Causa da Explosão Cambriana: terrestre ou cósmica???

segunda-feira, maio 21, 2018

Progress in Biophysics and Molecular Biology

Available online 13 March 2018

In Press, Corrected Proof What are Corrected Proof articles?

Progress in Biophysics and Molecular Biology

Cause of Cambrian Explosion - Terrestrial or Cosmic?

Author Edward J. Steele a j Shirwan Al-Mufti b Kenneth A. Augustyn c Rohana Chandrajith d John P. Coghlan e S. G. Coulson b Sudipto Ghosh f Mark Gillman g Reginald M. Gorczynski h Brig Klyce b Godfrey Louis i Kithsiri Mahanama  j Keith R. Oliver k Julio Padron l Jiangwen Qu m John A. Schuster n W. E. Smith o Duane P. Snyder b…Yongsheng Liu v w


Under a Creative Commons license open access


Source/Fonte: Nature

Abstract

We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion – life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.

Keywords

Cosmic biology Cambrian Explosion Retroviruses Panspermia Hypermutation & evolution Origin epidemics & pandemics

Último artigo de Stephen Hawking: uma saída simples da inflação eterna do universo???

domingo, maio 20, 2018

Journal of High Energy Physics

April 2018, 2018:147 | Cite as

A smooth exit from eternal inflation?

Authors and affiliations

S. W. Hawking 1

Thomas Hertog 2

Email author

1.DAMTP, CMS Cambridge U.K.

2.Institute for Theoretical Physics University of Leuven Leuven Belgium

Open AccessRegular Article - Theoretical Physics

First Online: 27 April 2018

Source/Fonte: Universe Review CA

Abstract

The usual theory of inflation breaks down in eternal inflation. We derive a dual description of eternal inflation in terms of a deformed Euclidean CFT located at the threshold of eternal inflation. The partition function gives the amplitude of different geometries of the threshold surface in the no-boundary state. Its local and global behavior in dual toy models shows that the amplitude is low for surfaces which are not nearly conformal to the round three-sphere and essentially zero for surfaces with negative curvature. Based on this we conjecture that the exit from eternal inflation does not produce an infinite fractal-like multiverse, but is finite and reasonably smooth.

Keywords

AdS-CFT Correspondence Gauge-gravity correspondence Models of Quantum Gravity Spacetime Singularities

Primeira pesquisa anatômica detalhada de bonobos revela e expõe as estórias da carochinha da evolução humana, bipedalismo e uso de ferramentas

REVIEW ARTICLE

Front. Ecol. Evol., 26 April 2018 | https://doi.org/10.3389/fevo.2018.00053

First Detailed Anatomical Study of Bonobos Reveals Intra-Specific Variations and Exposes Just-So Stories of Human Evolution, Bipedalism, and Tool Use

Rui Diogo*

Department of Anatomy, Howard University, Washington, DC, United States

Figure 1. Differences between head muscles of common chimps, bonobos, and humans, based and modified from Diogo et al. (2017b).

Just-so stories are prominent in human evolution literature because of our tendency to create simple progressionist narratives about our “special” place in nature, despite the fact that these stories are almost exclusively based on hard tissue data. How can we be so certain about the evolution of human facial communication, bipedalism, tool use, or speech without detailed knowledge of the internal anatomy of for instance, one of the two extant species more closely related to us, the bonobos? Here I show how many of these stories now become obsolete, after such a comprehensive knowledge on the anatomy of bonobos and other primates is finally put together. Each and every muscle that has been long accepted to be “uniquely human” and to provide “crucial singular functional adaptations” for our bipedalism, tool use and/or vocal/facial communication, is actually present as an intra-specific variant or even as normal phenotype in bonobos and/or other apes.

Just-so stories (Smith, 2016) are frequent in the literature about human evolution because of our tendency to build simple progressionist narratives about our “special” evolutionary history and place in nature (Gould, 1993, 2002). This is particularly striking because these stories are in reality almost exclusively based on hard tissue data. In fact, descriptions of the soft tissues of apes have been relatively scarce and mainly referred to just a few muscles of the head or limbs of a single taxon, in most cases (e.g., Tyson, 1699; Bischoff, 1880; Raven, 1950; Swindler and Wood, 1973; Diogo and Wood, 2011, 2012; Persaud and Loukas, 2014). For instance, the only study that specifically focused on the musculature of bonobos (Pan paniscus) was that of Miller (1952), which was based on dissections of a single adult and did not provide information for numerous head and limb muscles (Diogo and Wood, 2011, 2012). Strikingly, despite this scarcity of information, biologists and anthropologists have displayed a remarkable confidence in their stories about the origin and evolution of human soft tissues, including their phylogenetic distribution and “singular functional adaptations.”

To illustrate this fact, in this short paper I will refer here briefly to seven muscles that have long been generally seen as “unique human features” and linked with specific adaptations for our bipedalism, tool use, and vocal or facial communication. Firstly, the facial expression muscle risorius (Figure 1) has been generally accepted as a unique feature crucial for the evolution of our “gracile” smile and “specially sophisticated” facial communication abilities (Huber, 1931). In a very influential paper, Susman et al. argued—although (fortunately) not as confidently as the assertions done by some of the other authors cited here—that the hand muscle adductor pollicis accessorius (Figure 2; “Henle” or “interosseous volaris primus” muscle: Bello-Hellegouarch et al., 2013) is a unique feature likely related to our increased ability to manufacture and/or use tools (Susman et al., 1999). Similarly, the foot muscle adductor hallucis accessorius—which topologically corresponds to the adductor pollicis accessorius of the hand—is also often considered to be uniquely found in our bipedal species, being at least consistently present at early stages of our ontogenetic development (Cihak, 1972). The foot muscle fibularis tertius (Figure 3) is, according to Lewis' (1989) highly influential monograph on the evolution of our limbs, a unique feature most likely associated with our bipedal evolution (Lewis, 1989). The flexor pollicis longus and extensor pollicis brevis (Figure 2) are forearm muscles that insert onto the thumb and that are generally considered to be unique adaptations for human tool manufacture and use (Lewis, 1989). For instance, it has been experimentally shown that the recruitment to these two muscles allows human subjects to maintain the metacarpophalangeal joint in extension while flexing the distal phalanx of the thumb, i.e., two primary movements usually done when we grab/manipulate objects (Marzke et al., 1998; Williams et al., 2012). Lastly, the laryngeal muscle arytenoideus obliquus has long been considered to be a unique feature of humans—which also have an arytenoideus transversus, in contrast to the single arytenoideus muscle said to occur in all other primates—associated to our enhanced vocal communication (reviewed in Diogo and Wood, 2012).

Usando e navegando a árvore da vida das plantas

Using and navigating the plant tree of life

Douglas E. Soltis Michael J. Moore Emily B. Sessa Stephen A. Smith Pamela S. Soltis

First published: 27 April 2018 https://doi.org/10.1002/ajb2.1071


Image result for plants tree of life
Source/Fonte: One Zoom Tree of Life

Abstract

The “tree of life” has become a metaphor for the interconnectivity and breadth of all life on Earth. It also has come to symbolize the broad investigation of biodiversity, including both the reconstruction of phylogeny and the numerous downstream analyses that are possible with a firm phylogenetic underpinning. Only a few decades ago, the construction of large phylogenetic trees of hundreds of taxa (or more) was considered an impossible task due to the immense computational challenges posed by analyses of large data sets. And no wonder—the number of possible trees that can describe the relationships of just 200 species exceeds the number of atoms in the universe (Hillis, 1996). As a result, building the tree of all named life, including the green plant branch (Viridiplantae)—a major clade with perhaps 500,000 species—has long been considered a grand challenge in biology. However, a perfect storm of algorithm development, increases in computational power, and DNA sequencing improvements over the last decade has not only made the construction of large trees more feasible, but also allowed us to attain some far‐reaching goals—a noteworthy example being the recent publication of a first draft tree of all life (Hinchcliff et al., 2015).

In plant biology, the frequent reconstruction of large phylogenetic trees has had an immense impact on the field. Large trees have helped to resolve deep‐level relationships and resulted in the revision of classifications, including some of the most profound changes in our view of plant relationships over the past 200 years (e.g., reviewed in part by Gitzendanner et al., 2018, in this issue). Large trees have also ushered in a renaissance in the study of conservation, ecology, methods development, crop improvement, genome evolution, and much more. Building the plant tree of life has come to represent the biodiversity equivalent of the human genome project, with numerous and often unanticipated downstream outcomes.

Accompanying these exciting advances are equally significant challenges that remain for the construction of a better and more complete picture of the evolution of plant lineages. In addition to the computational challenges of larger data sets, these include conceptual and methodological barriers. For example, where it was once thought that simply increasing DNA sequence data would increase resolution of relationships, we now understand that increasing data leads to increasing analytical complexity. Furthermore, this complexity is not due solely to limitations in computational power and methodology, but in part reflects the underlying complexity of the evolutionary process and its impact on genomes. Nevertheless, current conceptual and computational limitations present fantastic opportunities for transformative developments in our understanding of plant evolution. In this special issue, we explore many of the uses and challenges of big trees and big data in plant biology. Diverse papers provide overviews of the current status of the green plant tree of life and describe some of the myriad applications of the knowledge of phylogenetic relationships as well as some of the challenges inherent in handling plant phylogenomic data.

FREE PDF GRATIS: American Journal of Botany

Movimento unidirecional em torno de ligações duplas em motores moleculares rotativos: buscando ideias no mero acaso, fortuita necessidade ou no design inteligente?

quinta-feira, maio 03, 2018

Molecular rotary motors: Unidirectional motion around double bonds

Diederik Roke, Sander J. Wezenberg, and Ben L. Feringa

PNAS April 30, 2018. 201712784; published ahead of print April 30, 2018. https://doi.org/10.1073/pnas.1712784115

Edited by J. Fraser Stoddart, Northwestern University, Evanston, IL, and approved April 6, 2018 (received for review January 17, 2018)


Abstract

The field of synthetic molecular machines has quickly evolved in recent years, growing from a fundamental curiosity to a highly active field of chemistry. Many different applications are being explored in areas such as catalysis, self-assembled and nanostructured materials, and molecular electronics. Rotary molecular motors hold great promise for achieving dynamic control of molecular functions as well as for powering nanoscale devices. However, for these motors to reach their full potential, many challenges still need to be addressed. In this paper we focus on the design principles of rotary motors featuring a double-bond axle and discuss the major challenges that are ahead of us. Although great progress has been made, further design improvements, for example in terms of efficiency, energy input, and environmental adaptability, will be crucial to fully exploit the opportunities that these rotary motors offer.

molecular motor alkene molecular machine

FREE PDF GRATIS: PNAS

Insight na remodelagem estrutural do anel FlhA responsável pela exportação de proteína do flagelo bacteriano tipo III

Insight into structural remodeling of the FlhA ring responsible for bacterial flagellar type III protein export

Naoya Terahara1,*, Yumi Inoue1,*, Noriyuki Kodera2, Yusuke V. Morimoto1,3,4, Takayuki Uchihashi2,5,6, Katsumi Imada7, Toshio Ando2,8, Keiichi Namba1,3,† and Tohru Minamino1,†

See all authors and affiliations

Science Advances 25 Apr 2018: Vol. 4, no. 4, eaao7054



Abstract

The bacterial flagellum is a supramolecular motility machine. Flagellar assembly begins with the basal body, followed by the hook and finally the filament. A carboxyl-terminal cytoplasmic domain of FlhA (FlhAC) forms a nonameric ring structure in the flagellar type III protein export apparatus and coordinates flagellar protein export with assembly. However, the mechanism of this process remains unknown. We report that a flexible linker of FlhAC (FlhAL) is required not only for FlhAC ring formation but also for substrate specificity switching of the protein export apparatus from the hook protein to the filament protein upon completion of the hook structure. FlhAL was required for cooperative ring formation of FlhAC. Alanine substitutions of residues involved in FlhAC ring formation interfered with the substrate specificity switching, thereby inhibiting filament assembly at the hook tip. These observations lead us to propose a mechanistic model for export switching involving structural remodeling of FlhAC.

Copyright © 2018 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).

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

FREE PDF GRATIS: Science Advances

100% teleologia: usando a genômica de única célula para compreender processos de desenvolvimento e as decisões de destino celular

Using single‐cell genomics to understand developmental processes and cell fate decisions

Jonathan A Griffiths Antonio Scialdone John C Marioni

First published: 16 April 2018 https://doi.org/10.15252/msb.20178046


Abstract

High‐throughput ‐omics techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision‐making is inherently a unicellular process to which “bulk” ‐omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single‐cell methods bridge this gap, allowing high‐throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single‐cell gene expression data and highlight areas of developmental biology where single‐cell techniques have made important contributions. These include understanding of cell‐to‐cell heterogeneity, the tracing of differentiation pathways, quantification of gene expression from specific alleles, and the future directions of cell lineage tracing and spatial gene expression analysis.

FREE PDF GRATIS: Molecular Systems Biology

Esteganografia: reações de multicomponentes fornecem moléculas chaves para comunicação secreta

Multicomponent reactions provide key molecules for secret communication

Andreas C. Boukis, Kevin Reiter, Maximiliane Frölich, Dennis Hofheinz & Michael A. R. Meier

Nature Communications volume 9, Article number: 1439 (2018)


Download Citation

Chemical libraries Information technology

Received: 27 September 2017 Accepted: 13 March 2018

Published online: 12 April 2018


Abstract

A convenient and inherently more secure communication channel for encoding messages via specifically designed molecular keys is introduced by combining advanced encryption standard cryptography with molecular steganography. The necessary molecular keys require large structural diversity, thus suggesting the application of multicomponent reactions. Herein, the Ugi four-component reaction of perfluorinated acids is utilized to establish an exemplary database consisting of 130 commercially available components. Considering all permutations, this combinatorial approach can unambiguously provide 500,000 molecular keys in only one synthetic procedure per key. The molecular keys are transferred nondigitally and concealed by either adsorption onto paper, coffee, tea or sugar as well as by dissolution in a perfume or in blood. Re-isolation and purification from these disguises is simplified by the perfluorinated sidechains of the molecular keys. High resolution tandem mass spectrometry can unequivocally determine the molecular structure and thus the identity of the key for a subsequent decryption of an encoded message.

Acknowledgements

We thank PD Dr. Weiss, T. Neck, and Dr. N. Boukis for the discussions and comments on early versions of this manuscript. A.B. is grateful for the Chemie Fonds fellowship from the VCI. This work was financially supported in part by SFB 1176 (Projects A3 and Q5). We thank Prof. Podlech for sharing lab space with us. We acknowledge support by Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of Karlsruhe Institute of Technology.

Author information

Affiliations

Laboratory of Applied Chemistry, Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, Karlsruhe, 76131, Germany

Andreas C. Boukis, Maximiliane Frölich & Michael A. R. Meier

Institute of Nano Technology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344, Germany

Kevin Reiter

Institute for Theoretical Informatics (ITI), Karlsruhe Institute of Technology (KIT), Am Fasanengarten 5, Karlsruhe, 76131, Germany

Dennis Hofheinz

Contributions

A.B. and M.M. conceived and designed the project. A.B. designed the experiments with input from M.M. K.R. programed the analysis script. M.F. synthesized the molecular keys under the supervision of A.B. D.H. optimized the cryptography integration and programed the molecular encryption script. A.B. analyzed data, prepared the figures and wrote the paper, with feedback from all the authors.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Michael A. R. Meier.





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NOTA DESTE BLOGGER: A esteganografia (em grego significa “escrita oculta). É o estudo de técnicas que permitam esconder informações dentro de outros arquivos, sejam imagens, músicas, vídeos ou mesmo textos. A teoria do Design Inteligente tem na esteganografia um campo fértil de pesquisas.

Atenção guardas-cancelas epistêmicos da Nomenklatura científica: a importância científica da liberdade de expressão!

sexta-feira, abril 27, 2018

Published on April 13, 2018

The Scientific Importance of Free Speech

written by Adam Perkins


Editor’s note: this is a shortened version of a speech that the author was due to give last month at King’s College London which was canceled because the university deemed the event to be too ‘high risk’.

A quick Google search suggests that free speech is a regarded as an important virtue for a functional, enlightened society. For example, according to George Orwell: “If liberty means anything at all, it means the right to tell people what they do not want to hear.” Likewise, Ayaan Hirsi Ali remarked: “Free speech is the bedrock of liberty and a free society, and yes, it includes the right to blaspheme and offend.” In a similar vein, Bill Hicks declared: “Freedom of speech means you support the right of people to say exactly those ideas which you do not agree with”.

But why do we specifically need free speech in science? Surely we just take measurements and publish our data? No chit chat required. We need free speech in science because science is not really about microscopes, or pipettes, or test tubes, or even Large Hadron Colliders. These are merely tools that help us to accomplish a far greater mission, which is to choose between rival narratives, in the vicious, no-holds-barred battle of ideas that we call “science”.

For example, stomach problems such as gastritis and ulcers were historically viewed as the products of stress. This opinion was challenged in the late 1970s by the Australian doctors Robin Warren and Barry Marshall, who suspected that stomach problems were caused by infection with the bacteria Helicobacter pylori. Frustrated by skepticism from the medical establishment and by difficulties publishing his academic papers, in 1984, Barry Marshall appointed himself his own experimental subject and drank a Petri dish full of H. pylori culture. He promptly developed gastritis which was then cured with antibiotics, suggesting that H. pylori has a causal role in this type of illness. You would have thought that given this clear-cut evidence supporting Warren and Marshall’s opinion, their opponents would immediately concede defeat. But scientists are only human and opposition to Warren and Marshall persisted. In the end it was two decades before their crucial work on H. pylori gained the recognition it deserved, with the award of the 2005 Nobel Prize in Physiology or Medicine.

From this episode we can see that even in situations where laboratory experiments can provide clear evidence in favour of a particular scientific opinion, opponents will typically refuse to accept it. Instead scientists tend cling so stubbornly to their pet theories that no amount of evidence will change their minds and only death can bring an end to the argument, as famously observed by Max Planck:

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.

It is a salutary lesson that even in a society that permits free speech, Warren and Marshall had difficulty publishing their results. If their opponents had the legal power to silence them their breakthrough would have taken even longer to have become clinically accepted and even more people would have suffered unnecessarily with gastric illness that could have been cured quickly and easily with a course of antibiotics. But scientific domains in which a single experiment can provide a definitive answer are rare. For example, Charles Darwin’s principle of evolution by natural selection concerns slow, large-scale processes that are unsuited to testing in a laboratory. In these cases, we take a bird’s eye view of the facts of the matter and attempt to form an opinion about what they mean.

This allows a lot of room for argument, but as long as both sides are able to speak up, we can at least have a debate: when a researcher disagrees with the findings of an opponent’s study, they traditionally write an open letter to the journal editor critiquing the paper in question and setting out their counter-evidence. Their opponent then writes a rebuttal, with both letters being published in the journal with names attached so that the public can weigh up the opinions of the two parties and decide for themselves whose stance they favour. I recently took part in just such an exchange of letters in the elite journal Trends in Cognitive Sciences. The tone is fierce and neither side changed their opinions, but at least there is a debate that the public can observe and evaluate.

The existence of scientific debate is also crucial because as the Nobel Prize-winning physicist Richard Feynman remarked in 1963: “There is no authority who decides what is a good idea.” The absence of an authority who decides what is a good idea is a key point because it illustrates that science is a messy business and there is no absolute truth. This was articulated in Tom Schofield’s posthumously published essay in which he wrote:

[S]cience is not about finding the truth at all, but about finding better ways of being wrong. The best scientific theory is not the one that reveals the truth — that is impossible. It is the one that explains what we already know about the world in the simplest way possible, and that makes useful predictions about the future. When I accepted that I would always be wrong, and that my favourite theories are inevitably destined to be replaced by other, better, theories — that is when I really knew that I wanted to be a scientist.

When one side of a scientific debate is allowed to silence the other side, this is an impediment to scientific progress because it prevents bad theories being replaced by better theories. Or, even worse, it causes civilization to go backward, such as when a good theory is replaced by a bad theory that it previously displaced. The latter situation is what happened in the most famous illustration of the dire consequences that can occur when one side of a scientific debate is silenced. This occurred in connection with the theory that acquired characteristics are inherited. This idea had been out of fashion for decades, in part due to research in the 1880s by August Weismann. He conducted an experiment that entailed amputating the tails of 68 white mice, over 5 generations. He found that no mice were born without a tail or even with a shorter tail. He stated: “901 young were produced by five generations of artificially mutilated parents, and yet there was not a single example of a rudimentary tail or of any other abnormality in this organ.”

These findings and others like them led to the widespread acceptance of Mendelian genetics. Unfortunately for the people of the USSR, Mendelian genetics are incompatible with socialist ideology and so in the 1930s USSR were replaced with Trofim Lysenko’s socialism-friendly idea that acquired characteristics are inherited. Scientists who disagreed were imprisoned or executed. Soviet agriculture collapsed and millions starved.

Henceforth the tendency to silence scientists with inconvenient opinions has been labeled Lysenkoism since it provides the most famous example of the harm that can be done when competing scientific opinions cannot be expressed equally freely. Left-wingers tend to be the most prominent Lysenkoists but the suppression of scientific opinions can occur in other contexts too. The Space Shuttle Challenger disaster in 1986 is a famous example.
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Evolução molecular: como os blocos construtores da vida podem se formar no espaço

quinta-feira, abril 26, 2018

Glycine formation in CO2:CH4:NH3 ices induced by 0-70 eV electrons featured

The Journal of Chemical Physics 148, 164702 (2018); https://doi.org/10.1063/1.5021596

Sasan Esmaili, Andrew D. Bass, Pierre Cloutier, Léon Sanche, and Michael A. Huelsa)

Affiliations

Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada

a)Author to whom correspondence should be addressed: Michael.Huels@usherbrooke.ca and huels@kth.se. Tel.: 1-819-821-8000 (74776).

Source/Fonte: Science Daily

ABSTRACT

Glycine (Gly), the simplest amino-acid building-block of proteins, has been identified on icy dust grains in the interstellar medium, icy comets, and ice covered meteorites. These astrophysical ices contain simple molecules (e.g., CO2, H2O, CH4, HCN, and NH3) and are exposed to complex radiation fields, e.g., UV, γ, or X-rays, stellar/solar wind particles, or cosmic rays. While much current effort is focused on understanding the radiochemistry induced in these ices by high energy radiation, the effects of the abundant secondary low energy electrons (LEEs) it produces have been mostly assumed rather than studied. Here we present the results for the exposure of multilayer CO2:CH4:NH3 ice mixtures to 0-70 eV electrons under simulated astrophysical conditions. Mass selected temperature programmed desorption (TPD) of our electron irradiated films reveals multiple products, most notably intactglycine, which is supported by control measurements of both irradiated or un-irradiated binary mixture films, and un-irradiated CO2:CH4:NH3ices spiked with Gly. The threshold of Gly formation by LEEs is near 9 eV, while the TPD analysis of Gly film growth allows us to determine the “quantum” yield for 70 eV electrons to be about 0.004 Gly per incident electron. Our results show that simple amino acids can be formed directly from simple molecular ingredients, none of which possess preformed C—C or C—N bonds, by the copious secondary LEEs that are generated by ionizing radiation in astrophysical ices.

Inflação cosmológica reproduzida em laboratório?

A Rapidly Expanding Bose-Einstein Condensate: An Expanding Universe in the Lab

S. Eckel, A. Kumar, T. Jacobson, I. B. Spielman, and G. K. Campbell

Phys. Rev. X 8, 021021 – Published 19 April 2018


Source/Fonte: LeCosPa

ABSTRACT

We study the dynamics of a supersonically expanding, ring-shaped Bose-Einstein condensate both experimentally and theoretically. The expansion redshifts long-wavelength excitations, as in an expanding universe. After expansion, energy in the radial mode leads to the production of bulk topological excitations—solitons and vortices—driving the production of a large number of azimuthal phonons and, at late times, causing stochastic persistent currents. These complex nonlinear dynamics, fueled by the energy stored coherently in one mode, are reminiscent of a type of “preheating” that may have taken place at the end of inflation.

Revised 3 February 2018 Received 16 October 2017


Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.

Published by the American Physical Society

Physics Subject Headings (PhySH)

Research Areas Acoustic phonons Physical Systems Bose-Einstein condensates Solitons Superfluids Vortices Properties Distances, redshifts, & velocities Gravitation, Cosmology & Astrophysics Atomic, Molecular & Optical 

FREE PDF GRATIS: Phys Rev X

Adaptação estocasticamente bombeada e movimento direcional de máquinas moleculares: mero acaso, fortuita necessidade ou design inteligente?

terça-feira, abril 24, 2018

Stochastically pumped adaptation and directional motion of molecular machines

R. Dean Astumian

PNAS March 9, 2018. 201714498; published ahead of print March 9, 2018. https://doi.org/10.1073/pnas.1714498115

Edited by J. Fraser Stoddart, Northwestern University, Evanston, IL, and approved February 5, 2018 (received for review November 7, 2017)


Abstract

Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment—walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium.

molecular machinestochastic pumpingkinetic asymmetry

FREE PDF GRATIS: PNAS

Rotação de endossomos demonstra coordenação de motores moleculares durante o transporte axonal: mero acaso, fortuita necessidade ou design inteligente?

Rotation of endosomes demonstrates coordination of molecular motors during axonal transport

Luke Kaplan1, Athena Ierokomos1, Praveen Chowdary2, Zev Bryant3,4 and Bianxiao Cui2,*

See all authors and affiliations

Science Advances 07 Mar 2018: Vol. 4, no. 3, e1602170



Abstract

Long-distance axonal transport is critical to the maintenance and function of neurons. Robust transport is ensured by the coordinated activities of multiple molecular motors acting in a team. Conventional live-cell imaging techniques used in axonal transport studies detect this activity by visualizing the translational dynamics of a cargo. However, translational measurements are insensitive to torques induced by motor activities. By using gold nanorods and multichannel polarization microscopy, we simultaneously measure the rotational and translational dynamics for thousands of axonally transported endosomes. We find that the rotational dynamics of an endosome provide complementary information regarding molecular motor activities to the conventionally tracked translational dynamics. Rotational dynamics correlate with translational dynamics, particularly in cases of increased rotation after switches between kinesin- and dynein-mediated transport. Furthermore, unambiguous measurement of nanorod angle shows that endosome-contained nanorods align with the orientation of microtubules, suggesting a direct mechanical linkage between the ligand-receptor complex and the microtubule motors.

Copyright © 2018 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).

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

FREE PDF GRATIS: Science Advances

Descoberta a origem genética dos sexos... em algas

Anisogamy evolved with a reduced sex-determining region in volvocine green algae

Takashi Hamaji, Hiroko Kawai-Toyooka, Haruka Uchimura, Masahiro Suzuki, Hideki Noguchi, Yohei Minakuchi, Atsushi Toyoda, Asao Fujiyama, Shin-ya Miyagishima, James G. Umen & Hisayoshi Nozaki

Communications Biology volume 1, Article number: 17 (2018)


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Comparative genomics Evolutionary biology Evolutionary genetics

Received: 16 November 2017 Accepted: 08 February 2018

Published online: 08 March 2018



Abstract

Male and female gametes differing in size—anisogamy—emerged independently from isogamous ancestors in various eukaryotic lineages, although genetic bases of this emergence are still unknown. Volvocine green algae are a model lineage for investigating the transition from isogamy to anisogamy. Here we focus on two closely related volvocine genera that bracket this transition—isogamous Yamagishiella and anisogamous Eudorina. We generated de novo nuclear genome assemblies of both sexes of Yamagishiella and Eudorina to identify the dimorphic sex-determining chromosomal region or mating-type locus (MT) from each. In contrast to the large (>1 Mb) and complex MT of oogamous Volvox, Yamagishiella and Eudorina MT are smaller (7–268 kb) and simpler with only two sex-limited genes—the minus/male-limited MID and the plus/female-limited FUS1. No prominently dimorphic gametologs were identified in either species. Thus, the first step to anisogamy in volvocine algae presumably occurred without an increase in MT size and complexity.

Acknowledgements

We thank the staff of Comparative Genomics Laboratory at NIG for supporting genome sequencing. Computations were partially performed on the NIG supercomputer at ROIS National Institute of Genetics. This work was supported by a Grants-in-Aid for Scientific Research on Innovative Areas “Genome Science” (grant number 221S0002; to A.T. and A.F.), Scientific Research (A) (grant number 16H02518; to H.Nozaki), Research Activity Startup grants (grant number 16H06734 to T.H.), Scientific Research (C) (grant number 17K07510 to H.K.-T.), Grant-in-Aid for Scientific Research on Innovative Areas (grant number 17H05840 to T.H.) from MEXT/JSPS KAKENHI, and National Institutes of Health (grant number GM 078376 to J.G.U.).

Author information

Author notes

Takashi Hamaji

Present address: Department of Biological Sciences, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan

These authors contributed equally: Takashi Hamaji, Hiroko Kawai-Toyooka.

Affiliations

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan

Takashi Hamaji, Hiroko Kawai-Toyooka, Haruka Uchimura & Hisayoshi Nozaki

Kobe University Research Center for Inland Seas, Awaji, Hyogo, 656-2401, Japan

Masahiro Suzuki

Center for Genome Informatics, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan

Hideki Noguchi

Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan

Hideki Noguchi, Atsushi Toyoda & Asao Fujiyama

Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan

Yohei Minakuchi & Atsushi Toyoda

Department of Cell Genetics, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan

Shin-ya Miyagishima

Donald Danforth Plant Science Center, 975 N Warson Rd, St. Louis, MO, 63132, USA

James G. Umen

Contributions

Conceived the study: H.Nozaki. Designed the study: T.H., H.K.-T., H.Nozaki. Prepared genomic DNA: M.S. Performed whole-genome sequencing and assembly: H.Noguchi., Y.M. A.T., A.F. Performed the experiments: T.H., H.K.-T., H.U. Analyzed the data: T.H., H.K.-T., H.Nozaki. Contributed materials: S.-y.M. Wrote and edited the manuscript: T.H., H.K.-T., A.T., J.G.U., H.Nozaki.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Hiroko Kawai-Toyooka or Hisayoshi Nozaki.

A evolução da "vida": uma abordagem metadarwinista integrativa

Communicative & Integrative Biology Volume 10, 2017 - Issue 3

The evolution of “Life”: A Metadarwinian integrative approach

Arnold De Loof

Article: e1301335 | Received 14 Feb 2017, Accepted 24 Feb 2017, Accepted author version posted online: 13 Mar 2017, Published online: 13 Mar 2017

Download citation https://doi.org/10.1080/19420889.2017.1301335


ABSTRACT

It is undeniably very logical to first formulate an unambiguous definition of “Life” before engaging in defining the parameters instrumental to Life's evolution. Because nearly everybody assumes, erroneously in my opinion, that catching Life's essence in a single sentence is impossible, this way of thinking remained largely unexplored in evolutionary theory. Upon analyzing what exactly happens at the transition from “still alive” to “just dead,” the following definition emerged. What we call “Life” (L) is an activity. It is nothing other than the total sum (∑) of all communication acts (C) executed, at moment t, by entities organized as sender-receiver compartments: L = ∑C Such “living” entities are self-electrifying and talking ( = communicating) aggregates of fossil stardust operating in an environment heavily polluted by toxic calcium. Communication is a multifaceted, complex process that is seldom well explained in introductory textbooks of biology. Communication is instrumental to adaptation because, at the cellular level, any act of communication is in fact a problem-solving act. It can be logically deduced that not Natural Selection itself but communication/problem-solving activity preceding selection is the universal driving force of evolution. This is against what textbooks usually claim, although doubt on the status of Natural Selection as driving force has been around for long. Finally, adopting the sender-receiver with its 2 memory systems (genetic and cognitive, both with their own rules) and 2 types of progeny (”physical children” and “pupils”) as the universal unit of architecture and function of all living entities, also enables the seamless integration of cultural and organic evolution, another long-standing tough problem in evolutionary theory. Paraphrasing Theodosius Dobzhansky, the very essence of biology is: “Nothing in biology and evolutionary theory makes sense except in the light of the ability of living matter to communicate, and by doing so, to solve problems.”

KEYWORDS: adaptation, Calcigender, cultural evolution, definition of Life, EES, electrome, evo-devo, Metadarwinism, Neo-Darwinism, selection

Descoberta uma nova forma de DNA em nossas células

segunda-feira, abril 23, 2018

I-motif DNA structures are formed in the nuclei of human cells

Mahdi Zeraati, David B. Langley, Peter Schofield, Aaron L. Moye, Romain Rouet, William E. Hughes, Tracy M. Bryan, Marcel E. Dinger & Daniel Christ

Nature Chemistry (2018)

doi:10.1038/s41557-018-0046-3

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Bioanalytical chemistry DNA DNA probes Molecular biology

Received: 29 June 2017 Accepted: 14 March 2018

Published online: 23 April 2018

Source/Fonte: Chris Hammang - Science Daily


Abstract

Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

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Nocautes naturais: a seleção natural de Darwin nocauteada

Biology 2017, 6(4), 43; doi:10.3390/biology6040043

Natural Knockouts: Natural Selection Knocked Out

Peter Borger

The Independent Research Initiative on Information & Origins, 79540 Loerrach, Germany

Academic Editor: Hirofumi Akari

Received: 13 September 2017 / Revised: 17 October 2017 / Accepted: 25 October 2017 / Published: 12 December 2017

(This article belongs to the Special Issue Biology in the Early 21st Century: Evolution Beyond Selection)

Image result for knockout

Abstract

In functional genomics studies, research is dedicated to unveiling the function of genes using gene-knockouts, model organisms in which a gene is artificially inactivated. The idea is that, by knocking out the gene, the provoked phenotype would inform us about the function of the gene. Still, the function of many genes cannot be elucidated, because disruption of conserved sequences, including protein-coding genes, often does not directly affect the phenotype. Since the phenomenon was first observed in the early nineties of the last century, these so-called ‘no-phenotype knockouts’ have met with great skepticism and resistance by died-in-the-wool selectionists. Still, functional genomics of the late 20th and early 21st centuries has taught us two important lessons. First, two or more unrelated genes can often substitute for each other; and second, some genes are only present in the genome in a silent state. In the laboratory, the disruption of such genes does not negatively influence reproductive success, and does not show measurable fitness effects of the species. The genes are redundant. Genetic redundancy, one of the big surprises of modern biology, can thus be defined as the condition in which the inactivation of a gene is selectively neutral. The no-phenotype knockout is not just a freak of the laboratory. Genetic variants known as homozygous loss-of-function (HLOF) variants are of considerable scientific and clinical interest, as they represent experiments of nature qualifying as “natural knockouts”. Such natural knockouts challenge the conventional NeoDarwinian appraisal that genetic information is the result of natural selection acting on random genetic variation

Keywords: genetic redundancy; natural knockout; natural selection; homozygous loss-of-function

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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