Físicos revertem o tempo em pequenas partículas dentro de um computador quântico

sábado, março 16, 2019

Arrow of time and its reversal on the IBM quantum computer

G. B. Lesovik, I. A. Sadovskyy, M. V. Suslov, A. V. Lebedev & V. M. Vinokur 

Scientific Reportsvolume 9, Article number: 4396 (2019) 

Source/Fonte: Wired

Abstract

Uncovering the origin of the “arrow of time” remains a fundamental scientific challenge. Within the framework of statistical physics, this problem was inextricably associated with the Second Law of Thermodynamics, which declares that entropy growth proceeds from the system’s entanglement with the environment. This poses a question of whether it is possible to develop protocols for circumventing the irreversibility of time and if so to practically implement these protocols. Here we show that, while in nature the complex conjugation needed for time reversal may appear exponentially improbable, one can design a quantum algorithm that includes complex conjugation and thus reverses a given quantum state. Using this algorithm on an IBM quantum computer enables us to experimentally demonstrate a backward time dynamics for an electron scattered on a two-level impurity.

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Investigação bioinformática exploratória revela a IMPORTÂNCIA do DNA “lixo” no desenvolvimento embrionário inicial

quinta-feira, março 14, 2019

Exploratory bioinformatics investigation reveals importance of “junk” DNA in early embryo development

Steven Xijin Ge

BMC Genomics201718:200


Received: 13 October 2016 Accepted: 7 February 2017 Published: 23 February 2017



Abstract

Background

Instead of testing predefined hypotheses, the goal of exploratory data analysis (EDA) is to find what data can tell us. Following this strategy, we re-analyzed a large body of genomic data to study the complex gene regulation in mouse pre-implantation development (PD).

Results

Starting with a single-cell RNA-seq dataset consisting of 259 mouse embryonic cells derived from zygote to blastocyst stages, we reconstructed the temporal and spatial gene expression pattern during PD. The dynamics of gene expression can be partially explained by the enrichment of transposable elements in gene promoters and the similarity of expression profiles with those of corresponding transposons. Long Terminal Repeats (LTRs) are associated with transient, strong induction of many nearby genes at the 2-4 cell stages, probably by providing binding sites for Obox and other homeobox factors. B1 and B2 SINEs (Short Interspersed Nuclear Elements) are correlated with the upregulation of thousands of nearby genes during zygotic genome activation. Such enhancer-like effects are also found for human Alu and bovine tRNA SINEs. SINEs also seem to be predictive of gene expression in embryonic stem cells (ESCs), raising the possibility that they may also be involved in regulating pluripotency. We also identified many potential transcription factors underlying PD and discussed the evolutionary necessity of transposons in enhancing genetic diversity, especially for species with longer generation time.

Conclusions

Together with other recent studies, our results provide further evidence that many transposable elements may play a role in establishing the expression landscape in early embryos. It also demonstrates that exploratory bioinformatics investigation can pinpoint developmental pathways for further study, and serve as a strategy to generate novel insights from big genomic data.

Keywords Single-cell RNA-seq Exploratory data analysis Pre-implantation development Early embryogenesis Transposons Repetitive DNA Background

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A biologia e a evolução da fala: por que só os seres humanos falam?

The Biology and Evolution of Speech: A Comparative Analysis
Annual Review of Linguistics

Vol. 4:255-279 (Volume publication date January 2018) 


W. Tecumseh Fitch

Department of Cognitive Biology, University of Vienna, Vienna 1090, Austria

Copyright © 2018 by W. Tecumseh Fitch. This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 (CC-BY) International License, which permits unrestricted use, distribution, and reproduction in any medium and any derivative work is made available under the same, similar, or a compatible license. See credit lines of images or other third-party material in this article for license information.


Abstract

I analyze the biological underpinnings of human speech from a comparative perspective. By first identifying mechanisms that are evolutionarily derived relative to other primates, we obtain members of the faculty of language, derived components (FLD). Understanding when and why these evolved is central to understanding the evolution of speech. There is little evidence for human-specific mechanisms in auditory perception, and the hypothesis that speech perception is “special” is poorly supported by comparative data. Regarding speech production, human peripheral vocal anatomy includes several derived characteristics (permanently descended larynx, loss of air sacs), but their importance has been overestimated. In contrast, the central neural mechanisms underlying speech production involve crucial derived characteristics (direct monosynaptic connections from motor cortex to laryngeal motor neurons, derived intracortical dorsal circuitry between auditory and motor regions). Paleo-DNA from fossil hominins provides an exciting new opportunity to determine when these derived speech production mechanisms arose during evolution.

Keywords human evolution, speech perception, speech production, evolution of language, monosynaptic connections, paleo-DNA

A matemática que diz às células o que elas são: mero acaso, fortuita necessidade ou design inteligente?

MATHEMATICAL BIOLOGY

The Math That Tells Cells What They Are

During development, cells seem to decode their fate through optimal information processing, which could hint at a more general principle of life.



Cells in embryos need to make their way across a “developmental landscape” to their eventual fate. New findings bear on how they may do this so efficiently.

Adrian du Buisson for Quanta Magazine

In 1891, when the German biologist Hans Driesch split two-cell sea urchin embryos in half, he found that each of the separated cells then gave rise to its own complete, albeit smaller, larva. Somehow, the halves “knew” to change their entire developmental program: At that stage, the blueprint for what they would become had apparently not yet been drawn out, at least not in ink.

Since then, scientists have been trying to understand what goes into making this blueprint, and how instructive it is. (Driesch himself, frustrated at his inability to come up with a solution, threw up his hands and left the field entirely.) It’s now known that some form of positional information makes genes variously switch on and off throughout the embryo, giving cells distinct identities based on their location. But the signals carrying that information seem to fluctuate wildly and chaotically — the opposite of what you might expect for an important guiding influence.

“The [embryo] is a noisy environment,” said Robert Brewster, a systems biologist at the University of Massachusetts Medical School. “But somehow it comes together to give you a reproducible, crisp body plan.”

I don’t think optimization is an aesthetic or philosophical idea. It’s a very concrete idea.

William Bialek, Princeton University

The same precision and reproducibility emerge from a sea of noise again and again in a range of cellular processes. That mounting evidence is leading some biologists to a bold hypothesis: that where information is concerned, cells might often find solutions to life’s challenges that are not just good but optimal — that cells extract as much useful information from their complex surroundings as is theoretically possible. Questions about optimal decoding, according to Aleksandra Walczak, a biophysicist at the École Normale Supérieure in Paris, “are everywhere in biology.”

Biologists haven’t traditionally cast analyses of living systems as optimization problems because the complexity of those systems makes them hard to quantify, and because it can be difficult to discern what would be getting optimized. Moreover, while evolutionary theory suggests that evolving systems can improve over time, nothing guarantees that they should be driven to an optimal level.

Yet when researchers have been able to appropriately determine what cells are doing, many have been surprised to see clear indications of optimization. Hints have turned up in how the brain responds to external stimuli and how microbes respond to chemicals in their environments. Now some of the best evidence has emerged from a new study of fly larva development, reported recently in Cell.

Cells That Understand Statistics

For decades, scientists have been studying fruit fly larvae for clues about how development unfolds. Some details became apparent early on: A cascade of genetic signals establishes a pattern along the larva’s head-to-tail axis. Signaling molecules called morphogens then diffuse through the embryonic tissues, eventually defining the formation of body parts.

Particularly important in the fly are four “gap” genes, which are expressed separately in broad, overlapping domains along the axis. The proteins they make in turn help regulate the expression of “pair-rule” genes, which create an extremely precise, periodic striped pattern along the embryo. The stripes establish the groundwork for the later division of the body into segments.
...

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A estrutura de uma ATP sintase bacteriana: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, março 13, 2019

Structure of a bacterial ATP synthase

Hui Guo, Toshiharu Suzuki, John L Rubinstein The Hospital for Sick Children Research Institute, Canada; The University of Toronto, Canada; Tokyo Institute of Technology, Japan; Kyoto-Sangyo University, Japan

RESEARCH ARTICLE Feb 6, 2019


Abstract

ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the Bacillus PS3 ATP synthase in Eschericia coli, purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit ε shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.

https://doi.org/10.7554/eLife.43128.001

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Como "conversas secretas" dentro das células estão transformando a biologia

NEWS FEATURE  11 MARCH 2019

How secret conversations inside cells are transforming biology

Organelles — the cell’s workhorses — mingle far more than scientists ever appreciated.

Illustration by Serge Bloch

Elie Dolgin

Nobody paid much attention to Jean Vance 30 years ago, when she discovered something fundamental about the building blocks inside cells. She even doubted herself, at first.

The revelation came after a series of roadblocks. The cell biologist had just set up her laboratory at the University of Alberta in Edmonton, Canada, and was working alone. She thought she had isolated a pure batch of structures called mitochondria — the power plants of cells — from rat livers. But tests revealed that her sample contained something that wasn’t supposed to be there. “I thought I’d made a big mistake,” Vance recalls.

After additional purification steps, she found extra bits of the cells’ innards clinging to mitochondria like wads of chewing gum stuck to a shoe. The interlopers were part of the endoplasmic reticulum (ER) — an assembly line for proteins and fatty molecules. Other biologists had seen this, too, and dismissed it as an artefact of the preparation. But Vance realized that the pieces were glued together for a reason, and that this could solve one of cell biology’s big mysteries.

In a 1990 paper, Vance showed that the meeting points between the ER and mitochondria were crucibles for the synthesis of lipids1. By bringing the two organelles together, these junctions could serve as portals for the transfer of newly made fats. This would answer the long-standing question of how mitochondria receive certain lipids — they are directly passed from the ER.

Yet most of her contemporaries, schooled in the idea that the gummy bits of ER were nothing more than contamination, doubted that such unions were important to cells. “I gave several presentations,” says Vance, “and people were sceptical.”

Not any more. Close to three decades later, Vance’s paper is seen as a landmark — one that has come to transform scientists’ understanding of how cells maintain order and function in their crowded interiors, which buzz with various types of organelles, including mitochondria, nuclei and the ER. Researchers now recognize that interactions between organelles are ubiquitous, with almost every type coming into close conversation with every other type. Probing those connections is also leading biologists to discover proteins that are responsible for holding the organelles together and maintaining a healthy cell.
...

FREE PDF GRATIS: Nature
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https://www.nature.com/magazine-assets/d41586-019-00792-9/d41586-019-00792-9.pdf

Fora do tópico deste blog: transplante de úteros em mulheres que são geneticamente XY

sexta-feira, março 08, 2019

Uterus transplantation in women who are genetically XY

Amani Sampson1, Laura L. Kimberly2,3, Kara N. Goldman1, David L. Keefe1, Gwendolyn P. Quinn1,3

Author affiliations

Department of Obstetrics and Gynecology, New York University School of Medicine, New York City, New York, USA

Hansjörg Wyss Department of Plastic Surgery, New York University School of Medicine, New York City, New York, USA

Division of Medical Ethics, Department of Population Health, New York University School of Medicine, New York City, New York, USA

Correspondence to

Dr Gwendolyn P. Quinn, Obstetrics and Gynecology, NYU School of Medicine, New York NY 10016, USA; gwendolyn.quinn@nyumc.org


Abstract

Uterus transplantation is an emerging technology adding to the arsenal of treatments for infertility; specifically the only available treatment for uterine factor infertility. Ethical investigations concerning risks to uteri donors and transplant recipients have been discussed in the literature. However, missing from the discourse is the potential of uterus transplantation in other groups of genetically XY women who experience uterine factor infertility. There have been philosophical inquiries concerning uterus transplantation in genetically XY women, which includes transgender women and women with complete androgen insufficiency syndrome. We discuss the potential medical steps necessary and associated risks for uterus transplantation in genetically XY women. Presently, the medical technology does not exist to make uterus transplantation a safe and effective option for genetically XY women, however this group should not be summarily excluded from participation in trials. Laboratory research is needed to better understand and reduce medical risk and widen the field to all women who face uterine factor infertility.

+++++

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Contra Jerry Coyne et al: porque a ciência precisa da filosofia

Opinion: Why science needs philosophy

Lucie Laplane, Paolo Mantovani, Ralph Adolphs, Hasok Chang, Alberto Mantovani, Margaret McFall-Ngai, Carlo Rovelli, Elliott Sober, and Thomas Pradeu

PNAS March 5, 2019 116 (10) 3948-3952; 



Article

A knowledge of the historic and philosophical background gives that kind of independence from prejudices of his generation from which most scientists are suffering. This independence created by philosophical insight is—in my opinion—the mark of distinction between a mere artisan or specialist and a real seeker after truth.

Albert Einstein, Letter to Robert Thornton, 1944

Despite the tight historical links between science and philosophy, present-day scientists often perceive philosophy as completely different from, and even antagonistic to, science. We argue here that, to the contrary, philosophy can have an important and productive impact on science.



Despite the tight historical links between science and philosophy, hearkening back to Plato, Aristotle, and others (here evoked with Raphael’s famous School of Athens), present-day scientists often perceive philosophy as completely different from, and even antagonistic to, science. To the contrary, we believe philosophy can have an important and productive impact on science. Image credit: Shutterstock.com/Isogood_patrick.

We illustrate our point with three examples taken from various fields of the contemporary life sciences. Each bears on cutting-edge scientific research, and each has been explicitly acknowledged by practicing researchers as a useful contribution to science. These and other examples show that philosophy’s contribution can take at least four forms: the clarification of scientific concepts, the critical assessment of scientific assumptions or methods, the formulation of new concepts and theories, and the fostering of dialogue between different sciences, as well as between science and society.

FREE PDF GRATIS: PNAS

Eficiência da primeira lei da termodinâmica das proteínas de membrana: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, março 06, 2019

Thermodynamic first law efficiency of membrane proteins

Mert Gur, Mert Golcuk, Sema Zeynep Yilmaz & Elhan Taka

Received 15 Oct 2018, Accepted 29 Jan 2019, Accepted author version posted online: 06 Feb 2019, Published online: 04 Mar 2019

Source/Fonte: Nature


Abstract

Proteins are nature’s biomolecular machines. Proteins, such as transporters, pumps and motors, have complex function/operating-machinery/mechanisms, comparable to the macro-scaled machines that we encounter in our daily life. These proteins, as it is for their macro-scaled counterparts, convert (part of) other/various forms of energy into work. In this study, we are performing the first law analysis on a set of proteins, including the dopamine transporter, glycine transporters I and II, glutamate transporter, sodium–potassium pump and Ca2+ ATPase. Each of these proteins operates on a thermodynamic/mechanic cycle to perform their function. In each of these cycles, they receive energy from a source, convert part of this energy into work and reject the remaining part of the energy to the environment. Conservation of energy principle was applied to the thermodynamic/mechanic cycle of each protein, and thermodynamic first law efficiency was evaluated for each cycle, which shows how much of the energy input per cycle was converted into useful work. Interestingly, calculations based on experimental data indicate that proteins can operate under a range of efficiencies, which vary based on the extracellular and intracellular ion and substrate concentrations. The lowest observed first law efficiency was 50%, which is a very high value if compared to the efficiency of the macro-scaled heat engines we encounter in our daily lives.

Communicated by Ramaswamy H. Sarma

Keywords: Thermodynamics, first law analysis, first law efficiency, biomolecular machines, proteins, neurotransmitter transporters, ATP-powered pumps

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Origem da vida: um cenário geoquímico universal para condensação de formamida e a química prebiótica

Chemistry – A European Journal Volume 25, Issue 13
 
Review

Open Access

A Universal Geochemical Scenario for Formamide Condensation and Prebiotic Chemistry

Prof. Raffaele Saladino, Prof. Ernesto Di Mauro, Prof. Juan Manuel García‐Ruiz
 
First published: 19 September 2018


Abstract

The condensation of formamide has been shown to be a robust chemical pathway affording molecules necessary for the origin of life. It has been experimentally demonstrated that condensation reactions of formamide are catalyzed by a number of minerals, including silicates, phosphates, sulfides, zirconia, and borates, and by cosmic dusts and meteorites. However, a critical discussion of the catalytic power of the tested minerals, and the geochemical conditions under which the condensation would occur, is still missing. We show here that mineral self‐assembled structures forming under alkaline silica‐rich solutions are excellent catalysts for the condensation of formamide with respect to other minerals. We also propose that these structures were likely forming as early as 4.4 billion years ago when the whole earth surface was a reactor, a global scale factory, releasing large amounts of organic compounds. Our experimental results suggest that the conditions required for the synthesis of the molecular bricks from which life self‐assembles, rather than being local and bizarre, appears to be universal and geologically rather conventional
.
 
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Células usam açúcares para se comunicar em nível molecular

terça-feira, março 05, 2019

Encoding biological recognition in a bicomponent cell-membrane mimic

Cesar Rodriguez-Emmenegger, Qi Xiao, Nina Yu. Kostina, Samuel E. Sherman, Khosrow Rahimi, Benjamin E. Partridge, Shangda Li, Dipankar Sahoo, Aracelee M. Reveron Perez, Irene Buzzacchera, Hong Han, Meir Kerzner, Ishita Malhotra, Martin Möller, Christopher J. Wilson, Matthew C. Good, Mark Goulian, Tobias Baumgart, Michael L. Klein, and Virgil Percec

PNAS published ahead of print February 28, 2019 

Contributed by Michael L. Klein, January 22, 2019 (sent for review December 27, 2018; reviewed by Stephen Z. D. Cheng and Timothy J. Deming)

Models of nanosegregated bilayer structures

Significance

The seminal fluid mosaic model of the cell membranes suggests a lipid bilayer sea, in which cholesterol, proteins, glycoconjugates, and other components are swimming. Complementing this view, a microsegregated rafts model predicts clusters of components that function as relay stations for intracellular signaling and trafficking. However, elucidating the arrangement of glycoconjugates responsible for communication and recognition between cells, and cells with proteins remains a challenge. Herein, designed dendritic macromolecules are shown to self-assemble into vesicles that function as biological-membrane mimics with controlled density of sugar moieties on their periphery. Surprisingly, lowering sugar density elicits higher bioactivity to sugar-binding proteins. This finding informs a design principle for active complex soft matter with potential for applications in cellular biology and nanomedicine.

Abstract

Self-assembling dendrimers have facilitated the discovery of periodic and quasiperiodic arrays of supramolecular architectures and the diverse functions derived from them. Examples are liquid quasicrystals and their approximants plus helical columns and spheres, including some that disregard chirality. The same periodic and quasiperiodic arrays were subsequently found in block copolymers, surfactants, lipids, glycolipids, and other complex molecules. Here we report the discovery of lamellar and hexagonal periodic arrays on the surface of vesicles generated from sequence-defined bicomponent monodisperse oligomers containing lipid and glycolipid mimics. These vesicles, known as glycodendrimersomes, act as cell-membrane mimics with hierarchical morphologies resembling bicomponent rafts. These nanosegregated morphologies diminish sugar–sugar interactions enabling stronger binding to sugar-binding proteins than densely packed arrangements of sugars. Importantly, this provides a mechanism to encode the reactivity of sugars via their interaction with sugar-binding proteins. The observed sugar phase-separated hierarchical arrays with lamellar and hexagonal morphologies that encode biological recognition are among the most complex architectures yet discovered in soft matter. The enhanced reactivity of the sugar displays likely has applications in material science and nanomedicine, with potential to evolve into related technologies.

Janus glycodendrimers lipid rafts nanosegregation atomic force microscopy galectin

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Colin Patterson perguntou: Vocês podem me dizer algo sobre a evolução, qualquer coisa, que seja verdade?" 2/2

quinta-feira, fevereiro 28, 2019





No dia 5 de novembro de 1981, Patterson deu uma palestra para o Grupo de Discussão de Sistemática no Museu Americano de História Natural, Nova York: 

"It's true that for the last eighteen months or so, I've been kicking around non-evolutionary or even anti-evolutionary ideas. I think always before in my life, when I've got up to speak on a subject, I've been confident of one thing – that I know more about it than anybody in the room, because I've worked on it.

Well, this time that isn't true. I'm speaking on two subjects, evolutionism and creationism, and I believe it's true to say that I know nothing whatever about either of them. One or the reasons I started taking this anti-evolutionary view, or let's call it non-evolutionary, was last year I had a sudden realization that for over twenty years I had thought that I was working on evolution in some way. Then one morning I woke up, and something had happened in the night, and it struck me that I had been working on this stuff for twenty years, and there was not one thing I knew about it. That's quite a shock, to learn that one can be so misled for so long.

So either there was something wrong with me, or there was something wrong with evolutionary theory. Naturally, I know there is nothing wrong with me, so for the last few weeks, I've tried putting a simple question to various people and groups of people.

The question is: Can you tell me anything you know about evolution, any one thing, any one thing that is true? I tried that question on the geology staff in the Field Museum of Natural History, and the only answer I got was silence. I tried it on the members of the Evolutionary Morphology Seminar at the University of Chicago, a very prestigious body of evolutionists, and all I got there was silence for a long time, and then eventually one person said, "Yes, I do know one thing. It ought not to be taught in high school.” [laughter]"

Colin Patterson perguntou: Vocês podem me dizer algo sobre a evolução, qualquer coisa, que seja verdade?" 1/2



No dia 5 de novembro de 1981, Patterson deu uma palestra para o Grupo de Discussão de Sistemática no Museu Americano de História Natural, Nova York: 

"It's true that for the last eighteen months or so, I've been kicking around non-evolutionary or even anti-evolutionary ideas. I think always before in my life, when I've got up to speak on a subject, I've been confident of one thing – that I know more about it than anybody in the room, because I've worked on it.

Well, this time that isn't true. I'm speaking on two subjects, evolutionism and creationism, and I believe it's true to say that I know nothing whatever about either of them. One or the reasons I started taking this anti-evolutionary view, or let's call it non-evolutionary, was last year I had a sudden realization that for over twenty years I had thought that I was working on evolution in some way. Then one morning I woke up, and something had happened in the night, and it struck me that I had been working on this stuff for twenty years, and there was not one thing I knew about it. That's quite a shock, to learn that one can be so misled for so long.

So either there was something wrong with me, or there was something wrong with evolutionary theory. Naturally, I know there is nothing wrong with me, so for the last few weeks, I've tried putting a simple question to various people and groups of people.

The question is: Can you tell me anything you know about evolution, any one thing, any one thing that is true? I tried that question on the geology staff in the Field Museum of Natural History, and the only answer I got was silence. I tried it on the members of the Evolutionary Morphology Seminar at the University of Chicago, a very prestigious body of evolutionists, and all I got there was silence for a long time, and then eventually one person said, "Yes, I do know one thing. It ought not to be taught in high school.” [laughter]"

Cresce o número de cientistas com Ph. D. céticos da teoria da evolução de Darwin

quarta-feira, fevereiro 27, 2019

Darwin, mais complexidade: arquiteturas supramoleculares de camadas molecularmente finas independentes, mas robustas

sexta-feira, fevereiro 22, 2019

Supramolecular architectures of molecularly thin yet robust free-standing layers

Mina Moradi1,2, Nadia L. Opara2,3, Ludovico G. Tulli1, Christian Wäckerlin4, Scott J. Dalgarno5, Simon J. Teat6, Milos Baljozovic2, Olha Popova7, Eric van Genderen2,*, Armin Kleibert8, Henning Stahlberg3, Jan Pieter Abrahams9,10, Celestino Padeste2, Philippe F.-X. Corvini1, Thomas A. Jung2,† and Patrick Shahgaldian1,†

1Institute of Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 35, CH-4132 Muttenz, Switzerland.

2Laboratory for Micro- and Nano-technology, Paul Scherrer Institute, Villigen CH-5232, Switzerland.

3Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.

4Empa–Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland.

5Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, Scotland EH14 4AS, UK.

6Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS6R2100, Berkeley, CA 94720, USA.

7Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland.

8Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland.

9Biozentrum, University of Basel, Switzerland and Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.

10Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands.

↵†Corresponding author. Email: patrick.shahgaldian@fhnw.ch (P.S.); thomas.jung@psi.ch (T.A.J.)

↵* Present address: Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.

Science Advances 22 Feb 2019: Vol. 5, no. 2, eaav4489



Fig. 3
Molecular resolution AFM imaging of the monolayer of 1.
(A) AFM images of the monolayer of 1 transferred onto HOPG via the LS method. (B) The high-resolution image of the crystalline network of the monolayer shows a highly ordered network formed from the single molecules of 1. [C (top view) and D (side view)] Molecular model of the building blocks of 1 interacting via the proposed dipole-dipole interaction in the well-ordered monolayer.

Abstract

Stable, single-nanometer thin, and free-standing two-dimensional layers with controlled molecular architectures are desired for several applications ranging from (opto-)electronic devices to nanoparticle and single-biomolecule characterization. It is, however, challenging to construct these stable single molecular layers via self-assembly, as the cohesion of those systems is ensured only by in-plane bonds. We herein demonstrate that relatively weak noncovalent bonds of limited directionality such as dipole-dipole (–CN⋅⋅⋅NC–) interactions act in a synergistic fashion to stabilize crystalline monomolecular layers of tetrafunctional calixarenes. The monolayers produced, demonstrated to be free-standing, display a well-defined atomic structure on the single-nanometer scale and are robust under a wide range of conditions including photon and electron radiation. This work opens up new avenues for the fabrication of robust, single-component, and free-standing layers via bottom-up self-assembly.

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Darwin, mais complexidade, mano: descobrindo elementos químicos nas células

Chemical and Topographical Single‐Cell Imaging by Near‐Field Desorption Mass Spectrometry

Dr. Zhibin Yin Xiaoling Cheng Rong Liu Xiaoping Li Le Hang Prof. Wei Hang Jingyi Xu Prof. Xiaomei Yan Prof. Jianfeng Li Prof. Zhongqun Tian

First published: 02 January 2019


 

Abstract

Simultaneously acquiring chemical and topographical information within a single cell at nanoscale resolutions is vital to cellular biology, yet it remains a great challenge due to limited lateral resolutions and detection sensitivities. Herein, the development of near‐field desorption mass spectrometry for correlated chemical and topographical imaging is reported, thereby bridging the gap between laser‐based mass spectrometry (MS) methods and multimodal single‐cell imaging. Using this integrated platform, an imaging resolution of 250 nm and 3D topographically reconstructed chemical single‐cell imaging were achieved. This technique offers more in‐depth cellular information than micrometer‐range laser‐based MS imaging methods. Considering the simplicity and compact size of the near‐field device, this technique can be introduced to MALDI‐MS, expanding the multimodal abilities of MS at nanoscale resolutions.

Taxas evolutivas de trilobitas restringem a duração da explosão cambriana

quarta-feira, fevereiro 20, 2019

Trilobite evolutionary rates constrain the duration of the Cambrian explosion

John R. Paterson, Gregory D. Edgecombe, and Michael S. Y. Lee

PNAS published ahead of print February 19, 2019 


Add to Cart ($10)

Edited by Andrew H. Knoll, Harvard University, Cambridge, MA, and approved January 9, 2019 (received for review November 12, 2018)


Significance

The Cambrian explosion was arguably the most important biological event after the origin of life. Extensive research has been devoted to understanding when it began but far less on when this burst of evolution ended. We present a quantitative study that addresses these issues, using a large new dataset of Cambrian trilobites, the most abundant and diverse organisms during this time. Using probabilistic clock methods, we calculate rates of evolution in the earliest trilobites virtually identical to those throughout their Cambrian fossil history. We conclude that the Cambrian explosion was over by the time the typical Cambrian fossil record commences and reject an unfossilized Precambrian history for trilobites, solving a problem that had long troubled biologists since Darwin.

Abstract

Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (∼521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early Cambrian, thereby shortening the phylogenetic fuse. Furthermore, comparatively little research has been devoted to understanding the duration of the Cambrian explosion, after which normal Phanerozoic evolutionary rates were established. We test these hypotheses by applying Bayesian tip-dating methods to a comprehensive dataset of Cambrian trilobites. We show that trilobites have a Cambrian origin, as supported by the trace fossil record and molecular clocks. Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all aspects of the preserved phenotype: discrete, meristic, and continuous morphological traits. Our data therefore provide robust, quantitative evidence that by the time the typical Cambrian fossil record begins (∼521 Ma), the Cambrian explosion had already largely concluded. This suggests that a modern-style marine biosphere had rapidly emerged during the latest Ediacaran and earliest Cambrian (∼20 million years), followed by broad-scale evolutionary stasis throughout the remainder of the Cambrian.

Cambrian explosion evolutionary rates trilobites Bayesian tip-dating morphological clock

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Cálculo direto de mutações em grandes símios reconcilia a datação filogenética

Direct estimation of mutations in great apes reconciles phylogenetic dating

Søren Besenbacher, Christina Hvilsom, Tomas Marques-Bonet, Thomas Mailund & Mikkel Heide Schierup 

Nature Ecology & Evolution volume 3, pages 286–292 (2019) 


Abstract

The human mutation rate per generation estimated from trio sequencing has revealed an almost linear relationship with the age of the father and the age of the mother, with fathers contributing about three times as many mutations per year as mothers. The yearly trio-based mutation rate estimate of around 0.43 × 10−9 is markedly lower than previous indirect estimates of about 1 × 10−9 per year from phylogenetic comparisons of the great apes calibrated by fossil evidence. This suggests either a slowdown in the accumulation of mutations per year in the human lineage over the past 10 million years or an inaccurate interpretation of the fossil record. Here we inferred de novo mutations in chimpanzee, gorilla, and orangutan parent-offspring trios. Extrapolating the relationship between the mutation rate and the age of parents from humans to these other great apes, we estimated that each species has higher mutation rates per year by factors of 1.50 ± 0.10, 1.51 ± 0.23, and 1.42 ± 0.22 for chimpanzee, gorilla, and orangutan, respectively, and by a factor of 1.48 ± 0.08 for the three species combined. These estimates suggest an appreciable slowdown in the yearly mutation rate in the human lineage that is likely to be recent as genome comparisons almost adhere to a molecular clock. If the nonhuman rates rather than the human rate are extrapolated over the phylogeny of the great apes, we estimate divergence and speciation times that are much more in line with the fossil record and the biogeography.

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Nature Ecology & Evolution

Análise de leitura longa de DNA pode dar origem a erros

Correspondence | Published: 22 January 2019

Errors in long-read assemblies can critically affect protein prediction

Mick Watson & Amanda Warr

Nature Biotechnology volume 37, pages124–126 (2019)

Source/Fonte: QiagenScience

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Nature Biotechnology

Senciência e Consciência em Células Únicas: Como as Primeiras Mentes Surgiram nas Espécies Unicelulares

terça-feira, fevereiro 19, 2019

Sentience and Consciousness in Single Cells: How the First Minds Emerged in Unicellular Species

František Baluška Arthur Reber

First published: 04 February 2019


Source/Fonte: Internet

Abstract

A reductionistic, bottom‐up, cellular‐based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. It emerges as an inherent feature of, and contemporaneously with, the very first life‐forms. All other varieties of mentation are the result of evolutionary mechanisms based on this singular event. Therefore, all forms of sentience and consciousness evolve from this original instantiation in prokaryotes. It has also been identified that three cellular structures and mechanisms that likely play critical roles here are excitable membranes, oscillating cytoskeletal polymers, and structurally flexible proteins. Finally, basic biophysical principles are proposed to guide those processes that underly the emergence of supracellular sentience from cellular sentience in multicellular organisms.

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Richard Dawkins, ateu militante: “Tomando a coragem de Darwin para combater a arrogância da fé”

Zoológicos humanos: A história esquecida do racismo científico dos Estados Unidos

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

segunda-feira, fevereiro 18, 2019

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

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

PNAS published ahead of print February 13, 2019


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


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

Significance

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

Abstract

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

mitochondria ATP synthase membrane curvature electron cryotomography subtomogram averaging

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

quinta-feira, fevereiro 14, 2019

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

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

See all authors and affiliations

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



Source/Fonte: Spark Notes

Abstract

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

Acknowledgments: 

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

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

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

quarta-feira, fevereiro 13, 2019

Grammar of protein domain architectures

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

PNAS published ahead of print February 7, 2019


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


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

Significance

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

Abstract

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

n-grambigramprotein domainlanguagedomain architecture

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