Os fundamentos das visões de concordância da filogenia numa era discordante

quinta-feira, janeiro 28, 2021

The Foundations of Concordance Views of Phylogeny

Joel D. Velasco, Department of Philosophy, Texas Tech University, 2500 Broadway, Lubbock, Texas 79409, USA

email: joel@joelvelasco.net


Clade, Concordance Tree, Phylogeny, Plurality Consensus


Volume 11, No. 020, 2019

Received 21 November 2017; Revised 25 November 2018; Accepted 8 March 2019


Despite the enormous importance and widespread use of the term, it is unclear exactly what a phylogeny is and what a phylogenetic tree represents. A natural thought is that a phylogeny should represent the “dominant history” of the flow of genetic information. Here, I will focus on methods in which a tree is determined by input gene trees. I compare various possibilities of how to do this including consensus trees, the R* triplet method, and concordance methods. I make precise the notion of a concordance factor and then compare concordance trees to species trees, which attempt to track population histories through time. I show that even in the most idealized circumstances, it is possible for the primary concordance tree to differ from the species tree. I argue that when these trees differ, there are reasons to think of the primary concordance tree as a better representation of phylogenetic history than the species tree and that when these highly idealized conditions break down, it is especially plausible that we should take concordance trees seriously as an interpretation of phylogeny and as the basis for taxonomic grouping.

Part of the special issue Species in the Age of Discordance, guest-edited by Matthew H. Haber and Daniel J. Molter.


Topoisomerases de DNA - Análise da estrutura-função dos papéis celulares e complexos multiproteicos: mero acaso, fortuita necessidade ou design inteligente?

segunda-feira, janeiro 25, 2021

DNA topoisomerases: Advances in understanding of cellular roles and multi‐protein complexes via structure‐function analysis

Shannon J. McKie Keir C. Neuman Anthony Maxwell

First published: 22 January 2021 https://doi.org/10.1002/bies.202000286

DNA topology and DNA topoisomerase mechanisms. 


DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA‐topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single‐molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA‐associated proteins, supporting the idea that they often function as part of multi‐enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini‐A. These new findings are advancing our understanding of DNA‐related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.


Quantas moléculas de água são necessárias para solvatar uma molécula?

quinta-feira, janeiro 21, 2021

How many water molecules are needed to solvate one?† 

Alessandro Rognoni, ORCID logo a Riccardo Conte ORCID logo a and Michele Ceotto *a 

Author affiliations


Many efforts undertaken to study the solvation process have led to general theories that may describe mean properties, but are unable to provide a detailed understanding at the molecular level. Remarkably, the basic question of how many solvent molecules are necessary to solvate one solute molecule is still open. By exploring several water aggregates of increasing complexity, in this contribution we employ semiclassical spectroscopy to determine on quantum dynamical grounds the minimal network of surrounding water molecules to make the central one display the same vibrational features of liquid water. We find out that double-acceptor double-donor tetrahedral coordination constituting the standard picture is necessary but not sufficient, and that particular care must be reserved for the quantum description of the combination band due to the coupling of the central monomer bending mode with network librations. It is actually our ability to investigate the combination band with a quantum-derived approach that allows us to answer the titular question. The minimal structure eventually responsible for proper solvation is made of a total of 21 water molecules and includes two complete solvation shells, of which the whole first one is tetrahedrally coordinated to the central molecule.

FREE PDF GRATIS: Chemical Science Sup. Info.

Orientando a formação de proteínas: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, janeiro 06, 2021

Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients

Lakshmi E Miller-Vedam, Bastian Bräuning, Katerina D Popova, Nicole T Schirle Oakdale, Jessica L Bonnar, Jesuraj R Prabu, Elizabeth A Boydston, Natalia Sevillano, Matthew J Shurtleff, Robert M Stroud, Charles S Craik, Brenda A Schulman Is a corresponding author, Adam Frost Is a corresponding author, Jonathan S Weissman Is a corresponding author s

Molecular, Cellular, and Computational Biophysics Graduate Program, University of California, San Francisco, United States; Department of Biochemistry and Biophysics, University of California, San Francisco, United States; Department of Biology, Whitehead Institute, MIT, United States; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, United States; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Germany; Biomedical Sciences Graduate Program, University of California, San Francisco, United States; Department of Pharmaceutical Chemistry, University of California, San Francisco, United States; Howard Hughes Medical Institute, United States

Three identical snapshots of the structure of human EMC:
Image credit: Lakshmi E Miller-Vedam, Bastian Bräuning and Katerina D Popova, created using UCSF ChimeraX (CC BY 4.0)


Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC’s multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.

eLife digest

Cells are surrounded and contained by a plasma membrane consisting of a double layer of fats and proteins. These proteins monitor and facilitate the movement of food, oxygen and messages in and out of the cell, and help neighboring cells communicate. Membrane proteins are manufactured in a cell compartment called the endoplasmic reticulum. Cellular machines called ribosomes visit this compartment’s membrane to manufacture proteins that need to be secreted or embedded into the cell’s membranes. As these proteins are made, they are pulled into the endoplasmic reticulum so they can be folded correctly and inserted in the membrane. A cellular machine in this compartment’s membrane that aids this process is the endoplasmic reticulum membrane protein complex (EMC). Many steps can go wrong during protein assembly, so to control protein quality, the EMC has to accommodate the variety of complex physical features that proteins can have.

To explore the activity of the EMC, Miller-Vedam, Bräuning, Popova et al. studied the normal structure of the EMC in both yeast and human cells grown in the lab. These snapshots of the complex in different species had a lot in common, including how the complex was arranged within and around the membrane.

Next, Miller-Vedam, Bräuning, Popova et al. generated 50 mutant versions of the EMC in human cells to determine how changing different parts of the complex affected the production of three proteins that rely on the EMC to fold correctly. These proteins were an enzyme called squalene synthase, a signaling protein called the beta adrenergic receptor and sigma intracellular receptor 2, a protein involved in the regulation of cholesterol levels.

Mutations in the section of the EMC outside of the endoplasmic reticulum, within the main cellular compartment, negatively impacted the stability of squalene synthase. This section of the EMC provides a platform where proteins can associate before entering the membrane.

The part of EMC that spans the membrane contains both a fat-filled cavity and a cavity with a ‘door’ that is either open or closed. Mutations in this section disrupted the insertion of both squalene synthase and the beta adrenergic receptor into the membrane, a role performed by the cavity with the door. The specific role of the fat-filled cavity is still not fully understood, but a mutation affecting this cavity disrupts the correct production of all three proteins studied.

The largest section of the complex, which sits inside the endoplasmic reticulum, protected proteins as they folded, ensuring they were not destroyed for being folded incorrectly before they were fully formed. Mutations in this part of the EMC negatively impacted the stability of sigma intracellular receptor 2 without negatively affecting the other proteins.

This molecular dissection of the activity of the EMC provides insights into how membrane proteins are manufactured, stabilized, coordinated, and monitored for quality. These findings could contribute towards the development of new treatments for certain congenital diseases. For example, cystic fibrosis, retinitis pigmentosa, and Charcot-Marie-Tooth disease are all thought to be caused by mutations within membrane proteins that require the EMC during their production.


Gilbert 'falou e disse': a teoria da seleção natural de Darwin não funciona e precisa da teoria da recompensa natural!

terça-feira, janeiro 05, 2021

Natural reward drives the advancement of life

Owen M. Gilbert

Comparison of theories of natural selection and natural reward. A The theory of natural selection includes A only. B The theory of natural reward includes A and B, and the connection between them.


Throughout the history of life on earth, rare and complex innovations have periodically increased the efficiency with which abiotic free energy and biotic resources are converted to biomass and organismal diversity. Such macroevolutionary expansions have increased the total amount of abiotic free energy utilized by life and shaped the earth’s ecosystems. Meanwhile, Darwin’s theory of natural selection assumes a historical, worldwide state of effective resource limitation, which could not possibly be true if life evolved from one or a few original ancestors. In this paper, I analyze the self-contradiction in Darwin’s theory that comes from viewing the world and universe as effectively resource limited. I then extend evolutionary theory to include a second deterministic evolutionary force, natural reward. Natural reward operates on complex inventions produced by natural selection and is analogous to the reward for innovation in human economic systems. I hypothesize that natural reward, when combined with climate change and extinction, leads to the increased innovativeness, or what I call the advancement, of life with time. I then discuss applications of the theory of natural reward to the evolution of evolvability, the apparent sudden appearance of new forms in the fossil record, and human economic evolution. I conclude that the theory of natural reward holds promise as an explanation for the historical advancement of life on earth.


invention, entrepreneurship, innovation, success, progress, advancement

FREE PDF GRATIS: Rethinking Ecology

Nem todos os dinossauros morreram no impacto do grande asteroide Chicxulub há 66 milhões de anos!

domingo, janeiro 03, 2021

Over 13,000 elements from a single bonebed help elucidate disarticulation and transport of an Edmontosaurus thanatocoenosis

Keith Snyder, Matthew McLain, Jared Wood, Arthur Chadwick


Over twenty years of work on the Hanson Ranch (HR) Bonebed in the Lance Formation of eastern Wyoming has yielded over 13,000 individual elements primarily of the hadrosaurid dinosaur Edmontosaurus annectens. The fossil bones are found normally-graded within a fine-grained (claystone to siltstone) bed that varies from one to two meters in thickness. Almost all specimens exhibit exquisite preservation (i.e., little to no abrasion, weathering, and breakage), but they are disarticulated which, combined with our sedimentological observations, suggests that the bones were remobilized and buried after a period of initial decay and disarticulation of Edmontosaurus carcasses. Because of the large number of recovered fossil elements, we have been able to gain deeper insight into Edmontosaurus biostratigraphy including disarticulation and transport of skeletal elements. The most common postcranial elements in the bonebed are pubes, ischia, scapulae, ribs, and limb bones. By contrast, vertebrae, ilia, and chevrons are rare. The most common craniomandibular bones include dentaries, nasals, quadrates, and jugals, whereas the premaxillae, predentaries, and braincase bones are underrepresented. Thus, overall, chondrocranial and axial elements, as well as distal elements of the limbs, are distinctly underrepresented. We hypothesize that following decay and disarticulation, hydraulic winnowing removed the articulated sections (e.g., vertebral columns) and the small, distal-most elements before, or at the same time, the remaining bones were swept up in a subaqueous debris flow that generated the deposit. Comparison of the HR Bonebed with other widely dispersed Upper Cretaceous hadrosaurid-dominated bonebeds reveals many shared attributes, which suggests similar processes at work in the formation of these bonebeds across space and time. This in turn reflects similar behavior by populations of these species around the world resulting in similar modes of death, becoming interred in similar depositional settings.



NOTA DESTE BLOGGER: O Dr. Arthur Chadwick é amigo pessoal deste blogger.