cite this: Biochemistry 2022, 61, 9, 749–751

Publication Date:April 7, 2022

https://doi.org/10.1021/acs.biochem.2c00121

Copyright © 2022 The Author. Published by American Chemical Society



Abstract

The ribozyme world is thought to have evolved the burdensome complexity of peptide and protein synthesis because the 20 amino acid side chains are catalytically superior. Instead, I propose that the Achilles heel of the RNA world that led to the extinction of riboorganisms was RNA’s polyanionic charges that could not be covalently neutralized stably by phosphotriester formation. These charges prevented development of hydrophobic cores essential for integration into membranes and many enzymatic reactions. In contrast, the phosphotriester modification of DNA is stable. So, the fact that the charge was never removed in DNA evolution gives further credence to proteins coming before DNA.

FREE PDF GRATIS: Biochemistry

Reflexões sobre a historiografia de Darwin: uma figura-chave científica sendo desconstruída.

sexta-feira, agosto 19, 2022

Reflections on Darwin Historiography

Janet Browne 

Journal of the History of Biology

Getty Images

Abstract

Much has happened in the Darwin field since the Correspondence began publishing in 1985. This overview of historiography suggests that the richness of the letters generates fresh scholarly questions and that Darwin, paradoxically, is becoming progressively deconstructed as a key figure in the history of science.

Subscription or payment needed/Requer assinatura ou pagamento: 

Journal of the History of Biology

Otodus megalodon, um extinto tubarão superpredador transoceânico

The extinct shark Otodus megalodon was a transoceanic superpredator: Inferences from 3D modeling

Jack A. Cooper, John R. Hutchinson, David C. Bernvi, Geremy Cliff, Rory P. Wilson, Matt L. Dicken, Jan Menzel, Stephen Wroe, Jeanette Pirlo, and Catalina Pimiento Authors Info & Affiliations

SCIENCE ADVANCES 17 Aug 2022 Vol 8, Issue 33 DOI: 10.1126/sciadv.abm9424


 

Abstract

Although shark teeth are abundant in the fossil record, their bodies are rarely preserved. Thus, our understanding of the anatomy of the extinct Otodus megalodon remains rudimentary. We used an exceptionally well-preserved fossil to create the first three-dimensional model of the body of this giant shark and used it to infer its movement and feeding ecology. We estimate that an adult O. megalodon could cruise at faster absolute speeds than any shark species today and fully consume prey the size of modern apex predators. A dietary preference for large prey potentially enabled O. megalodon to minimize competition and provided a constant source of energy to fuel prolonged migrations without further feeding. Together, our results suggest that O. megalodon played an important ecological role as a transoceanic superpredator. Hence, its extinction likely had large impacts on global nutrient transfer and trophic food webs.

FREE PDF GRATIS: Science Advances Sup. Info.

Darwin, nós temos um problema: uma breve história das histórias da carochinha em ciência evolucionária - explanação de narrativa implausível

sábado, agosto 13, 2022

A Brief (Hi)Story of Just-So Stories in Evolutionary Science

Michal Hubálek

First Published August 6, 2020 

https://doi.org/10.1177/0048393120944223

Volume: 51 issue: 5, page(s): 447-468

Article first published online: August 6, 2020; Issue published: September 1, 2021

Michal Hubálek 1

1 University of Hradec Králové, Hradec Králové, Czech Republic

Corresponding Author:

Michal Hubálek, Department of Philosophy and Social Sciences, University of Hradec Králové, Hradec Králové, EU 500 03, Czech Republic. Email: hubalek.michal.42@gmail.com



Abstract

In this essay, I examine the usage of the term “just-so story.” I attempt to show that just-so storytelling can be seen as an epistemic concept that, in various ways, tackles the epistemological and methodological problems relating to evolutionary explanations qua historical/narrative explanations. I identify two main, yet mutually exclusive, strategies of employing the concept of a just-so story: a negative strategy and a positive strategy. Subsequently, I argue that these strategies do not satisfactorily capture the core of the “original” meaning advanced by Stephen Jay Gould and Richard Lewontin at the end of the 1970s. I revisit the foundation(s) of their anti-adaptationist critique in order to reframe it as a critique of distinctive methodological manners and epistemic maxims related to historical inquiry. Last but not least, I suggest that contemporary evolutionary thinkers have two conceptually different options: they can either adhere to the “original” meaning of the term “just-so story” or accept that “just-so story” is a term equivalent to “implausible narrative explanation.”

Keywords just-so story, narrative explanation, adaptationism, Stephen Jay Gould, Richard Lewontin

Subscription or payment needed/Requer assinatura ou pagamento: Philosophy of the Social Sciences 

Darwin, nós temos um problema - o neodarwinismo é um paradigma falido!

sábado, agosto 06, 2022

The fight for the future of biology

The broken paradigm of Neo-Darwinism



4th August 2022

Denis Noble | World-renowned physiologist and Emeritus Professor of Cardiovascular Physiology at Oxford University. He is the author of Dance to the Tune of Life: Biological Relativity (CUP 2016).

The Neo-Darwinist paradigm maintains that natural selection is the sole driving force in evolution.  This paradigm is not only wrong, but untrue to Darwin’s theory of evolution which made room for  Lamarck’s suggestion that acquired characteristics can also be inherited. The side-lining any research into Lamarckian evolution has stifled the fruitful work of generations of researchers, limiting our understanding of how inheritance really works, argues Denis Noble.

The Neo-Darwinist paradigm of evolutionary biology is almost defined by its view of inheritance. That view is that acquired characteristics cannot be inherited, and that the organism itself has no active role in the evolution of the species. One of its founders, August Weismann, created the break with the ideas of Charles Darwin in 1883, just a year following Darwin’s death in 1882. He did so by inventing the Weismann Barrier, which he claimed protects the germ-line, the future eggs and sperm, from any influences of use-disuse features acquired by the organism during its lifetime. He was therefore going against the Lamarckian idea of inheritance of acquired characteristics that Darwin had accepted and later expanded upon in his writings on heredity. There was no experimental evidence for Weismann’s idea. He even wrote that it was a “necessary” idea, whether or not any experiments supported it.

...

Read more here: IAI News

Vendo a célula em uma dimensão totalmente nova: mero acaso, fortuita necessidade ou design inteligente?

sexta-feira, julho 29, 2022

Journal of Molecular Biology

Volume 434, Issue 2, 30 January 2022, 167351

Research Article

Building Structural Models of a Whole Mycoplasma Cell

Martina Maritan 1†Ludovic Autin 1†Jonathan Karr 2 Markus W.Covert 3 Arthur J.Olson 1 David S.Goodsell14

1 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA

2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA

4 RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA

Received 5 August 2021, Revised 4 November 2021, Accepted 5 November 2021, Available online 10 November 2021, Version of Record 22 November 2021.

Edited by Amy Keating

https://doi.org/10.1016/j.jmb.2021.167351 


Image of a 3D model of a Mycoplasma cell by Martina Maritan

Highlights

• 3D whole cell modeling requires new bioinformatics and computational methods.

• Information for generating 3D cell models is gathered and curated with Mesoscope.

• A multi-step workflow generates structural models of an entire proteome.

• Entire bacterial cells are interactively modeled and visualized with CellPACKgpu.

• This work demonstrates the feasibility of building 3D models of an entire cell.

Abstract

Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of integration between multiple sources of biological data and enhanced methods for computational modeling and visualization. Here, we present the first 3D structural models of an entire Mycoplasma genitalium (MG) cell, built using the CellPACK suite of computational modeling tools. Our model recapitulates the data described in recent whole-cell system biology simulations and provides a structural representation for all MG proteins, DNA and RNA molecules, obtained by combining experimental and homology-modeled structures and lattice-based models of the genome. We establish a framework for gathering, curating and evaluating these structures, exposing current weaknesses of modeling methods and the boundaries of MG structural knowledge, and visualization methods to explore functional characteristics of the genome and proteome. We compare two approaches for data gathering, a manually-curated workflow and an automated workflow that uses homologous structures, both of which are appropriate for the analysis of mesoscale properties such as crowding and volume occupancy. Analysis of model quality provides estimates of the regularization that will be required when these models are used as starting points for atomic molecular dynamics simulations.

FREE PDF GRATIS: Journal of Molecular Biology

Uma nova teoria da formação da Terra

Stochastic accretion of the Earth

Paolo A. Sossi, Ingo L. Stotz, Seth A. Jacobson, Alessandro Morbidelli & Hugh St. C. O’Neill 

Nature Astronomy (2022)

Artist’s impression of the forming Earth – from chondritic asteroids on the left, and from planetesimals on the right. Credit: Tobias Stierli / flaeck.ch


Abstract

Chondritic meteorites are thought to be representative of the material that formed the Earth. However, the Earth is depleted in volatile elements in a manner unlike that observed in any chondrite, and yet these elements retain chondritic isotope ratios. Here we use N-body simulations to show that the Earth did not form only from chondrites, but by stochastic accretion of many precursor bodies whose variable compositions reflect the temperatures at which they formed. Earth’s composition is reproduced when the initial temperatures of planetesimal- to embryo-sized bodies are set by disk accretion rates of (1.08 ± 0.17) × 10−7 solar masses per year, although they may be perturbed by 26Al heating on bodies formed at different times. Our model implies that a heliocentric gradient in composition was present in the protoplanetary disk and that planetesimals formed rapidly within ~1 Myr, consistent with radiometric volatile depletion ages of the Earth.

Subscription or payment needed/Requer assinatura ou pagamento: Nature Astronomy

Preprint available/Pre-impressão disponível: arXiv

A evolução química reimaginada

quarta-feira, julho 27, 2022

Chemical Evolution Reimagined

WORKING PAPER 

Moran Frenkel Pinter, Hebrew University of Jerusalem ,Kavita Matange, Georgia Institute of Technology, Vahab Rajaei, Georgia Institute of Technology, John T Costner, Georgia Institute of Technology, Adelaide Robertson, Georgia Institute of Technology, Jennifer Seoyoung Kim, Georgia Institute of Technology, Anton S Petrov, Georgia Institute of Technology, Jessica C. Bowman, Georgia Institute of Technology, Loren Dean, Williams Georgia Institute of Technology 


Image/Imagem: Chemistry World

Abstract

Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of new complex and functional chemical species. The spectacular polymers that underlay biology demonstrate an untapped, by modern science, creative potential. We hypothesized that prebiotic chemical evolutionary processes leading to biopolymers were not idiosyncratic one-off events. We have developed an experimental platform that accomplishes chemical evolution in the laboratory. In this paper we describe this platform and report empirical outcomes, some of which were not foreseen. We have constructed experimental platform to study evolution of chemical systems that: (i) undergo continuous recursive change with transitions to new chemical spaces while not converging, (ii) demonstrate stringent chemical selection, during which combinatorial explosion is avoided, (iii) maintain synchronicity of molecular sub-populations, and (iv) harvest environmental energy that is invested in chemical reactions. We have established general guidelines for conducting chemical evolution. Our results suggest that chemical evolution can be adapted to produce a broad array of molecules with novel structures and functions.

FREE PDF GRATIS: ChemRxiv Sup. Info.

A interpretação de embriões fósseis requer avaliação razoável da idade de desenvolvimento.

Interpretation of fossil embryos requires reasonable assessment of developmental age

Published online by Cambridge University Press:  20 July 2022

D. Charles Deeming and Martin Kundrát 

Figure 1. Three-dimensional mapping of real consectutive positioning and developmental geometry of cranial and postcranial elements in Crocodylus niloticus embryos. The incubation period is around 90 days. Note the position of the skull inside the egg, overall curling patterns, and in ovo space left unoccupied by 55- and 68-day-old embryos.

Abstract

Dinosaur embryos cause a lot of excitement in the scientific literature and are often widely reported because of the general public's interest in dinosaur biology. Well-preserved, articulated oviraptorosaur embryos in eggs are usually interpreted as representing a stage of development close to hatching because of their large size and good level of skeletal ossification. Based on this evidence, a recent report suggested that the position of the one embryo's head was reminiscent of an avian-like hatching position. Here we explore how the developmental stage of well-preserved oviraptorosaur embryos can be estimated, rather than assumed. This will help in our understanding of their developmental biology and its evolutionary consequences. Using quantitative methods and comparison with modern crocodilian embryos, we show that all articulated oviraptorosaur embryos are small relative to the egg and most likely at a stage of development equivalent to around 50%–60% of the developmental period, that is, not even close to hatching. This conclusion is supported by the fact that many elements of the crocodilian skeleton are well ossified many weeks before hatching and the position of oviraptorosaur embryos’ heads was also comparable to a crocodilian embryo many days before hatching. Misunderstandings about the stage of the developmental biology of these well-preserved oviraptorosaur embryos hampers our understanding of the true nature of their reproductive biology. We urge a more conservative approach to their interpretation. This is important, because misunderstandings in the minds of the public about dinosaur biology are hard to counter once poorly evidenced ideas have been reported around the world.

FREE PDF GRATIS: Palaeobiology

Se o design na natureza é mera ilusão, por que procurar design na natureza?

terça-feira, julho 26, 2022

A DNA origami rotary ratchet motor

Anna-Katharina Pumm, Wouter Engelen, Enzo Kopperger, Jonas Isensee, Matthias Vogt, Viktorija Kozina, Massimo Kube, Maximilian N. Honemann, Eva Bertosin, Martin Langecker, Ramin Golestanian, Friedrich C. Simmel & Hendrik Dietz 

Nature volume 607, pages492–498 (2022)


Fig. 1: Motor design and experimental setup.

Abstract

To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry1,2,3,4,5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6,7,8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. 3) and also in artificial molecular motors created by organic chemical synthesis9,10,11,12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14,15,16,17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20,21,22,23,24,25,26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F1F0-ATPase.

FREE PDF GRATIS: Nature Sup. Info.