Y chromosome evolution: emerging insights into processes of Y chromosome degeneration

PubMed Central

Bachtrog, Doris

2014-01-01

The human Y chromosome is intriguing not only because it harbours the master-switch gene determining gender but also because of its unusual evolutionary trajectory. Previously an autosome, Y chromosome evolution has been characterized by massive gene decay. Recent whole-genome and transcriptome analyses of Y chromosomes in humans and other primates, in Drosophila species as well as in plants have shed light on the current gene content of the Y, its origins and its long-term fate. Comparative analysis of young and old Y chromosomes have given further insights into the evolutionary and molecular forces triggering Y degeneration and its evolutionary destiny. PMID:23329112

Doping dependence of low-energy quasiparticle excitations in superconducting Bi2212.

PubMed

Ino, Akihiro; Anzai, Hiroaki; Arita, Masashi; Namatame, Hirofumi; Taniguchi, Masaki; Ishikado, Motoyuki; Fujita, Kazuhiro; Ishida, Shigeyuki; Uchida, Shinichi

2013-12-05

: The doping-dependent evolution of the d-wave superconducting state is studied from the perspective of the angle-resolved photoemission spectra of a high-Tc cuprate, Bi2Sr2CaCu2 O8+δ (Bi2212). The anisotropic evolution of the energy gap for Bogoliubov quasiparticles is parametrized by critical temperature and superfluid density. The renormalization of nodal quasiparticles is evaluated in terms of mass enhancement spectra. These quantities shed light on the strong coupling nature of electron pairing and the impact of forward elastic or inelastic scatterings. We suggest that the quasiparticle excitations in the superconducting cuprates are profoundly affected by doping-dependent screening.

Brownian model of transcriptome evolution and phylogenetic network visualization between tissues.

PubMed

Gu, Xun; Ruan, Hang; Su, Zhixi; Zou, Yangyun

2017-09-01

While phylogenetic analysis of transcriptomes of the same tissue is usually congruent with the species tree, the controversy emerges when multiple tissues are included, that is, whether species from the same tissue are clustered together, or different tissues from the same species are clustered together. Recent studies have suggested that phylogenetic network approach may shed some lights on our understanding of multi-tissue transcriptome evolution; yet the underlying evolutionary mechanism remains unclear. In this paper we develop a Brownian-based model of transcriptome evolution under the phylogenetic network that can statistically distinguish between the patterns of species-clustering and tissue-clustering. Our model can be used as a null hypothesis (neutral transcriptome evolution) for testing any correlation in tissue evolution, can be applied to cancer transcriptome evolution to study whether two tumors of an individual appeared independently or via metastasis, and can be useful to detect convergent evolution at the transcriptional level. Copyright © 2017. Published by Elsevier Inc.

Microphysics of liquid complex plasmas in equilibrium and non-equilibrium systems

NASA Astrophysics Data System (ADS)

Piel, Alexander; Block, Dietmar; Melzer, André; Mulsow, Matthias; Schablinski, Jan; Schella, André; Wieben, Frank; Wilms, Jochen

2018-05-01

The dynamic evolution of the microscopic structure of solid and liquid phases of complex plasmas is studied experimentally and by means of molecular dynamics (MD) simulations. In small finite systems, the cooperative motion can be described in terms of discrete modes. These modes are studied with different experimental approaches. Using diffuse scattered laser light, applying laser tweezer forces to individual particles, and periodic laser pulses, the excitation of modes is investigated. The instantaneous normal mode analysis of experimental data from two-dimensional liquid clusters gives access to the local dynamics of the liquid phase. Our investigations shed light on the role of compressional and shear modes as well as the determination of diffusion constants and melting temperatures in finite systems. Special attention is paid to hydrodynamic situations with a stationary inhomogeneous dust flow. MD simulations allow to study the collective motion in the shell of nearest neighbors, which can be linked to smooth and sudden changes of the macroscopic flow. Finally, the observed micro-motion in all situations above allows to shed light on the preference of shear-like over compressional motion in terms of a minimized potential energy and a dynamic incompressibility.

Morphology-dependent photo-induced polarization recovery in ferroelectric thin films

NASA Astrophysics Data System (ADS)

Wang, J. Y.; Liu, G.; Sando, D.; Nagarajan, V.; Seidel, J.

2017-08-01

We investigate photo-induced ferroelectric domain switching in a series of Pb(Zr0.2Ti0.8)O3/La0.7Sr0.3MnO3 (PZT/LSMO) bilayer thin films with varying surface morphologies by piezoresponse force microscopy under light illumination. We demonstrate that reverse poled ferroelectric regions can be almost fully recovered under laser irradiation of the PZT layer and that the recovery process is dependent on the surface morphology on the nanometer scale. The recovery process is well described by the Kolmogorov-Avrami-Ishibashi model, and the evolution speed is controlled by light intensity, sample thickness, and initial write voltage. Our findings shed light on optical control of the domain structure in ferroelectric thin films with different surface morphologies.

Toward understanding early Earth evolution: Prescription for approach from terrestrial noble gas and light element records in lunar soils

PubMed Central

Ozima, Minoru; Yin, Qing-Zhu; Podosek, Frank A.; Miura, Yayoi N.

2008-01-01

Because of the almost total lack of geological record on the Earth's surface before 4 billion years ago, the history of the Earth during this period is still enigmatic. Here we describe a practical approach to tackle the formidable problems caused by this lack. We propose that examinations of lunar soils for light elements such as He, N, O, Ne, and Ar would shed a new light on this dark age in the Earth's history and resolve three of the most fundamental questions in earth science: the onset time of the geomagnetic field, the appearance of an oxygen atmosphere, and the secular variation of an Earth–Moon dynamical system. PMID:19001263

The SOAPS project - Spin-orbit alignment of planetary systems. Exoplanets' evolution histories in systems with different architectures

NASA Astrophysics Data System (ADS)

Faedi, F.; Gómez Maqueo Chew, Y.; Fossati, L.; Pollacco, D.; McQuillan, A.; Hebb, L.; Chaplin, W. J.; Aigrain, S.

2013-04-01

The wealth of information rendered by Kepler planets and planet candidates is indispensable for statistically significant studies of distinct planet populations, in both single and multiple systems. Empirical evidences suggest that Kepler's planet population shows different physical properties as compared to the bulk of known exoplanets. The SOAPS project, aims to shed light on Kepler's planets formation, their migration and architecture. By measuring v sini accurately for Kepler hosts with rotation periods measured from their high-precision light curves, we will assess the alignment of the planetary orbit with respect to the stellar spin axis. This degree of alignment traces the formation history and evolution of the planetary systems, and thus, allows to distinguish between different proposed migration theories. SOAPS will increase by a factor of 2 the number of spin-orbit alignment measurements pushing the parameters space down to the SuperEarth domain. Here we present our preliminary results.

Chapter 4. New model systems for the study of developmental evolution in plants.

PubMed

Kramer, Elena M

2009-01-01

The number of genetically tractable plant model systems is rapidly increasing, thanks to the decreasing cost of sequencing and the wide amenability of plants to stable transformation and other functional approaches. In this chapter, I discuss emerging model systems from throughout the land plant phylogeny and consider how their unique attributes are contributing to our understanding of development, evolution, and ecology. These new models are being developed using two distinct strategies: in some cases, they are selected because of their close relationship to the established models, while in others, they are chosen with the explicit intention of exploring distantly related plant lineages. Such complementary approaches are yielding exciting new results that shed light on both micro- and macroevolutionary processes in the context of developmental evolution.

Evolution of sex: Using experimental genomics to select among competing theories.

PubMed

Sharp, Nathaniel P; Otto, Sarah P

2016-08-01

Few topics have intrigued biologists as much as the evolution of sex. Understanding why sex persists despite its costs requires not just rigorous theoretical study, but also empirical data on related fundamental issues, including the nature of genetic variance for fitness, patterns of genetic interactions, and the dynamics of adaptation. The increasing feasibility of examining genomes in an experimental context is now shedding new light on these problems. Using this approach, McDonald et al. recently demonstrated that sex uncouples beneficial and deleterious mutations, allowing selection to proceed more effectively with sex than without. Here we discuss the insights provided by this study, along with other recent empirical work, in the context of the major theoretical models for the evolution of sex. © 2016 WILEY Periodicals, Inc.

N-body simulations of collective effects in spiral and barred galaxies

NASA Astrophysics Data System (ADS)

Zhang, X.

2016-10-01

We present gravitational N-body simulations of the secular morphological evolution of disk galaxies induced by density wave modes. In particular, we address the demands collective effects place on the choice of simulation parameters, and show that the common practice of the use of a large gravity softening parameter was responsible for the failure of past simulations to correctly model the secular evolution process in galaxies, even for those simulations where the choice of basic state allows an unstable mode to emerge, a prerequisite for obtaining the coordinated radial mass flow pattern needed for secular evolution of galaxies along the Hubble sequence. We also demonstrate that the secular evolution rates measured in our improved simulations agree to an impressive degree with the corresponding rates predicted by the recently-advanced theories of dynamically-driven secular evolution of galaxies. The results of the current work, besides having direct implications on the cosmological evolution of galaxies, also shed light on the general question of how irreversibility emerges from a nominally reversible physical system.

Effect of self-interaction on the evolution of cooperation in complex topologies

NASA Astrophysics Data System (ADS)

Wu, Yu'e.; Zhang, Zhipeng; Chang, Shuhua

2017-09-01

Self-interaction, as a significant mechanism explaining the evolution of cooperation, has attracted great attention both theoretically and experimentally. In this text, we consider a new self-interaction mechanism in the two typical pairwise models including the prisoner's dilemma and the snowdrift games, where the cooperative agents will gain extra bonus for their selfless behavior. We find that under the mechanism the collective cooperation is elevated to a very high level especially after adopting the finite population analogue of replicator dynamics for evolution. The robustness of the new mechanism is tested for different complex topologies for the prisoner's dilemma game. All the presented results demonstrate that the enhancement effects are independent of the structure of the applied spatial networks and the potential evolutionary games, and thus showing a high degree of universality. Our conclusions might shed light on the understanding of the evolution of cooperation in the real world.

Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration.

PubMed

Bachtrog, Doris

2013-02-01

The human Y chromosome is intriguing not only because it harbours the master-switch gene that determines gender but also because of its unusual evolutionary history. The Y chromosome evolved from an autosome, and its evolution has been characterized by massive gene decay. Recent whole-genome and transcriptome analyses of Y chromosomes in humans and other primates, in Drosophila species and in plants have shed light on the current gene content of the Y chromosome, its origins and its long-term fate. Furthermore, comparative analysis of young and old Y chromosomes has given further insights into the evolutionary and molecular forces triggering Y-chromosome degeneration and into the evolutionary destiny of the Y chromosome.

The enigma of the magnetic pulsar SXP1062: a new look with XMM-Newton

NASA Astrophysics Data System (ADS)

Oskinova, Lidia

2012-10-01

SXP 1062 is an exceptional case of a young neutron star with known age in a wind-fed HMXB. A unique combination of measured spin period, its derivative, luminosity and young age makes this source a key probe for the physics of accretion and neutron star evolution. All current accretion scenarios encounter major difficulties explaining the spin-down rate of this accretion-powered pulsar. This study will allow us to construct a spin period-luminosity relation as a powerful tool for distinguishing between different accretion and evolution scenarios. The XMM-Newton observations of SXP 1062 will thus shed new light on the physics of accreting neutron stars.

Dark Candles of the Universe: Black Hole Observations

NASA Astrophysics Data System (ADS)

Aykutalp, Aycin

2016-03-01

In 1916, when Karl Schwarzschild solved the Einstein field equations of general relativity for a spherically symmetric, non-rotating mass no one anticipated the impact black holes would have on astrophysics. I will review the main formation channels for black hole seeds and their evolution through cosmic time. In this, emphasis will be placed on the observational diagnostics of astrophysical black holes and their role on the assembly of galaxy formation and evolution. I then review how these observations put constrain on the seed black hole formation theories. Finally, I present an outlook for how future observations can shed light on our understanding of black holes. This work is supported by NSF Grant AST-1333360.

Doping dependence of low-energy quasiparticle excitations in superconducting Bi2212

PubMed Central

2013-01-01

The doping-dependent evolution of the d-wave superconducting state is studied from the perspective of the angle-resolved photoemission spectra of a high-Tc cuprate, Bi2Sr2CaCu2 O8+δ (Bi2212). The anisotropic evolution of the energy gap for Bogoliubov quasiparticles is parametrized by critical temperature and superfluid density. The renormalization of nodal quasiparticles is evaluated in terms of mass enhancement spectra. These quantities shed light on the strong coupling nature of electron pairing and the impact of forward elastic or inelastic scatterings. We suggest that the quasiparticle excitations in the superconducting cuprates are profoundly affected by doping-dependent screening. PMID:24314035

Biofilms 2015: Multidisciplinary Approaches Shed Light into Microbial Life on Surfaces

PubMed Central

Yildiz, Fitnat

2016-01-01

The 7th ASM Conference on Biofilms was held in Chicago, Illinois, from 24 to 29 October 2015. The conference provided an international forum for biofilm researchers across academic and industry platforms, and from different scientific disciplines, to present and discuss new findings and ideas. The meeting covered a wide range of topics, spanning environmental sciences, applied biology, evolution, ecology, physiology, and molecular biology of the biofilm lifestyle. This report summarizes the presentations with regard to emerging biofilm-related themes. PMID:26977109

Auxology: when auxin meets plant evo-devo.

PubMed

Finet, Cédric; Jaillais, Yvon

2012-09-01

Auxin is implicated throughout plant growth and development. Although the effects of this plant hormone have been recognized for more than a century, it is only in the past two decades that light has been shed on the molecular mechanisms that regulate auxin homeostasis, signaling, transport, crosstalk with other hormonal pathways as well as its roles in plant development. These discoveries established a molecular framework to study the role of auxin in land plant evolution. Here, we review recent advances in auxin biology and their implications in both micro- and macro-evolution of plant morphology. By analogy to the term 'hoxology', which refers to the critical role of HOX genes in metazoan evolution, we propose to introduce the term 'auxology' to take into account the crucial role of auxin in plant evo-devo. Copyright © 2012 Elsevier Inc. All rights reserved.

The function and evolution of the Aspergillus genome

PubMed Central

Gibbons, John G.; Rokas, Antonis

2012-01-01

Species in the filamentous fungal genus Aspergillus display a wide diversity of lifestyles and are of great importance to humans. The decoding of genome sequences from a dozen species that vary widely in their degree of evolutionary affinity has galvanized studies of the function and evolution of the Aspergillus genome in clinical, industrial, and agricultural environments. Here, we synthesize recent key findings that shed light on the architecture of the Aspergillus genome, on the molecular foundations of the genus’ astounding dexterity and diversity in secondary metabolism, and on the genetic underpinnings of virulence in Aspergillus fumigatus, one of the most lethal fungal pathogens. Many of these insights dramatically expand our knowledge of fungal and microbial eukaryote genome evolution and function and argue that Aspergillus constitutes a superb model clade for the study of functional and comparative genomics. PMID:23084572

Creep and slip: Seismic precursors to the Nuugaatsiaq landslide (Greenland)

NASA Astrophysics Data System (ADS)

Poli, Piero

2017-09-01

Precursory signals to material's failure are predicted by numerical models and observed in laboratory experiments or using field data. These precursory signals are a marker of slip acceleration on weak regions, such as crustal faults. Observation of these precursory signals of catastrophic natural events, such as earthquakes and landslides, is necessary for improving our knowledge about the physics of the nucleation process. Furthermore, observing such precursory signals may help to forecast these catastrophic events or reduce their hazard. I report here the observation of seismic precursors to the Nuugaatsiaq landslide in Greenland. Time evolution of the detected precursors implies that an aseismic slip event is taking place for hours before the landslide, with an exponential increase of slip velocity. Furthermore, time evolution of the precursory signals' amplitude sheds light on the evolution of the fault physics during the nucleation process.

Facies Analysis of the Tandoǧdu Travertines, Van, Eastern Anatolia, Turkey: implications for the active tectonic deformation behind the formation and evolution of the travertines

NASA Astrophysics Data System (ADS)

Yesilova, Cetin; Yesilova, Pelin; Aclan, Mustafa; Gülyüz, Nilay

2017-04-01

In this study, stratigraphic and sedimentologic characteristics of Tandoǧdu travertines exposing at the 13 km southwest of Başkale, Van were examined. In this respect, we shed light on their formation conditions and depositional environment by determining their morphological characteristics and analyzing their facies distribution. In addition, kinematic studies were conducted by collecting structural data from the structures hosting the travertines. Tandoǧdu travertines having bed type and ridge type travertines have 5 distinct lithofacies based on the studies conducted. These are: (1) crystalline crust facies, (2) coated bubble facies, (3) paper-thin raft type facies, (4) lithoclast - breccia facies and (5) paleosoil facies. According to the examination of their morphologies and lithofacies; lithofacies were developed depending on the temperature of fluids forming the travertines. Distal from the source field of the hydrothermal fluids, paper-thin raft type facies were developed in shallow pools. Proximal to the source field of the hydrothermal fluids, crystalline crust facies and coated bubble facies were deposited. Existence of breccia facies indicates the effects of active tectonism during the formation of travertines. Hot hydrothermal pools on the ridge type travertines prove the still active tectonic activities. On-going studies aim to date growth of the travertines by U-Th dating method which will also shed some light on the tectonic scenario behind the evolution of the travertines.

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

PubMed Central

de los Reyes, Pedro; Romero-Campero, Francisco J.; Ruiz, M. Teresa; Romero, José M.; Valverde, Federico

2017-01-01

Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions. PMID:28751903

The use of a GIS for the identification of geologic structures in the region of Santa María Amajac, Hidalgo, Mexico

NASA Astrophysics Data System (ADS)

Casas, José C. Escamilla; Muñetón, Gustavo Murillo; Piñán-Llamas, Aránzazu; López, Salvador Cruz

2008-05-01

A prominent semicircular structure bounded by circular normal faults and a northeast-southwest trending, active normal fault are the main structures identified in Santa Maria Amajac, south central Hidalgo, Mexico, in the Trans Mexican Volcanic Belt. Fieldwork, assisted by a Geographic Information System helped to refine the traces of the identified geologic structures. The field evidences supports our hypothesis that the lacustrine deposits in the area are associated with the evolution of a possible volcanic collapse caldera. Our results are the base for a geological risk map and will shed light on the understanding of the mechanisms that governed the evolution of the suspect collapse caldera.

On the Crossover from Classical to Fermi Liquid Behavior in Dense Plasmas

NASA Astrophysics Data System (ADS)

Daligault, Jerome

2017-10-01

We explore the crossover from classical plasma to quantum Fermi liquid behavior of electrons in dense plasmas. To this end, we analyze the evolution with density and temperature of the momentum lifetime of a test electron introduced in a dense electron gas. This allows us 1) to determine the boundaries of the crossover region in the temperature-density plane and to shed light on the evolution of scattering properties across it, 2) to quantify the role of the fermionic nature of electrons on electronic collisions across the crossover region, and 3) to explain how the concept of Coulomb logarithm emerges at high enough temperature but disappears at low enough temperature. Work supported by LDRD Grant No. 20170490ER.

Systems Engineering Design Via Experimental Operation Research: Complex Organizational Metric for Programmatic Risk Environments (COMPRE)

NASA Technical Reports Server (NTRS)

Mog, Robert A.

1999-01-01

Unique and innovative graph theory, neural network, organizational modeling, and genetic algorithms are applied to the design and evolution of programmatic and organizational architectures. Graph theory representations of programs and organizations increase modeling capabilities and flexibility, while illuminating preferable programmatic/organizational design features. Treating programs and organizations as neural networks results in better system synthesis, and more robust data modeling. Organizational modeling using covariance structures enhances the determination of organizational risk factors. Genetic algorithms improve programmatic evolution characteristics, while shedding light on rulebase requirements for achieving specified technological readiness levels, given budget and schedule resources. This program of research improves the robustness and verifiability of systems synthesis tools, including the Complex Organizational Metric for Programmatic Risk Environments (COMPRE).

The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

PubMed Central

2015-01-01

Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses. PMID:26683838

1. Shed, keeper's house and light tower, view west northwest, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. Shed, keeper's house and light tower, view west northwest, south and east sides - Ram Island Light Station, Ram Island, south of Ocean Point & just north of Fisherman Island, marking south side of Fisherman Island Passage, Ocean Point, Lincoln County, ME

Sm-Nd isotopic systematics of the ancient Gneiss complex, southern Africa

NASA Technical Reports Server (NTRS)

Carlson, R. W.; Hunter, D. R.; Barker, F.

1983-01-01

In order to shed some new light on the question of the absolute and relative ages of the Ancient Gneiss Complex and Onverwacht Group, a Sm-Nd whole-rock and mineral isochron study of the AGC was begun. At this point, the whole-rock study of samples from the Bimodal Suite selected from those studied for their geochemical characteristics by Hunter et al., is completed. These results and their implications for the chronologic evolution of the Kaapvaal craton and the sources of these ancient rocks are discussed.

Life and evolution as physics

PubMed Central

Bejan, Adrian

2016-01-01

ABSTRACT What is evolution and why does it exist in the biological, geophysical and technological realms — in short, everywhere? Why is there a time direction — a time arrow — in the changes we know are happening every moment and everywhere? Why is the present different than the past? These are questions of physics, about everything, not just biology. The answer is that nothing lives, flows and moves unless it is driven by power. Physics sheds light on the natural engines that produce the power destroyed by the flows, and on the free morphing that leads to flow architectures naturally and universally. There is a unifying tendency across all domains to evolve into flow configurations that provide greater access for movement. This tendency is expressed as the constructal law of evolutionary flow organization everywhere. Here I illustrate how this law of physics accounts for and unites the life and evolution phenomena throughout nature, animate and inanimate. PMID:27489579

Anatomy of scientific evolution.

PubMed

Yun, Jinhyuk; Kim, Pan-Jun; Jeong, Hawoong

2015-01-01

The quest for historically impactful science and technology provides invaluable insight into the innovation dynamics of human society, yet many studies are limited to qualitative and small-scale approaches. Here, we investigate scientific evolution through systematic analysis of a massive corpus of digitized English texts between 1800 and 2008. Our analysis reveals great predictability for long-prevailing scientific concepts based on the levels of their prior usage. Interestingly, once a threshold of early adoption rates is passed even slightly, scientific concepts can exhibit sudden leaps in their eventual lifetimes. We developed a mechanistic model to account for such results, indicating that slowly-but-commonly adopted science and technology surprisingly tend to have higher innate strength than fast-and-commonly adopted ones. The model prediction for disciplines other than science was also well verified. Our approach sheds light on unbiased and quantitative analysis of scientific evolution in society, and may provide a useful basis for policy-making.

Anatomy of Scientific Evolution

PubMed Central

Yun, Jinhyuk; Kim, Pan-Jun; Jeong, Hawoong

2015-01-01

The quest for historically impactful science and technology provides invaluable insight into the innovation dynamics of human society, yet many studies are limited to qualitative and small-scale approaches. Here, we investigate scientific evolution through systematic analysis of a massive corpus of digitized English texts between 1800 and 2008. Our analysis reveals great predictability for long-prevailing scientific concepts based on the levels of their prior usage. Interestingly, once a threshold of early adoption rates is passed even slightly, scientific concepts can exhibit sudden leaps in their eventual lifetimes. We developed a mechanistic model to account for such results, indicating that slowly-but-commonly adopted science and technology surprisingly tend to have higher innate strength than fast-and-commonly adopted ones. The model prediction for disciplines other than science was also well verified. Our approach sheds light on unbiased and quantitative analysis of scientific evolution in society, and may provide a useful basis for policy-making. PMID:25671617

Evolution of the Human Pelvis.

PubMed

Rosenberg, Karen R; DeSilva, Jeremy M

2017-05-01

No bone in the human postcranial skeleton differs more dramatically from its match in an ape skeleton than the pelvis. Humans have evolved a specialized pelvis, well-adapted for the rigors of bipedal locomotion. Precisely how this happened has been the subject of great interest and contention in the paleoanthropological literature. In part, this is because of the fragility of the pelvis and its resulting rarity in the human fossil record. However, new discoveries from Miocene hominoids and Plio-Pleistocene hominins have reenergized debates about human pelvic evolution and shed new light on the competing roles of bipedal locomotion and obstetrics in shaping pelvic anatomy. In this issue, 13 papers address the evolution of the human pelvis. Here, we summarize these new contributions to our understanding of pelvic evolution, and share our own thoughts on the progress the field has made, and the questions that still remain. Anat Rec, 300:789-797, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The evolution of speech: a comparative review.

PubMed

Fitch

2000-07-01

The evolution of speech can be studied independently of the evolution of language, with the advantage that most aspects of speech acoustics, physiology and neural control are shared with animals, and thus open to empirical investigation. At least two changes were necessary prerequisites for modern human speech abilities: (1) modification of vocal tract morphology, and (2) development of vocal imitative ability. Despite an extensive literature, attempts to pinpoint the timing of these changes using fossil data have proven inconclusive. However, recent comparative data from nonhuman primates have shed light on the ancestral use of formants (a crucial cue in human speech) to identify individuals and gauge body size. Second, comparative analysis of the diverse vertebrates that have evolved vocal imitation (humans, cetaceans, seals and birds) provides several distinct, testable hypotheses about the adaptive function of vocal mimicry. These developments suggest that, for understanding the evolution of speech, comparative analysis of living species provides a viable alternative to fossil data. However, the neural basis for vocal mimicry and for mimesis in general remains unknown.

The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes

PubMed Central

Xu, Guang-Hui; Zhao, Li-Jun; Coates, Michael I.

2014-01-01

The Halecomorphi are a major subdivision of the ray-finned fishes. Although living halecomorphs are represented solely by the freshwater bowfin, Amia calva, this clade has a rich fossil history, and the resolution of interrelationships among extinct members is central to the problem of understanding the origin of the Teleostei, the largest clade of extant vertebrates. The Ionoscopiformes are extinct marine halecomorphs that were inferred to have originated in the Late Jurassic of Europe, and subsequently dispersed to the Early Cretaceous of the New World. Here, we report the discovery of a new ionoscopiform, Robustichthys luopingensis gen. et sp. nov., based on eight well-preserved specimens from the Anisian (242–247 Ma), Middle Triassic marine deposits of Luoping, eastern Yunnan Province, China. The new species documents the oldest known ionoscopiform, extending the stratigraphic range of this group by approximately 90 Ma, and the geographical distribution of this group into the Middle Triassic of South China, a part of eastern Palaeotethys Ocean. These new data provide a minimum estimate for the split of Ionoscopiformes from its sister clade Amiiformes and shed new light on the origin of ionoscopiform fishes. PMID:24872460

Tracking the origin and divergence of cholinesterases and neuroligins: the evolution of synaptic proteins.

PubMed

Lenfant, Nicolas; Hotelier, Thierry; Bourne, Yves; Marchot, Pascale; Chatonnet, Arnaud

2014-07-01

A cholinesterase activity can be found in all kingdoms of living organism, yet cholinesterases involved in cholinergic transmission appeared only recently in the animal phylum. Among various proteins homologous to cholinesterases, one finds neuroligins. These proteins, with an altered catalytic triad and no known hydrolytic activity, display well-identified cell adhesion properties. The availability of complete genomes of a few metazoans provides opportunities to evaluate when these two protein families emerged during evolution. In bilaterian animals, acetylcholinesterase co-localizes with proteins of cholinergic synapses while neuroligins co-localize and may interact with proteins of excitatory glutamatergic or inhibitory GABAergic/glycinergic synapses. To compare evolution of the cholinesterases and neuroligins with other proteins involved in the architecture and functioning of synapses, we devised a method to search for orthologs of these partners in genomes of model organisms representing distinct stages of metazoan evolution. Our data point to a progressive recruitment of synaptic components during evolution. This finding may shed light on the common or divergent developmental regulation events involved into the setting and maintenance of the cholinergic versus glutamatergic and GABAergic/glycinergic synapses.

Greater than the sum of its parts: single-nucleus sequencing identifies convergent evolution of independent EGFR mutants in GBM.

PubMed

Gini, Beatrice; Mischel, Paul S

2014-08-01

Single-cell sequencing approaches are needed to characterize the genomic diversity of complex tumors, shedding light on their evolutionary paths and potentially suggesting more effective therapies. In this issue of Cancer Discovery, Francis and colleagues develop a novel integrative approach to identify distinct tumor subpopulations based on joint detection of clonal and subclonal events from bulk tumor and single-nucleus whole-genome sequencing, allowing them to infer a subclonal architecture. Surprisingly, the authors identify convergent evolution of multiple, mutually exclusive, independent EGFR gain-of-function variants in a single tumor. This study demonstrates the value of integrative single-cell genomics and highlights the biologic primacy of EGFR as an actionable target in glioblastoma. ©2014 American Association for Cancer Research.

Hydrozoan insights in animal development and evolution.

PubMed

Leclère, Lucas; Copley, Richard R; Momose, Tsuyoshi; Houliston, Evelyn

2016-08-01

The fresh water polyp Hydra provides textbook experimental demonstration of positional information gradients and regeneration processes. Developmental biologists are thus familiar with Hydra, but may not appreciate that it is a relatively simple member of the Hydrozoa, a group of mostly marine cnidarians with complex and diverse life cycles, exhibiting extensive phenotypic plasticity and regenerative capabilities. Hydrozoan species offer extensive opportunities to address many developmental mechanisms relevant across the animal kingdom. Here we review recent work from non-Hydra hydrozoans - hydromedusae, hydroids and siphonophores - shedding light on mechanisms of oogenesis, embryonic patterning, allorecognition, stem cell regulation and regeneration. We also highlight potential research directions in which hydrozoan diversity can illuminate the evolution of developmental processes at micro- and macro-evolutionary time scales. Copyright © 2016 Elsevier Ltd. All rights reserved.

Human MHC architecture and evolution: implications for disease association studies

PubMed Central

Traherne, J A

2008-01-01

Major histocompatibility complex (MHC) variation is a key determinant of susceptibility and resistance to a large number of infectious, autoimmune and other diseases. Identification of the MHC variants conferring susceptibility to disease is problematic, due to high levels of variation and linkage disequilibrium. Recent cataloguing and analysis of variation over the complete MHC has facilitated localization of susceptibility loci for autoimmune diseases, and provided insight into the MHC's evolution. This review considers how the unusual genetic characteristics of the MHC impact on strategies to identify variants causing, or contributing to, disease phenotypes. It also considers the MHC in relation to novel mechanisms influencing gene function and regulation, such as epistasis, epigenetics and microRNAs. These developments, along with recent technological advances, shed light on genetic association in complex disease. PMID:18397301

Evolution of speech-specific cognitive adaptations.

PubMed

de Boer, Bart

2015-01-01

This paper argues that an evolutionary perspective is natural when investigating cognitive adaptations related to language. This is because there appears to be correspondence between traits that linguists consider interesting and traits that have undergone selective pressure related to language. The paper briefly reviews theoretical results that shed light on what kind of adaptations we can expect to have evolved and then reviews concrete work related to the evolution of adaptations for combinatorial speech. It turns out that there is as yet no strong direct evidence for cognitive traits that have undergone selection related to speech, but there is indirect evidence that indicates selection. However, the traits that may have undergone selection are expected to be continuously variable ones, rather than the discrete ones that linguists have focused on traditionally.

Signaling Games and the Evolution of Structure in Language and Music: A Reply to Ravignani and Verhoef (2018) ‡.

PubMed

Lumaca, Massimo; Baggio, Giosuè

2018-01-01

In their commentary on our work, Ravignani and Verhoef (2018) raise concerns about two methodological aspects of our experimental paradigm (the signaling game): (1) the use of melodic signals of fixed length and duration, and (2) the fact that signals are endowed with meaning. They argue that music is hardly a semantic system and that our methodological choices may limit the capacity of our paradigm to shed light on the emergence and evolution of a number of putative musical universals. We reply that musical systems are semantic systems and that the aim of our research is not to study musical universals as such, but to compare more closely the kinds of principles that organize meaning and structure in linguistic and musical systems.

A stem-group cnidarian described from the mid-Cambrian of China and its significance for cnidarian evolution.

PubMed

Park, Tae-yoon; Woo, Jusun; Lee, Dong-Jin; Lee, Dong-Chan; Lee, Seung-bae; Han, Zuozhen; Chough, Sung Kwun; Choi, Duck K

2011-08-23

Palaeontological data of extinct groups often sheds light on the evolutionary sequences leading to extant groups, but has failed to resolve the basal metazoan phylogeny including the origin of the Cnidaria. Here we report the occurrence of a stem-group cnidarian, Cambroctoconus orientalis gen. et sp. nov., from the mid-Cambrian of China, which is a colonial organism with calcareous octagonal conical cup-shaped skeletons. It bears cnidarian features including longitudinal septa arranged in octoradial symmetry and colonial occurrence, but lacks a jelly-like mesenchyme. Such morphological characteristics suggest that the colonial occurrence with polyps of octoradial symmetry is the plesiomorphic condition of the Cnidaria and appeared earlier than the jelly-like mesenchyme during the course of evolution. © 2011 Macmillan Publishers Limited. All rights reserved.

A stem-group cnidarian described from the mid-Cambrian of China and its significance for cnidarian evolution

PubMed Central

Park, Tae-yoon; Woo, Jusun; Lee, Dong-Jin; Lee, Dong-Chan; Lee, Seung-bae; Han, Zuozhen; Chough, Sung Kwun; Choi, Duck K.

2011-01-01

Palaeontological data of extinct groups often sheds light on the evolutionary sequences leading to extant groups, but has failed to resolve the basal metazoan phylogeny including the origin of the Cnidaria. Here we report the occurrence of a stem-group cnidarian, Cambroctoconus orientalis gen. et sp. nov., from the mid-Cambrian of China, which is a colonial organism with calcareous octagonal conical cup-shaped skeletons. It bears cnidarian features including longitudinal septa arranged in octoradial symmetry and colonial occurrence, but lacks a jelly-like mesenchyme. Such morphological characteristics suggest that the colonial occurrence with polyps of octoradial symmetry is the plesiomorphic condition of the Cnidaria and appeared earlier than the jelly-like mesenchyme during the course of evolution. PMID:21863009

Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae).

PubMed

Litsios, Glenn; Pellissier, Loïc; Forest, Félix; Lexer, Christian; Pearman, Peter B; Zimmermann, Niklaus E; Salamin, Nicolas

2012-09-22

The rate of environmental niche evolution describes the capability of species to explore the available environmental space and is known to vary among species owing to lineage-specific factors. Trophic specialization is a main force driving species evolution and is responsible for classical examples of adaptive radiations in fishes. We investigate the effect of trophic specialization on the rate of environmental niche evolution in the damselfish, Pomacentridae, which is an important family of tropical reef fishes. First, phylogenetic niche conservatism is not detected in the family using a standard test of phylogenetic signal, and we demonstrate that the environmental niches of damselfishes that differ in trophic specialization are not equivalent while they still overlap at their mean values. Second, we estimate the relative rates of niche evolution on the phylogenetic tree and show the heterogeneity among rates of environmental niche evolution of the three trophic groups. We suggest that behavioural characteristics related to trophic specialization can constrain the evolution of the environmental niche and lead to conserved niches in specialist lineages. Our results show the extent of influence of several traits on the evolution of the environmental niche and shed new light on the evolution of damselfishes, which is a key lineage in current efforts to conserve biodiversity in coral reefs.

Trophic specialization influences the rate of environmental niche evolution in damselfishes (Pomacentridae)

PubMed Central

Litsios, Glenn; Pellissier, Loïc; Forest, Félix; Lexer, Christian; Pearman, Peter B.; Zimmermann, Niklaus E.; Salamin, Nicolas

2012-01-01

The rate of environmental niche evolution describes the capability of species to explore the available environmental space and is known to vary among species owing to lineage-specific factors. Trophic specialization is a main force driving species evolution and is responsible for classical examples of adaptive radiations in fishes. We investigate the effect of trophic specialization on the rate of environmental niche evolution in the damselfish, Pomacentridae, which is an important family of tropical reef fishes. First, phylogenetic niche conservatism is not detected in the family using a standard test of phylogenetic signal, and we demonstrate that the environmental niches of damselfishes that differ in trophic specialization are not equivalent while they still overlap at their mean values. Second, we estimate the relative rates of niche evolution on the phylogenetic tree and show the heterogeneity among rates of environmental niche evolution of the three trophic groups. We suggest that behavioural characteristics related to trophic specialization can constrain the evolution of the environmental niche and lead to conserved niches in specialist lineages. Our results show the extent of influence of several traits on the evolution of the environmental niche and shed new light on the evolution of damselfishes, which is a key lineage in current efforts to conserve biodiversity in coral reefs. PMID:22719034

Transcriptome comparisons shed light on the pre-condition and potential barrier for C4 photosynthesis evolution in eudicots.

PubMed

Tao, Yimin; Lyu, Ming-Ju Amy; Zhu, Xin-Guang

2016-05-01

C4 photosynthesis evolved independently from C3 photosynthesis in more than 60 lineages. Most of the C4 lineages are clustered together in the order Poales and the order Caryophyllales while many other angiosperm orders do not have C4 species, suggesting the existence of biological pre-conditions in the ancestral C3 species that facilitate the evolution of C4 photosynthesis in these lineages. To explore pre-adaptations for C4 photosynthesis evolution, we classified C4 lineages into the C4-poor and the C4-rich groups based on the percentage of C4 species in different genera and conducted a comprehensive comparison on the transcriptomic changes between the non-C4 species from the C4-poor and the C4-rich groups. Results show that species in the C4-rich group showed higher expression of genes related to oxidoreductase activity, light reaction components, terpene synthesis, secondary cell synthesis, C4 cycle related genes and genes related to nucleotide metabolism and senescence. In contrast, C4-poor group showed up-regulation of a PEP/Pi translocator, genes related to signaling pathway, stress response, defense response and plant hormone metabolism (ethylene and brassinosteroid). The implications of these transcriptomic differences between the C4-rich and C4-poor groups to C4 evolution are discussed.

Continuous measurement of two spatially separated superconducting qubits: quantum trajectories and statistics

NASA Astrophysics Data System (ADS)

Roch, Nicolas

2015-03-01

Measurement can be harnessed to probabilistically generate entanglement in the absence of local interactions, for example between spatially separated quantum objects. Continuous weak measurement allows us to observe the dynamics associated with this process. In particular, we perform joint dispersive readout of two superconducting transmon qubits separated by one meter of coaxial cable. We track the evolution of a joint quantum state under the influence of measurement, both as an ensemble and as a set of individual quantum trajectories. Analyzing the statistics of such quantum trajectories can shed new light on the underlying entangling mechanism.

Flame deformation and entrainment associated with an isothermal transverse fuel jet

NASA Technical Reports Server (NTRS)

Jenkins, D. W.; Karagozian, A. R.

1992-01-01

This paper describes an analytical model of an incompressible, isothermal reacting jet in crossflow. The model represents the flow in the jet cross-section by a counter rotating vortex pair, a flow structure that has been observed to dominate the jet behavior. The reaction surface surrounding the fuel jet is represented as a composite of strained diffusion flames that are stretched and deformed by the vortex pair flow. The results shed new light on the interaction between the vortex pair circulation and flame structure evolution and their relation to the concept of entrainment.

Earliest evolution of multituberculate mammals revealed by a new Jurassic fossil.

PubMed

Yuan, Chong-Xi; Ji, Qiang; Meng, Qing-Jin; Tabrum, Alan R; Luo, Zhe-Xi

2013-08-16

Multituberculates were successful herbivorous mammals and were more diverse and numerically abundant than any other mammal groups in Mesozoic ecosystems. The clade also developed diverse locomotor adaptations in the Cretaceous and Paleogene. We report a new fossil skeleton from the Late Jurassic of China that belongs to the basalmost multituberculate family. Dental features of this new Jurassic multituberculate show omnivorous adaptation, and its well-preserved skeleton sheds light on ancestral skeletal features of all multituberculates, especially the highly mobile joints of the ankle, crucial for later evolutionary success of multituberculates in the Cretaceous and Paleogene.

Emergence and Evolution of Cooperation Under Resource Pressure

PubMed Central

Pereda, María; Zurro, Débora; Santos, José I.; Briz i Godino, Ivan; Álvarez, Myrian; Caro, Jorge; Galán, José M.

2017-01-01

We study the influence that resource availability has on cooperation in the context of hunter-gatherer societies. This paper proposes a model based on archaeological and ethnographic research on resource stress episodes, which exposes three different cooperative regimes according to the relationship between resource availability in the environment and population size. The most interesting regime represents moderate survival stress in which individuals coordinate in an evolutionary way to increase the probabilities of survival and reduce the risk of failing to meet the minimum needs for survival. Populations self-organise in an indirect reciprocity system in which the norm that emerges is to share the part of the resource that is not strictly necessary for survival, thereby collectively lowering the chances of starving. Our findings shed further light on the emergence and evolution of cooperation in hunter-gatherer societies. PMID:28362000

Organogenesis in deep time: A problem in genomics, development, and paleontology.

PubMed

Pieretti, Joyce; Gehrke, Andrew R; Schneider, Igor; Adachi, Noritaka; Nakamura, Tetsuya; Shubin, Neil H

2015-04-21

The fossil record is a unique repository of information on major morphological transitions. Increasingly, developmental, embryological, and functional genomic approaches have also conspired to reveal evolutionary trajectory of phenotypic shifts. Here, we use the vertebrate appendage to demonstrate how these disciplines can mutually reinforce each other to facilitate the generation and testing of hypotheses of morphological evolution. We discuss classical theories on the origins of paired fins, recent data on regulatory modulations of fish fins and tetrapod limbs, and case studies exploring the mechanisms of digit loss in tetrapods. We envision an era of research in which the deep history of morphological evolution can be revealed by integrating fossils of transitional forms with direct experimentation in the laboratory via genome manipulation, thereby shedding light on the relationship between genes, developmental processes, and the evolving phenotype.

Emergence and Evolution of Cooperation Under Resource Pressure.

PubMed

Pereda, María; Zurro, Débora; Santos, José I; Briz I Godino, Ivan; Álvarez, Myrian; Caro, Jorge; Galán, José M

2017-03-31

We study the influence that resource availability has on cooperation in the context of hunter-gatherer societies. This paper proposes a model based on archaeological and ethnographic research on resource stress episodes, which exposes three different cooperative regimes according to the relationship between resource availability in the environment and population size. The most interesting regime represents moderate survival stress in which individuals coordinate in an evolutionary way to increase the probabilities of survival and reduce the risk of failing to meet the minimum needs for survival. Populations self-organise in an indirect reciprocity system in which the norm that emerges is to share the part of the resource that is not strictly necessary for survival, thereby collectively lowering the chances of starving. Our findings shed further light on the emergence and evolution of cooperation in hunter-gatherer societies.

Innovation: an emerging focus from cells to societies.

PubMed

Hochberg, Michael E; Marquet, Pablo A; Boyd, Robert; Wagner, Andreas

2017-12-05

Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability.This article is part of the theme issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

Innovation: an emerging focus from cells to societies

PubMed Central

Boyd, Robert

2017-01-01

Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability. This article is part of the theme issue ‘Process and pattern in innovations from cells to societies’. PMID:29061887

Emergence and Evolution of Cooperation Under Resource Pressure

NASA Astrophysics Data System (ADS)

Pereda, María; Zurro, Débora; Santos, José I.; Briz I Godino, Ivan; Álvarez, Myrian; Caro, Jorge; Galán, José M.

2017-03-01

We study the influence that resource availability has on cooperation in the context of hunter-gatherer societies. This paper proposes a model based on archaeological and ethnographic research on resource stress episodes, which exposes three different cooperative regimes according to the relationship between resource availability in the environment and population size. The most interesting regime represents moderate survival stress in which individuals coordinate in an evolutionary way to increase the probabilities of survival and reduce the risk of failing to meet the minimum needs for survival. Populations self-organise in an indirect reciprocity system in which the norm that emerges is to share the part of the resource that is not strictly necessary for survival, thereby collectively lowering the chances of starving. Our findings shed further light on the emergence and evolution of cooperation in hunter-gatherer societies.

Randomly biased investments and the evolution of public goods on interdependent networks

NASA Astrophysics Data System (ADS)

Chen, Wei; Wu, Te; Li, Zhiwu; Wang, Long

2017-08-01

Deciding how to allocate resources between interdependent systems is significant to optimize efficiency. We study the effects of heterogeneous contribution, induced by such interdependency, on the evolution of cooperation, through implementing the public goods games on two-layer networks. The corresponding players on different layers try to share a fixed amount of resources as the initial investment properly. The symmetry breaking of investments between players located on different layers is able to either prevent investments from, or extract them out of the deadlock. Results show that a moderate investment heterogeneity is best favorable for the evolution of cooperation, and random allocation of investment bias suppresses the cooperators at a wide range of the investment bias and the enhancement effect. Further studies on time evolution with different initial strategy configurations show that the non-interdependent cooperators along the interface of interdependent cooperators also are an indispensable factor in facilitating cooperative behavior. Our main results are qualitatively unchanged even diversifying investment bias that is subject to uniform distribution. Our study may shed light on the understanding of the origin of cooperative behavior on interdependent networks.

Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats.

PubMed

Teske, Peter R; Beheregaray, Luciano B

2009-08-23

Seahorses (Syngnathidae: Hippocampus) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses' upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species.

A new giant titanosaur sheds light on body mass evolution among sauropod dinosaurs.

PubMed

Carballido, José L; Pol, Diego; Otero, Alejandro; Cerda, Ignacio A; Salgado, Leonardo; Garrido, Alberto C; Ramezani, Jahandar; Cúneo, Néstor R; Krause, Javier M

2017-08-16

Titanosauria was the most diverse and successful lineage of sauropod dinosaurs. This clade had its major radiation during the middle Early Cretaceous and survived up to the end of that period. Among sauropods, this lineage has the most disparate values of body mass, including the smallest and largest sauropods known. Although recent findings have improved our knowledge on giant titanosaur anatomy, there are still many unknown aspects about their evolution, especially for the most gigantic forms and the evolution of body mass in this clade. Here we describe a new giant titanosaur, which represents the largest species described so far and one of the most complete titanosaurs. Its inclusion in an extended phylogenetic analysis and the optimization of body mass reveals the presence of an endemic clade of giant titanosaurs inhabited Patagonia between the Albian and the Santonian. This clade includes most of the giant species of titanosaurs and represents the major increase in body mass in the history of Titanosauria. © 2017 The Author(s).

Vertical Wave Coupling associated with Stratospheric Sudden Warming Events analyzed in an Isentropic-Coordinate NWP Model.

NASA Astrophysics Data System (ADS)

Bleck, R.; Sun, S.; Benjamin, S.; Brown, J. M.

2017-12-01

Two- to four-week predictions of stratospheric sudden warming events during the winter seasons of 1999-2014, carried out with a high-resolution icosahedral NWP model using potential temperature as vertical coordinate, are inspected for commonalities in the evolution of both minor and major warmings. Emphasis is on the evolution of the potential vorticity field at different levels in the stratosphere, as well as on the sign and magnitude of the vertical component of the Eliassen-Palm flux vector suggestive of wave forcing in either direction. Material is presented shedding light on the skill of the model (FIM, developed at NOAA/ESRL) in predicting stratospheric warmings generally 2 weeks in advance. With an icosahedral grid ideally suited for studying polar processes, and a vertical coordinate faithfully reproducing details in the evolution of the potential vorticity and EP flux vector fields, FIM is found to be a good tool for investigating the SSW mechanism.

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

PubMed Central

Li, Ci-Xiu; Shi, Mang; Tian, Jun-Hua; Lin, Xian-Dan; Kang, Yan-Jun; Chen, Liang-Jun; Qin, Xin-Cheng; Xu, Jianguo; Holmes, Edward C; Zhang, Yong-Zhen

2015-01-01

Although arthropods are important viral vectors, the biodiversity of arthropod viruses, as well as the role that arthropods have played in viral origins and evolution, is unclear. Through RNA sequencing of 70 arthropod species we discovered 112 novel viruses that appear to be ancestral to much of the documented genetic diversity of negative-sense RNA viruses, a number of which are also present as endogenous genomic copies. With this greatly enriched diversity we revealed that arthropods contain viruses that fall basal to major virus groups, including the vertebrate-specific arenaviruses, filoviruses, hantaviruses, influenza viruses, lyssaviruses, and paramyxoviruses. We similarly documented a remarkable diversity of genome structures in arthropod viruses, including a putative circular form, that sheds new light on the evolution of genome organization. Hence, arthropods are a major reservoir of viral genetic diversity and have likely been central to viral evolution. DOI: http://dx.doi.org/10.7554/eLife.05378.001 PMID:25633976

Evolution of consciousness: Phylogeny, ontogeny, and emergence from general anesthesia

PubMed Central

Mashour, George A.; Alkire, Michael T.

2013-01-01

Are animals conscious? If so, when did consciousness evolve? We address these long-standing and essential questions using a modern neuroscientific approach that draws on diverse fields such as consciousness studies, evolutionary neurobiology, animal psychology, and anesthesiology. We propose that the stepwise emergence from general anesthesia can serve as a reproducible model to study the evolution of consciousness across various species and use current data from anesthesiology to shed light on the phylogeny of consciousness. Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution. Thus, in agreement with Darwin’s insight and the recent “Cambridge Declaration on Consciousness in Non-Human Animals,” a review of modern scientific data suggests that the differences between species in terms of the ability to experience the world is one of degree and not kind. PMID:23754370

PROPAGATION AND EVOLUTION OF THE JUNE 1st 2008 CME IN THE INTERPLANETARY MEDIUM

NASA Astrophysics Data System (ADS)

Nieves-Chinchilla, T.; Lamb, D. A.; Davila, J. M.; Vinas, A. F.; Moestl, C.; Hidalgo, M. A.; Farrugia, C. J.; Malandraki, O.; Dresing, N.; Gómez-Herrero, R.

2009-12-01

In this work we present a study of the coronal mass ejection (CME) of June 1st of 2008 in the interplanetary medium. This event has been extensively studied by others because of its favorable geometry and the possible consequences of its peculiar initiation for space weather forecasting. We show an analysis of the evolution of the CME in the interplanetary medium in order to shed some light on the propagation mechanism of the ICME. We have determined the typical shock associated characteristics of the ICME in order to understand the propagation properties. Using two different non force-free models of the magnetic cloud allows us to incorporate expansion of the cloud. We use in-situ measurements from STEREO B/IMPACT to characterize the ICME. In addition, we use images from STEREO A/SECCHI-HI to analyze the propagation and visual evolution of the associated flux rope in the interplanetary medium. We compare and contrast these observations with the results of the analytical models.

The Molecular Basis of Evolution and Disease: A Cold War Alliance.

PubMed

Suárez-Díaz, Edna

2017-03-28

This paper extends previous arguments against the assumption that the study of variation at the molecular level was instigated with a view to solving an internal conflict between the balance and classical schools of population genetics. It does so by focusing on the intersection of basic research in protein chemistry and the molecular approach to disease with the enactment of global health campaigns during the Cold War period. The paper connects advances in research on protein structure and function as reflected in Christian Anfinsen's The molecular basis of evolution, with a political reading of Emilé Zuckerkandl and Linus Pauling's identification of molecular disease and evolution. Beyond atomic fallout, these advances constituted a rationale for the promotion of genetic surveys of human populations in the Third World, in connection with international health programs. Light is shed not only on the experimental roots of the molecular challenge but on the broader geopolitical context where the rising role of biomedicine and public health (particularly the malaria eradication campaigns) had an impact on evolutionary biology.

Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP.

PubMed

Dugas, Diana V; Hernandez, David; Koenen, Erik J M; Schwarz, Erika; Straub, Shannon; Hughes, Colin E; Jansen, Robert K; Nageswara-Rao, Madhugiri; Staats, Martijn; Trujillo, Joshua T; Hajrah, Nahid H; Alharbi, Njud S; Al-Malki, Abdulrahman L; Sabir, Jamal S M; Bailey, C Donovan

2015-11-23

The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga, and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding, and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.

Lunar Orbit Anomaly

NASA Astrophysics Data System (ADS)

Riofrio, L.

2012-12-01

Independent experiments show a large anomaly in measurements of lunar orbital evolution, with applications to cosmology and the speed of light. The Moon has long been known to be slowly drifting farther from Earth due to tidal forces. The Lunar Laser Ranging Experiment (LLRE) indicates the Moon's semimajor axis increasing at 3.82 ± .07 cm/yr, anomalously high. If the Moon were today gaining angular momentum at this rate, it would have coincided with Earth less than 2 Gyr ago. Study of tidal rhythmites indicates a rate of 2.9 ± 0.6 cm/yr. Historical eclipse observations independently measure a recession rate of 2.82 ± .08 cm/yr. Detailed numerical simulation of lunar orbital evolution predicts 2.91 cm/yr. LLRE differs from three independent experiments by over12 sigma. A cosmology where speed of light c is related to time t by GM=tc^3 has been suggested to predict the redshifts of Type Ia supernovae, and a 4.507034% proportion of baryonic matter. If c were changing in the amount predicted, lunar orbital distance would appear to increase by an additional 0.935 cm/yr. An anomaly in the lunar orbit may be precisely calculated, shedding light on puzzles of 'dark energy'. In Planck units this cosmology may be summarized as M=R=t.Lunar Recession Rate;

Phototaxis and the origin of visual eyes

PubMed Central

Randel, Nadine

2016-01-01

Vision allows animals to detect spatial differences in environmental light levels. High-resolution image-forming eyes evolved from low-resolution eyes via increases in photoreceptor cell number, improvements in optics and changes in the neural circuits that process spatially resolved photoreceptor input. However, the evolutionary origins of the first low-resolution visual systems have been unclear. We propose that the lowest resolving (two-pixel) visual systems could initially have functioned in visual phototaxis. During visual phototaxis, such elementary visual systems compare light on either side of the body to regulate phototactic turns. Another, even simpler and non-visual strategy is characteristic of helical phototaxis, mediated by sensory–motor eyespots. The recent mapping of the complete neural circuitry (connectome) of an elementary visual system in the larva of the annelid Platynereis dumerilii sheds new light on the possible paths from non-visual to visual phototaxis and to image-forming vision. We outline an evolutionary scenario focusing on the neuronal circuitry to account for these transitions. We also present a comprehensive review of the structure of phototactic eyes in invertebrate larvae and assign them to the non-visual and visual categories. We propose that non-visual systems may have preceded visual phototactic systems in evolution that in turn may have repeatedly served as intermediates during the evolution of image-forming eyes. PMID:26598725

The oldest ionoscopiform from China sheds new light on the early evolution of halecomorph fishes.

PubMed

Xu, Guang-Hui; Zhao, Li-Jun; Coates, Michael I

2014-05-01

The Halecomorphi are a major subdivision of the ray-finned fishes. Although living halecomorphs are represented solely by the freshwater bowfin, Amia calva, this clade has a rich fossil history, and the resolution of interrelationships among extinct members is central to the problem of understanding the origin of the Teleostei, the largest clade of extant vertebrates. The Ionoscopiformes are extinct marine halecomorphs that were inferred to have originated in the Late Jurassic of Europe, and subsequently dispersed to the Early Cretaceous of the New World. Here, we report the discovery of a new ionoscopiform, Robustichthys luopingensis gen. et sp. nov., based on eight well-preserved specimens from the Anisian (242-247 Ma), Middle Triassic marine deposits of Luoping, eastern Yunnan Province, China. The new species documents the oldest known ionoscopiform, extending the stratigraphic range of this group by approximately 90 Ma, and the geographical distribution of this group into the Middle Triassic of South China, a part of eastern Palaeotethys Ocean. These new data provide a minimum estimate for the split of Ionoscopiformes from its sister clade Amiiformes and shed new light on the origin of ionoscopiform fishes. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Workforce Effects and the Evolution of Complex Sociality in Wild Damaraland Mole Rats.

PubMed

Young, Andrew J; Jarvis, Jennifer U M; Barnaville, James; Bennett, Nigel C

2015-08-01

Explaining the evolution of eusocial and cooperatively breeding societies demands that we understand the effects of workforce size on the reproductive success of breeders. This challenge has yet to be addressed in the family that arguably exhibits the most extreme outcomes of vertebrate social evolution, the African mole rats (Bathyergidae), leaving the ultimate causes of their many unusual adaptations open to debate. Here we report-using a 14-year field study of wild Damaraland mole rats, Fukomys damarensis-that workers appear to have strong but unusual effects on offspring. Groups with larger workforces exhibited substantially higher rates of offspring recruitment while maintaining high juvenile survival rates, relationships that may have favored the evolution of the delayed dispersal, cooperation, morphological specialization, and unusual patterns of longevity that characterize such societies. Offspring reared by larger workforces also showed slower growth, however. That reduced offspring growth in larger groups has also been documented under ad lib. food conditions in the laboratory raises the possibility that this reflects socially induced growth restraint rather than simple constraints on resource availability. Our findings shed new light on the evolution of complex sociality in this enigmatic clade and highlight further departures from the norms reported for other cooperative vertebrates.

Epidermal differentiation in embryos of the tuatara Sphenodon punctatus (Reptilia, Sphenodontidae) in comparison with the epidermis of other reptiles.

PubMed

Alibardi, L; Gill, B J

2007-07-01

Studying the epidermis in primitive reptiles can provide clues regarding evolution of the epidermis during land adaptation in vertebrates. With this aim, the development of the skin of the relatively primitive reptile Sphenodon punctatus in representative embryonic stages was studied by light and electron microscopy and compared with that of other reptiles previously studied. The dermis organizes into a superficial and deep portion when the epidermis starts to form the first layers. At embryonic stages comparable with those of lizards, only one layer of the inner periderm is formed beneath the outer periderm. This also occurs in lizards and snakes so far studied. The outer and inner periderm form the embryonic epidermis and accumulate thick, coarse filaments (25-30 nm thick) and sparse alpha-keratin filaments as in other reptiles. Beneath the embryonic epidermis an oberhautchen and beta-cells form small horny tips that represent overlapping borders along the margin of beta-cells that overlap other beta-cells (in a tile-like arrangement). The tips resemble those of agamine lizards but at a small scale, forming a lamellate-spinulated pattern as previously described in adult epidermis. The embryonic epidermis matures by the dispersion of coarse filaments among keratin at the end of embryonic development and is shed around hatching. The presence of these matrix organelles in the embryonic epidermis of this primitive reptile further indicates that amniote epidermis acquired interkeratin matrix proteins early for land adaptation. Unlike the condition in lizards and snakes, a shedding complex is not formed in the epidermis of embryonic S. punctatus that is like that of the adult. Therefore, as in chelonians and crocodilians, the epidermis of S. punctatus also represents an initial stage that preceded the evolution of the shedding complex for moulting.

Epidermal differentiation in embryos of the tuatara Sphenodon punctatus (Reptilia, Sphenodontidae) in comparison with the epidermis of other reptiles

PubMed Central

Alibardi, L; Gill, B J

2007-01-01

Studying the epidermis in primitive reptiles can provide clues regarding evolution of the epidermis during land adaptation in vertebrates. With this aim, the development of the skin of the relatively primitive reptile Sphenodon punctatus in representative embryonic stages was studied by light and electron microscopy and compared with that of other reptiles previously studied. The dermis organizes into a superficial and deep portion when the epidermis starts to form the first layers. At embryonic stages comparable with those of lizards, only one layer of the inner periderm is formed beneath the outer periderm. This also occurs in lizards and snakes so far studied. The outer and inner periderm form the embryonic epidermis and accumulate thick, coarse filaments (25–30 nm thick) and sparse alpha-keratin filaments as in other reptiles. Beneath the embryonic epidermis an oberhautchen and beta-cells form small horny tips that represent overlapping borders along the margin of beta-cells that overlap other beta-cells (in a tile-like arrangement). The tips resemble those of agamine lizards but at a small scale, forming a lamellate-spinulated pattern as previously described in adult epidermis. The embryonic epidermis matures by the dispersion of coarse filaments among keratin at the end of embryonic development and is shed around hatching. The presence of these matrix organelles in the embryonic epidermis of this primitive reptile further indicates that amniote epidermis acquired interkeratin matrix proteins early for land adaptation. Unlike the condition in lizards and snakes, a shedding complex is not formed in the epidermis of embryonic S. punctatus that is like that of the adult. Therefore, as in chelonians and crocodilians, the epidermis of S. punctatus also represents an initial stage that preceded the evolution of the shedding complex for moulting. PMID:17532799

Impact of doping on the carrier dynamics in graphene

PubMed Central

Kadi, Faris; Winzer, Torben; Knorr, Andreas; Malic, Ermin

2015-01-01

We present a microscopic study on the impact of doping on the carrier dynamics in graphene, in particular focusing on its influence on the technologically relevant carrier multiplication in realistic, doped graphene samples. Treating the time- and momentum-resolved carrier-light, carrier-carrier, and carrier-phonon interactions on the same microscopic footing, the appearance of Auger-induced carrier multiplication up to a Fermi level of 300 meV is revealed. Furthermore, we show that doping favors the so-called hot carrier multiplication occurring within one band. Our results are directly compared to recent time-resolved ARPES measurements and exhibit an excellent agreement on the temporal evolution of the hot carrier multiplication for n- and p-doped graphene. The gained insights shed light on the ultrafast carrier dynamics in realistic, doped graphene samples. PMID:26577536

7. Fog signal house and shed, view south, north and ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. Fog signal house and shed, view south, north and west sides of fog signal house, northeast and northwest sides of shed - Whitehead Light Station, Whitehead Island, East northeast of Tenants Harbor, Spruce Head, Knox County, ME

Effect of Heat Input on Inclusion Evolution Behavior in Heat-Affected Zone of EH36 Shipbuilding Steel

NASA Astrophysics Data System (ADS)

Sun, Jincheng; Zou, Xiaodong; Matsuura, Hiroyuki; Wang, Cong

2018-03-01

The effects of heat input parameters on inclusion and microstructure characteristics have been investigated using welding thermal simulations. Inclusion features from heat-affected zones (HAZs) were profiled. It was found that, under heat input of 120 kJ/cm, Al-Mg-Ti-O-(Mn-S) composite inclusions can act effectively as nucleation sites for acicular ferrites. However, this ability disappears when the heat input is increased to 210 kJ/cm. In addition, confocal scanning laser microscopy (CSLM) was used to document possible inclusion-microstructure interactions, shedding light on how inclusions assist beneficial transformations toward property enhancement.

Advanced X-ray Astrophysics Facility (AXAF) science instruments

NASA Technical Reports Server (NTRS)

Winkler, Carl E.; Dailey, Carroll C.; Cumings, Nesbitt P.

1991-01-01

The overall AXAF program is summarized, with particular emphasis given to its science instruments. The science objectives established for AXAF are to determine the nature of celestial objects, from normal stars to quasars, to elucidate the nature of the physical processes which take place in and between astronomical objects, and to shed light on the history and evolution of the universe. Attention is given to the AXAF CCD imaging spectrometer, which is to provide spectrally and temporally resolved imaging, or, in conjunction with transmission grating, high-resolution dispersed spectral images of celestial sources. A high-resolution camera, an X-ray spectrometer, and the Bragg Crystal Spectrometer are also discussed.

Sex and gender in psychoneuroimmunology research: Past, present and future

PubMed Central

Darnall, Beth D.; Suarez, Edward C.

2009-01-01

To date, research suggests that sex and gender impact pathways central to the foci of psychoneuroimmunology (PNI). This review provides a historical perspective on the evolution of sex and gender in psychoneuroimmunology research. Gender and sexually dimorphic pathways may have synergistic effects on health differences in men and women. We provide an overview of the literature of sex and gender differences in brain structure and function, sex steroids, gender role identification, hypothalamic-pituitary-adrenal axis function, genetics, immunology and cytokine response. Specific examples shed light on the importance of attending to sex and gender methodology in PNI research and recommendations are provided. PMID:19272440

Sex and gender in psychoneuroimmunology research: past, present and future.

PubMed

Darnall, Beth D; Suarez, Edward C

2009-07-01

To date, research suggests that sex and gender impact pathways central to the foci of psychoneuroimmunology (PNI). This review provides a historical perspective on the evolution of sex and gender in psychoneuroimmunology research. Gender and sexually dimorphic pathways may have synergistic effects on health differences in men and women. We provide an overview of the literature of sex and gender differences in brain structure and function, sex steroids, gender role identification, hypothalamic-pituitary-adrenal axis function, genetics, immunology and cytokine response. Specific examples shed light on the importance of attending to sex and gender methodology in PNI research and recommendations are provided.

Effect of Heat Input on Inclusion Evolution Behavior in Heat-Affected Zone of EH36 Shipbuilding Steel

NASA Astrophysics Data System (ADS)

Sun, Jincheng; Zou, Xiaodong; Matsuura, Hiroyuki; Wang, Cong

2018-06-01

The effects of heat input parameters on inclusion and microstructure characteristics have been investigated using welding thermal simulations. Inclusion features from heat-affected zones (HAZs) were profiled. It was found that, under heat input of 120 kJ/cm, Al-Mg-Ti-O-(Mn-S) composite inclusions can act effectively as nucleation sites for acicular ferrites. However, this ability disappears when the heat input is increased to 210 kJ/cm. In addition, confocal scanning laser microscopy (CSLM) was used to document possible inclusion-microstructure interactions, shedding light on how inclusions assist beneficial transformations toward property enhancement.

Localization-delocalization transition of electrons at the percolation threshold of semiconductor GaAs1-xNx alloys: The appearance of a mobility edge

NASA Astrophysics Data System (ADS)

Alberi, K.; Fluegel, B.; Beaton, D. A.; Ptak, A. J.; Mascarenhas, A.

2012-07-01

Electrons in semiconductor alloys have generally been described in terms of Bloch states that evolve from constructive interference of electron waves scattering from perfectly periodic potentials, despite the loss of structural periodicity that occurs on alloying. Using the semiconductor alloy GaAs1-xNx as a prototype, we demonstrate a localized to delocalized transition of the electronic states at a percolation threshold, the emergence of a mobility edge, and the onset of an abrupt perturbation to the host GaAs electronic structure, shedding light on the evolution of electronic structure in these abnormal alloys.

The evolution of sex roles in mate searching.

PubMed

Fromhage, Lutz; Jennions, Michael; Kokko, Hanna

2016-03-01

Searching for mates is a critical stage in the life cycle of most internally, and many externally, fertilizing species. Males usually invest more in this costly activity than females, but the reasons for this are poorly understood. Previous models have shown that female-biased parental investment, including anisogamy, does not by itself select for male-biased mate searching, so it requires additional explanations. Here, we correct and expand upon earlier models, and present two novel hypotheses that might explain the evolution of male-biased mate searching. The "carry-over hypothesis" states that females benefit less from searching if the associated costs affect other stages of the life cycle, rather than arising only while searching. It is relevant to the evolution of morphological traits that improve searching efficiency but are also expressed in other contexts. The "mating window hypothesis" states that females benefit less from searching if their life cycle includes intervals during which the exact timing of mating does not matter for the appropriate timing of reproduction (e.g., due to sperm storage or delayed embryo implantation). Such intervals are more likely to exist for females given the general pattern of greater female parental investment. Our models shed new light on classic arguments about sex role evolution. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

The nervous and visual systems of onychophorans and tardigrades: learning about arthropod evolution from their closest relatives.

PubMed

Martin, Christine; Gross, Vladimir; Hering, Lars; Tepper, Benjamin; Jahn, Henry; de Sena Oliveira, Ivo; Stevenson, Paul Anthony; Mayer, Georg

2017-08-01

Understanding the origin and evolution of arthropods requires examining their closest outgroups, the tardigrades (water bears) and onychophorans (velvet worms). Despite the rise of molecular techniques, the phylogenetic positions of tardigrades and onychophorans in the panarthropod tree (onychophorans + tardigrades + arthropods) remain unresolved. Hence, these methods alone are currently insufficient for clarifying the panarthropod topology. Therefore, the evolution of different morphological traits, such as one of the most intriguing features of panarthropods-their nervous system-becomes essential for shedding light on the origin and evolution of arthropods and their relatives within the Panarthropoda. In this review, we summarise current knowledge of the evolution of panarthropod nervous and visual systems. In particular, we focus on the evolution of segmental ganglia, the segmental identity of brain regions, and the visual system from morphological and developmental perspectives. In so doing, we address some of the many controversies surrounding these topics, such as the homology of the onychophoran eyes to those of arthropods as well as the segmentation of the tardigrade brain. Finally, we attempt to reconstruct the most likely state of these systems in the last common ancestors of arthropods and panarthropods based on what is currently known about tardigrades and onychophorans.

Evidence for adaptive evolution of low-temperature stress response genes in a Pooideae grass ancestor.

PubMed

Vigeland, Magnus D; Spannagl, Manuel; Asp, Torben; Paina, Cristiana; Rudi, Heidi; Rognli, Odd-Arne; Fjellheim, Siri; Sandve, Simen R

2013-09-01

Adaptation to temperate environments is common in the grass subfamily Pooideae, suggesting an ancestral origin of cold climate adaptation. Here, we investigated substitution rates of genes involved in low-temperature-induced (LTI) stress responses to test the hypothesis that adaptive molecular evolution of LTI pathway genes was important for Pooideae evolution. Substitution rates and signatures of positive selection were analyzed using 4330 gene trees including three warm climate-adapted species (maize (Zea mays), sorghum (Sorghum bicolor), and rice (Oryza sativa)) and five temperate Pooideae species (Brachypodium distachyon, wheat (Triticum aestivum), barley (Hordeum vulgare), Lolium perenne and Festuca pratensis). Nonsynonymous substitution rate differences between Pooideae and warm habitat-adapted species were elevated in LTI trees compared with all trees. Furthermore, signatures of positive selection were significantly stronger in LTI trees after the rice and Pooideae split but before the Brachypodium divergence (P < 0.05). Genome-wide heterogeneity in substitution rates was also observed, reflecting divergent genome evolution processes within these grasses. Our results provide evidence for a link between adaptation to cold habitats and adaptive evolution of LTI stress responses in early Pooideae evolution and shed light on a poorly understood chapter in the evolutionary history of some of the world's most important temperate crops. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

The structure of the bacteriophage PRD1 spike sheds light on the evolution of viral capsid architecture.

PubMed

Merckel, Michael C; Huiskonen, Juha T; Bamford, Dennis H; Goldman, Adrian; Tuma, Roman

2005-04-15

Comparisons of bacteriophage PRD1 and adenovirus protein structures and virion architectures have been instrumental in unraveling an evolutionary relationship and have led to a proposal of a phylogeny-based virus classification. The structure of the PRD1 spike protein P5 provides further insight into the evolution of viral proteins. The crystallized P5 fragment comprises two structural domains: a globular knob and a fibrous shaft. The head folds into a ten-stranded jelly roll beta barrel, which is structurally related to the tumor necrosis factor (TNF) and the PRD1 coat protein domains. The shaft domain is a structural counterpart to the adenovirus spike shaft. The structural relationships between PRD1, TNF, and adenovirus proteins suggest that the vertex proteins may have originated from an ancestral TNF-like jelly roll coat protein via a combination of gene duplication and deletion.

Miocene small-bodied ape from Eurasia sheds light on hominoid evolution.

PubMed

Alba, David M; Almécija, Sergio; DeMiguel, Daniel; Fortuny, Josep; Pérez de los Ríos, Miriam; Pina, Marta; Robles, Josep M; Moyà-Solà, Salvador

2015-10-30

Miocene small-bodied anthropoid primates from Africa and Eurasia are generally considered to precede the divergence between the two groups of extant catarrhines—hominoids (apes and humans) and Old World monkeys—and are thus viewed as more primitive than the stem ape Proconsul. Here we describe Pliobates cataloniae gen. et sp. nov., a small-bodied (4 to 5 kilograms) primate from the Iberian Miocene (11.6 million years ago) that displays a mosaic of primitive characteristics coupled with multiple cranial and postcranial shared derived features of extant hominoids. Our cladistic analyses show that Pliobates is a stem hominoid that is more derived than previously described small catarrhines and Proconsul. This forces us to reevaluate the role played by small-bodied catarrhines in ape evolution and provides key insight into the last common ancestor of hylobatids (gibbons) and hominids (great apes and humans). Copyright © 2015, American Association for the Advancement of Science.

Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria.

PubMed

Molina-Cruz, Alvaro; Zilversmit, Martine M; Neafsey, Daniel E; Hartl, Daniel L; Barillas-Mury, Carolina

2016-11-23

Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P. falciparum Pfs47 gene allows the parasite to evade mosquito immune detection. Here, we review the origin and globalization of P. falciparum and integrate this history with analysis of the biology, evolution, and dispersal of the main mosquito vectors. This new perspective broadens our understanding of P. falciparum population structure and the dispersal of important parasite genetic traits.

Role of Magnetosonic Solitons in Perpendicular Collisionless Shock Reformation

NASA Astrophysics Data System (ADS)

Gueroult, Renaud; Ohsawa, Yukiharu; Fisch, Nathaniel J.

2017-03-01

The nature of the magnetic structure arising from ion specular reflection in shock compression studies is examined by means of 1D particle-in-cell simulations. Propagation speed, field profiles, and supporting currents for this magnetic structure are shown to be consistent with a magnetosonic soliton. Coincidentally, this structure and its evolution are typical of foot structures observed in perpendicular shock reformation. To reconcile these two observations, we propose, for the first time, that shock reformation can be explained as the result of the formation, growth, and subsequent transition to a supercritical shock of a magnetosonic soliton. This argument is further supported by the remarkable agreement found between the period of the soliton evolution cycle and classical reformation results. This new result suggests that the unique properties of solitons can be used to shed new light on the long-standing issue of shock nonstationarity and its role on particle acceleration.

A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds.

PubMed

Knoll, Fabien; Chiappe, Luis M; Sanchez, Sophie; Garwood, Russell J; Edwards, Nicholas P; Wogelius, Roy A; Sellers, William I; Manning, Phillip L; Ortega, Francisco; Serrano, Francisco J; Marugán-Lobón, Jesús; Cuesta, Elena; Escaso, Fernando; Sanz, Jose Luis

2018-03-05

Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages of development. Comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.

Engineering Pt/Pd Interfacial Electronic Structures for Highly Efficient Hydrogen Evolution and Alcohol Oxidation.

PubMed

Fan, Jinchang; Qi, Kun; Zhang, Lei; Zhang, Haiyan; Yu, Shansheng; Cui, Xiaoqiang

2017-05-31

Tailoring the interfacial structure of Pt-based catalysts has emerged as an effective strategy to improve catalytic activity. However, little attention has been focused on investigating the relationship between the interfacial facets and their catalytic activity. Here, we design and implement Pd-Pt interfaces with controlled heterostructure features by epitaxially growing Pt nanoparticles on Pd nanosheets. On the basis of both density functional theory calculation and experimental results, we demonstrate that charge transfer from Pd to Pt is highly dependent on the interfacial facets of Pd substrates. Therefore, the Pd-Pt heterostructure with Pd(100)-Pt interface exhibits excellent activity and long-term stability for hydrogen evolution and methanol/ethanol oxidation reactions in alkaline medium, much better than that with Pd (111)-Pt interface or commercial Pt/C. Interfacial crystal facet-dependent electronic structural modulation sheds a light on the design and investigation of new heterostructures for high-activity catalysts.

Boundary Conditions for the Paleoenvironment: Chemical and Physical Processes in the Pre-Solar Nebula

NASA Technical Reports Server (NTRS)

Irvine, William M.; Schloerb, F. Peter

1997-01-01

The basic theme of this program is the study of molecular complexity and evolution in interstellar clouds and in primitive solar system objects. Research has included the detection and study of a number of new interstellar molecules and investigation of reaction pathways for astrochemistry from a comparison of theory and observed molecular abundances. The latter includes studies of cold, dark clouds in which ion-molecule chemistry should predominate, searches for the effects of interchange of material between the gas and solid phases in interstellar clouds, unbiased spectral surveys of particular sources, and systematic investigation of the interlinked chemistry and physics of dense interstellar clouds. In addition, the study of comets has allowed a comparison between the chemistry of such minimally thermally processed objects and that of interstellar clouds, shedding light on the evolution of the biogenic elements during the process of solar system formation.

Social interaction in synthetic and natural microbial communities.

PubMed

Xavier, Joao B

2011-04-12

Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same 'social interaction motifs' may be general to many cell populations.

Dimeric [Mo₂S₁₂]²⁻ Cluster: A Molecular Analogue of MoS₂ Edges for Superior Hydrogen-Evolution Electrocatalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, Zhongjie; Luo, Wenjia; Ma, Lu

2015-12-07

Proton reduction is one of the most fundamental and important reactions in nature. MoS2 edges have been identified as the active sites for hydrogen evolution reaction (HER) electrocatalysis. Designing molecular mimics of MoS2 edge sites is an attractive strategy to understand the underlying catalytic mechanism of different edge sites and improve their activities. Herein we report a dimeric molecular analogue [Mo₂S₁₂]²⁻, as the smallest unit possessing both the terminal and bridging disulfide ligands. Our electrochemical tests show that [Mo₂S₁₂]²⁻ is a superior heterogeneous HER catalyst under acidic conditions. Computations suggest that the bridging disulfide ligand of [Mo₂S₁₂]²⁻ exhibits a hydrogenmore » adsorption free energy near zero (-0.05eV). This work helps shed light on the rational design of HER catalysts and biomimetics of hydrogen-evolving enzymes.« less

Double Parton Fragmentation Function and its Evolution in Quarkonium Production

NASA Astrophysics Data System (ADS)

Kang, Zhong-Bo

2014-01-01

We summarize the results of a recent study on a new perturbative QCD factorization formalism for the production of heavy quarkonia of large transverse momentum pT at collider energies. Such a new factorization formalism includes both the leading power (LP) and next-to-leading power (NLP) contributions to the cross section in the mQ2/p_T^2 expansion for heavy quark mass mQ. For the NLP contribution, the so-called double parton fragmentation functions are involved, whose evolution equations have been derived. We estimate fragmentation functions in the non-relativistic QCD formalism, and found that their contribution reproduce the bulk of the large enhancement found in explicit NLO calculations in the color singlet model. Heavy quarkonia produced from NLP channels prefer longitudinal polarization, in contrast to the single parton fragmentation function. This might shed some light on the heavy quarkonium polarization puzzle.

15. GENERAL VIEW OF NORTHWEST SIDE OF SHED, WITH AN ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. GENERAL VIEW OF NORTHWEST SIDE OF SHED, WITH AN OBLIQUE VIEW OF THE STEP-DOWN ROOF AND TWO BANKS OF CLEARSTORY LIGHTS - Oakland Army Base, Transit Shed, East of Dunkirk Street & South of Burma Road, Oakland, Alameda County, CA

The Tragic Aspect of Teaching: Hope in Face of Uncertainty

ERIC Educational Resources Information Center

Scott, Kieran

2017-01-01

Educators throughout the ages have offered metaphors and analogies for teaching and teachers. Prominent among them are: gardener, midwife, facilitator, guide, sacrament. Each of these metaphors shed light, from a different angle, on the act of teaching. This article proposes the metaphor of tragedy as a way of shedding new light, from a totally…

The Evolution of Arthropod Body Plans: Integrating Phylogeny, Fossils, and Development-An Introduction to the Symposium.

PubMed

Chipman, Ariel D; Erwin, Douglas H

2017-09-01

The last few years have seen a significant increase in the amount of data we have about the evolution of the arthropod body plan. This has come mainly from three separate sources: a new consensus and improved resolution of arthropod phylogeny, based largely on new phylogenomic analyses; a wealth of new early arthropod fossils from a number of Cambrian localities with excellent preservation, as well as a renewed analysis of some older fossils; and developmental data from a range of model and non-model pan-arthropod species that shed light on the developmental origins and homologies of key arthropod traits. However, there has been relatively little synthesis among these different data sources, and the three communities studying them have little overlap. The symposium "The Evolution of Arthropod Body Plans-Integrating Phylogeny, Fossils and Development" brought together leading researchers in these three disciplines and made a significant contribution to the emerging synthesis of arthropod evolution, which will help advance the field and will be useful for years to come. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Evolution of Local Mutation Rate and Its Determinants.

PubMed

Terekhanova, Nadezhda V; Seplyarskiy, Vladimir B; Soldatov, Ruslan A; Bazykin, Georgii A

2017-05-01

Mutation rate varies along the human genome, and part of this variation is explainable by measurable local properties of the DNA molecule. Moreover, mutation rates differ between orthologous genomic regions of different species, but the drivers of this change are unclear. Here, we use data on human divergence from chimpanzee, human rare polymorphism, and human de novo mutations to predict the substitution rate at orthologous regions of non-human mammals. We show that the local mutation rates are very similar between human and apes, implying that their variation has a strong underlying cryptic component not explainable by the known genomic features. Mutation rates become progressively less similar in more distant species, and these changes are partially explainable by changes in the local genomic features of orthologous regions, most importantly, in the recombination rate. However, they are much more rapid, implying that the cryptic component underlying the mutation rate is more ephemeral than the known genomic features. These findings shed light on the determinants of mutation rate evolution. local mutation rate, molecular evolution, recombination rate. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Heptanuclear CoII5CoIII2 Cluster as Efficient Water Oxidation Catalyst.

PubMed

Xu, Jia-Heng; Guo, Ling-Yu; Su, Hai-Feng; Gao, Xiang; Wu, Xiao-Fan; Wang, Wen-Guang; Tung, Chen-Ho; Sun, Di

2017-02-06

Inspired by the transition-metal-oxo cubical Mn 4 CaO 5 in photosystem II, we herein report a disc-like heptanuclear mixed-valent cobalt cluster, [Co II 5 Co III 2 (mdea) 4 (N 3 ) 2 (CH 3 CN) 6 (OH) 2 (H 2 O) 2 ·4ClO 4 ] (1, H 2 mdea = N-methyldiethanolamine), for photocatalytic oxygen evolution. The topology of the Co 7 core resembles a small piece of cobaltate protected by terminal H 2 O, N 3 - , CH 3 CN, and multidentate N-methyldiethanolamine at the periphery. Under the optimal photocatalytic conditions, 1 exhibits water oxidation activity with a turnover number (TON) of 210 and a turnover frequency (TOF initial ) of 0.23 s -1 . Importantly, electrospray mass spectrometry (ESI-MS) was used to not only identify the possible main active species in the water oxidation reaction but also monitor the evolutions of oxidation states of cobalt during the photocatalytic reactions. These results shed light on the design concept of new water oxidation catalysts and mechanism-related issues such as the key active intermediate and oxidation state evolution in the oxygen evolution process. The magnetic properties of 1 were also discussed in detail.

Evolution of seahorses' upright posture was linked to Oligocene expansion of seagrass habitats

PubMed Central

Teske, Peter R.; Beheregaray, Luciano B.

2009-01-01

Seahorses (Syngnathidae: Hippocampus) are iconic marine teleosts that are readily identifiable by their upright posture. The fossil record is inadequate to shed light on the evolution of this trait because it lacks transitional forms. There are, however, extant syngnathid species (the pygmy pipehorses) that look like horizontally swimming seahorses and that might represent a surviving evolutionary link between the benthic seahorses and other, free-swimming members of the family Syngnathidae. Using sequence data from five nuclear loci, we confirm the sister taxon relationship between seahorses and pygmy pipehorses. Molecular dating indicates that the two taxa diverged during the Late Oligocene. During this time, tectonic events in the Indo-West Pacific resulted in the formation of vast amounts of new shallow-water areas and associated expansion of seagrass habitats that would have favoured the seahorses’ upright posture by improving their camouflage while not affecting their manoeuvrability negatively. The molecular techniques employed here provide new insights into the evolution of a taxon whose fossil record is incomplete, but whose evolutionary history is so recent that the major stages of morphological evolution are still represented in extant species. PMID:19451164

Doping evolution of spin and charge excitations in the Hubbard model

DOE PAGES

Kung, Y. F.; Nowadnick, E. A.; Jia, C. J.; ...

2015-11-05

We shed light on how electronic correlations vary across the phase diagram of the cuprate superconductors, examining the doping evolution of spin and charge excitations in the single-band Hubbard model using determinant quantum Monte Carlo (DQMC). In the single-particle response, we observe that the effects of correlations weaken rapidly with doping, such that one may expect the random phase approximation (RPA) to provide an adequate description of the two-particle response. In contrast, when compared to RPA, we find that significant residual correlations in the two-particle excitations persist up to 40% hole and 15% electron doping (the range of dopings achievedmore » in the cuprates). Ultimately, these fundamental differences between the doping evolution of single- and multi-particle renormalizations show that conclusions drawn from single-particle processes cannot necessarily be applied to multi-particle excitations. Eventually, the system smoothly transitions via a momentum-dependent crossover into a weakly correlated metallic state where the spin and charge excitation spectra exhibit similar behavior and where RPA provides an adequate description.« less

The evolution of Lachancea thermotolerans is driven by geographical determination, anthropisation and flux between different ecosystems

PubMed Central

Bely, Marina; Masneuf-Pomarede, Isabelle; Jiranek, Vladimir; Albertin, Warren

2017-01-01

The yeast Lachancea thermotolerans (formerly Kluyveromyces thermotolerans) is a species with remarkable, yet underexplored, biotechnological potential. This ubiquist occupies a range of natural and anthropic habitats covering a wide geographic span. To gain an insight into L. thermotolerans population diversity and structure, 172 isolates sourced from diverse habitats worldwide were analysed using a set of 14 microsatellite markers. The resultant clustering revealed that the evolution of L. thermotolerans has been driven by the geography and ecological niche of the isolation sources. Isolates originating from anthropic environments, in particular grapes and wine, were genetically close, thus suggesting domestication events within the species. The observed clustering was further validated by several means including, population structure analysis, F-statistics, Mantel’s test and the analysis of molecular variance (AMOVA). Phenotypic performance of isolates was tested using several growth substrates and physicochemical conditions, providing added support for the clustering. Altogether, this study sheds light on the genotypic and phenotypic diversity of L. thermotolerans, contributing to a better understanding of the population structure, ecology and evolution of this non-Saccharomyces yeast. PMID:28910346

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Wu, Wei-Sheng

2007-01-01

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective. PMID:19468310

Evolution and dynamics of shear-layer structures in near-wall turbulence

NASA Technical Reports Server (NTRS)

Johansson, Arne V.; Alfredsson, P. H.; Kim, John

1991-01-01

Near-wall flow structures in turbulent shear flows are analyzed, with particular emphasis on the study of their space-time evolution and connection to turbulence production. The results are obtained from investigation of a database generated from direct numerical simulation of turbulent channel flow at a Reynolds number of 180 based on half-channel width and friction velocity. New light is shed on problems associated with conditional sampling techniques, together with methods to improve these techniques, for use both in physical and numerical experiments. The results clearly indicate that earlier conceptual models of the processes associated with near-wall turbulence production, based on flow visualization and probe measurements need to be modified. For instance, the development of asymmetry in the spanwise direction seems to be an important element in the evolution of near-wall structures in general, and for shear layers in particular. The inhibition of spanwise motion of the near-wall streaky pattern may be the primary reason for the ability of small longitudinal riblets to reduce turbulent skin friction below the value for a flat surface.

The evolution of ethylene signaling in plant chemical ecology.

PubMed

Groen, Simon C; Whiteman, Noah K

2014-07-01

Ethylene is a key hormone in plant development, mediating plant responses to abiotic environmental stress, and interactions with attackers and mutualists. Here, we provide a synthesis of the role of ethylene in the context of plant ecology and evolution, and a prospectus for future research in this area. We focus on the regulatory function of ethylene in multi-organismal interactions. In general, plant interactions with different types of organisms lead to reduced or enhanced levels of ethylene. This in turn affects not only the plant's response to the interacting organism at hand, but also to other organisms in the community. These community-level effects become observable as enhanced or diminished relationships with future commensals, and systemic resistance or susceptibility to secondary attackers. Ongoing comparative genomic and phenotypic analyses continue to shed light on these interactions. These studies have revealed that plants and interacting organisms from separate kingdoms of life have independently evolved the ability to produce, perceive, and respond to ethylene. This signature of convergent evolution of ethylene signaling at the phenotypic level highlights the central role ethylene metabolism and signaling plays in plant interactions with microbes and animals.

Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics

PubMed Central

Howell, W. Mike

2018-01-01

To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal ‘rDNAome’ consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues. PMID:29443947

Success Factors in Higher Education-Industry Collaboration: A Case Study of Collaboration in the Engineering Field

ERIC Educational Resources Information Center

Thune, Taran

2011-01-01

This paper addresses the question of what potential success factors are relevant when developing and managing higher education-business partnerships. To shed light on this question, the paper presents a review of research literature on the possible success factors in university-industry relations. To shed further light on the factors identified in…

Traveling waves in a continuum model of 1D schools

NASA Astrophysics Data System (ADS)

Oza, Anand; Kanso, Eva; Shelley, Michael

2017-11-01

We construct and analyze a continuum model of a 1D school of flapping swimmers. Our starting point is a delay differential equation that models the interaction between a swimmer and its upstream neighbors' wakes, which is motivated by recent experiments in the Applied Math Lab at NYU. We coarse-grain the evolution equations and derive PDEs for the swimmer density and variables describing the upstream wake. We study the equations both analytically and numerically, and find that a uniform density of swimmers destabilizes into a traveling wave. Our model makes a number of predictions about the properties of such traveling waves, and sheds light on the role of hydrodynamics in mediating the structure of swimming schools.

Power to Explore: A History of the Marshall Space Flight Center, 1960-1990

NASA Technical Reports Server (NTRS)

Dunar, Andrew J.; Waring, Stephen P.

1999-01-01

This scholarly study of NASA's Marshall Space Flight Center places the institution in social, political, scientific and technological context. It traces the evolution of Marshall, located in Huntsville, Alabama, from its origins as an Army missile development organization to its status in 1990 as one of the most diversified of NASA's field Center. Chapters discuss military rocketry programs in Germany and the United States, Apollo-Saturn, Skylab, Space shuttle, Spacelab, the Space Station, and various scientific and technical projects including the Hubble Space Telescope. It sheds light not only on the history of space technology, science and exploration, but also on the Cold War, federal politics and complex organizations.

Evolution of ferroelectricity in tetrathiafulvalene-p-chloranil as a function of pressure and temperature

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dengl, Armin; Beyer, Rebecca; Peterseim, Tobias

2014-06-28

The neutral-to-ionic phase transition in the mixed-stack charge-transfer complex tetrathiafulvalene-p-chloranil (TTF-CA) has been studied by pressure-dependent infrared spectroscopy up to p = 11 kbar and down to low temperatures, T = 10 K. By tracking the C=O antisymmetric stretching mode of CA molecules, we accurately determine the ionicity of TTF-CA in the pressure-temperature phase diagram. At any point, the TTF-CA crystal bears only a single ionicity; there is no coexistence region or an exotic high-pressure phase. Our findings shed new light on the role of electron-phonon interaction in the neutral-ionic transition.

Ribosomes: Ribozymes that Survived Evolution Pressures but Is Paralyzed by Tiny Antibiotics

NASA Astrophysics Data System (ADS)

Yonath, Ada

An impressive number of crystal structures of ribosomes, the universal cellular machines that translate the genetic code into proteins, emerged during the last decade. The determination of ribosome high resolution structure, which was widely considered formidable, led to novel insights into the ribosomal function, namely, fidelity, catalytic mechanism, and polymerize activities. They also led to suggestions concerning its origin and shed light on the action, selectivity and synergism of ribosomal antibiotics; illuminated mechanisms acquiring bacterial resistance and provided structural information for drug improvement and design. These studies required the pioneering and implementation of advanced technologies, which directly influenced the remarkable increase of the number of structures deposited in the Protein Data Bank.

Black hole demography at the dawn of gravitational-wave astronomy: state-of-the art and future perspectives

NASA Astrophysics Data System (ADS)

Mapelli, Michela

2018-02-01

The first four LIGO detections have confirmed the existence of massive black holes (BHs), with mass 30-40 M⊙. Such BHs might originate from massive metal-poor stars (Z < 0:3 Z⊙) or from gravitational instabilities in the early Universe. The formation channels of merging BHs are still poorly constrained. The measure of mass, spin and redshift distribution of merging BHs will give us fundamental clues to distinguish between different models. In parallel, a better understanding of several astrophysical processes (e.g. common envelope, core-collapse SNe, and dynamical evolution of BHs) is decisive, to shed light on the formation channels of merging BHs.

Freezing Coherent Field Growth in a Cavity by the Quantum Zeno Effect

NASA Astrophysics Data System (ADS)

Bernu, J.; Deléglise, S.; Sayrin, C.; Kuhr, S.; Dotsenko, I.; Brune, M.; Raimond, J. M.; Haroche, S.

2008-10-01

We have frozen the coherent evolution of a field in a cavity by repeated measurements of its photon number. We use circular Rydberg atoms dispersively coupled to the cavity mode for an absorption-free photon counting. These measurements inhibit the growth of a field injected in the cavity by a classical source. This manifestation of the quantum Zeno effect illustrates the backaction of the photon number determination onto the field phase. The residual growth of the field can be seen as a random walk of its amplitude in the two-dimensional phase space. This experiment sheds light onto the measurement process and opens perspectives for active quantum feedback.

Reptiles: a new model for brain evo-devo research.

PubMed

Nomura, Tadashi; Kawaguchi, Masahumi; Ono, Katsuhiko; Murakami, Yasunori

2013-03-01

Vertebrate brains exhibit vast amounts of anatomical diversity. In particular, the elaborate and complex nervous system of amniotes is correlated with the size of their behavioral repertoire. However, the evolutionary mechanisms underlying species-specific brain morphogenesis remain elusive. In this review we introduce reptiles as a new model organism for understanding brain evolution. These animal groups inherited ancestral traits of brain architectures. We will describe several unique aspects of the reptilian nervous system with a special focus on the telencephalon, and discuss the genetic mechanisms underlying reptile-specific brain morphology. The establishment of experimental evo-devo approaches to studying reptiles will help to shed light on the origin of the amniote brains. Copyright © 2013 Wiley Periodicals, Inc.

Localization-delocalization transition of electrons at the percolation threshold of semiconductor GaAs 1–xN x alloys: The appearance of a mobility edge

DOE PAGES

Alberi, K.; Fluegel, B.; Beaton, D. A.; ...

2012-07-09

Electrons in semiconductor alloys have generally been described in terms of Bloch states that evolve from constructive interference of electron waves scattering from perfectly periodic potentials, despite the loss of structural periodicity that occurs on alloying. Using the semiconductor alloy GaAs₁₋ xN x as a prototype, we demonstrate a localized to delocalized transition of the electronic states at a percolation threshold, the emergence of a mobility edge, and the onset of an abrupt perturbation to the host GaAs electronic structure, shedding light on the evolution of electronic structure in these abnormal alloys.

4. Tower entrance wing, covered way, keeper's house and shed, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. Tower entrance wing, covered way, keeper's house and shed, view west northwest, northeast side of wing and covered way, southeast and northeast sides of keeper's house, southwest and southeast sides of shed - Burnt Island Light Station, Burnt Island, west side of entrance to Boothbay Harbor, Pine Cliff, Lincoln County, ME

Loss and gain of cone types in vertebrate ciliary photoreceptor evolution.

PubMed

Musser, Jacob M; Arendt, Detlev

2017-11-01

Ciliary photoreceptors are a diverse cell type family that comprises the rods and cones of the retina and other related cell types such as pineal photoreceptors. Ciliary photoreceptor evolution has been dynamic during vertebrate evolution with numerous gains and losses of opsin and phototransduction genes, and changes in their expression. For example, early mammals lost all but two cone opsins, indicating loss of cone receptor types in response to nocturnal lifestyle. Our review focuses on the comparison of specifying transcription factors and cell type-specific transcriptome data in vertebrate retinae to build and test hypotheses on ciliary photoreceptor evolution. Regarding cones, recent data reveal that a combination of factors specific for long-wavelength sensitive opsin (Lws)- cones in non-mammalian vertebrates (Thrb and Rxrg) is found across all differentiating cone photoreceptors in mice. This suggests that mammalian ancestors lost all but one ancestral cone type, the Lws-cone. We test this hypothesis by a correlation analysis of cone transcriptomes in mouse and chick, and find that, indeed, transcriptomes of all mouse cones are most highly correlated to avian Lws-cones. These findings underscore the importance of specifying transcription factors in tracking cell type evolution, and shed new light on the mechanisms of cell type loss and gain in retina evolution. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Hair shedding score may affect body temperature more than hair coat color during heat stress in weaned beef heifers.

USDA-ARS?s Scientific Manuscript database

The objective of this study was to evaluate the effect of hair shedding score and hair coat color on the vaginal temperature (VT) of calves during heat stress. Weaned Bos taurus beef heifers (n = 32; BW = 282 ± 6.4 kg) were assigned to a hair coat color class (BLACK; RED; or LIGHT, where LIGHT = yel...

Structural interpretation and physical property estimates based on COAST 2012 seismic reflection profiles offshore central Washington, Cascadia subduction zone

NASA Astrophysics Data System (ADS)

Webb, S. I.; Tobin, H. J.; Everson, E. D.; Fortin, W.; Holbrook, W. S.; Kent, G.; Keranen, K. M.

2014-12-01

The Cascadia subduction zone has a history of large magnitude earthquakes, but a near-total lack of plate interface seismicity, making the updip limit of the seismogenic zone difficult to locate. In addition, the central Cascadia accretionary prism is characterized by an extremely low wedge taper angle, landward vergent initial thrusting, and a flat midslope terrace between the inner and outer wedges, unlike most other accretionary prisms (e.g. the Nankai Trough, Japan). The Cascadia Open Access Seismic Transect (COAST) lines were shot by R/V Marcus Langseth in July of 2012 off central Washington to image this subduction zone. Two trench-parallel and nine trench-perpendicular lines were collected. In this study, we present detailed seismic interpretation of both time- and depth-migrated stacked profiles, focused on elucidating the deposition and deformation of both pre- and syn-tectonic sediment in the trench and slope. Distribution and timing of sediments and their deformation is used to unravel the evolution of the wedge through time. Initially, interpretation of the time-sections is carried out to support the building of tomographic velocity models to aid in the pre-stack depth migration (PSDM) of selected lines. In turn, we use PSDM velocity models to estimate porosity and pore pressure conditions at the base of the wedge and across the basal plate interface décollement where possible, using established velocity-porosity transforms. Interpretation in this way incorporates both accurate structural relationships and robust porosity models to document wedge development and present-day stress state, in particular regions of potential overpressure. Results shed light on the origin and evolution of the mid-slope terrace and the low taper angle for the forearc wedge. This work may shed light ultimately on the position of the potential updip limit of the seismogenic zone beneath the wedge.

In vitro monitoring of oxidative processes with self-aggregating gold nanoparticles using all-optical photoacoustic spectroscopy.

PubMed

Yasmin, Zannatul; Khachatryan, Edward; Lee, Yuan-Hao; Maswadi, Saher; Glickman, Randolph; Nash, Kelly L

2015-02-15

In this work, the assembly of gold nanoparticles of (AuNPs) is used to detect the presence of the biomolecule glutathione (GSH) using a novel technique called "all-optical photoacoustic spectroscopy" (AOPAS). The AOPAS technique coupled with AuNPs forms the basis of a biosensing technique capable of probing the dynamic evolution of nano-bio interfaces within a microscopic volume. Dynamic Light Scattering (DLS) and ultraviolet-visible (UV-vis) spectra were measured to describe the kinetics governing the interparticle interactions by monitoring the AuNPs assembly and evolution of the surface plasmon resonance (SPR) band. A comparison of the same dynamic evolution of AuNPs assembly was performed using the AOPAS technique to confirm the validity of this method. The fundamental study is complemented by a demonstration of the performance of this biosensing technique in the presence of cell culture medium containing fetal bovine serum (FBS), which forms a protein corona on the surface of the AuNPs. This work demonstrates that the in vitro monitoring capabilities of the AOPAS provides sensitive measurement at the microscopic level and low nanoparticle concentrations without the artifacts limiting the use of conventional biosensing methods, such as fluorescent indicators. The AOPAS technique not only provides a facile approach for in vitro biosensing, but also shed a light on the real-time detection of thiol containing oxidative stress biomarkers in live systems using AuNPs. Copyright © 2014 Elsevier B.V. All rights reserved.

Kinetic Modeling Sheds Light on the Mode of Action of Recombinant Factor VIIa on Thrombin Generation

DTIC Science & Technology

2011-01-01

Regular Article Kinetic modeling sheds light on the mode of action of recombinant factor VIIa on thrombin generation Alexander Y. Mitrophanov...its effects on the quantitative parameters of thrombin generation. For recombinant activated factor VII (rFVIIa) ― a promising hemostasis-inducing...modulate thrombin production , it is necessary to identify rFVIIa-induced effects that are compatible with the available biochemical knowledge about

This pineal gland does not mediate phase shifts in the disc shedding rhythm of the rat retina

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldman, A.I.

Albino rats were subjected to pinealectomy, superior cervical ganglionectomy, or the appropriate sham preparation and were placed in lighting conditions so that light onset was advanced by 10 hr. After 6 days of this regimen, all animals exhibited a complete shift in their outer segment disc shedding rhythm, indicating that the pineal gland is not a factor in mediating such a shift.

Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution

NASA Astrophysics Data System (ADS)

Kille, Sabrina; Zilly, Felipe E.; Acevedo, Juan P.; Reetz, Manfred T.

2011-09-01

A current challenge in synthetic organic chemistry is the development of methods that allow the regio- and stereoselective oxidative C-H activation of natural or synthetic compounds with formation of the corresponding alcohols. Cytochrome P450 enzymes enable C-H activation at non-activated positions, but the simultaneous control of both regio- and stereoselectivity is problematic. Here, we demonstrate that directed evolution using iterative saturation mutagenesis provides a means to solve synthetic problems of this kind. Using P450 BM3(F87A) as the starting enzyme and testosterone as the substrate, which results in a 1:1 mixture of the 2β- and 15β-alcohols, mutants were obtained that are 96-97% selective for either of the two regioisomers, each with complete diastereoselectivity. The mutants can be used for selective oxidative hydroxylation of other steroids without performing additional mutagenesis experiments. Molecular dynamics simulations and docking experiments shed light on the origin of regio- and stereoselectivity.

Microstructural Evolutions During Reversion Annealing of Cold-Rolled AISI 316 Austenitic Stainless Steel

NASA Astrophysics Data System (ADS)

Naghizadeh, Meysam; Mirzadeh, Hamed

2018-03-01

Microstructural evolutions during reversion annealing of a plastically deformed AISI 316 stainless steel were investigated and three distinct stages were identified: the reversion of strain-induced martensite to austenite, the primary recrystallization of the retained austenite, and the grain growth process. It was found that the slow kinetics of recrystallization at lower annealing temperatures inhibit the formation of an equiaxed microstructure and might effectively impair the usefulness of this thermomechanical treatment for the objective of grain refinement. By comparing the behavior of AISI 316 and 304 alloys, it was found that the mentioned slow kinetics is related to the retardation effect of solute Mo in the former alloy. At high reversion annealing temperature, however, an equiaxed austenitic microstructure was achieved quickly in AISI 316 stainless steel due to the temperature dependency of retardation effect of molybdenum, which allowed the process of recrystallization to happen easily. Conclusively, this work can shed some light on the issues of this efficient grain refining approach for microstructural control of austenitic stainless steels.

Genome evolution and speciation genetics of clawed frogs (Xenopus and Silurana).

PubMed

Evans, Ben J

2008-05-01

Speciation of clawed frogs occurred through bifurcation and reticulation of evolutionary lineages, and resulted in extant species with different ploidy levels. Duplicate gene evolution and expression in these animals provides a unique perspective into the earliest genomic transformations after vertebrate whole genome duplication (WGD) and suggests that functional constraints are relaxed compared to before duplication but still consistently strong for millions of years following WGD. Additionally, extensive quantitative expression divergence between duplicate genes occurred after WGD. Diversification of clawed frogs was potentially catalyzed by transposition and divergent resolution--processes that occur through different genetic mechanisms but that have analogous implications for genome structure. How sex determination is maintained after genome duplication is fundamental to our understanding of why allopolyploidization is so prevalent in this group, and why clawed frogs violate Haldane's Rule for hybrid sterility. Future studies of expression subfunctionalization in polyploids will shed light on the role and purviews of cis- and trans-regulatory elements in gene regulation.

Synoptic Factors Affecting Structure Predictability of Hurricane Alex (2016)

NASA Astrophysics Data System (ADS)

Gonzalez-Aleman, J. J.; Evans, J. L.; Kowaleski, A. M.

2016-12-01

On January 7, 2016, a disturbance formed over the western North Atlantic basin. After undergoing tropical transition, the system became the first hurricane of 2016 - and the first North Atlantic hurricane to form in January since 1938. Already an extremely rare hurricane event, Alex then underwent extratropical transition [ET] just north of the Azores Islands. We examine the factors affecting Alex's structural evolution through a new technique called path-clustering. In this way, 51 ensembles from the European Centre for Medium-Range Weather Forecasts Ensemble Prediction System (ECMWF-EPS) are grouped based on similarities in the storm's path through the Cyclone Phase Space (CPS). The differing clusters group various possible scenarios of structural development represented in the ensemble forecasts. As a result, it is possible to shed light on the role of the synoptic scale in changing the structure of this hurricane in the midlatitudes through intercomparison of the most "realistic" forecast of the evolution of Alex and the other physically plausible modes of its development.

Operando Evidence for a Universal Oxygen Evolution Mechanism on Thermal and Electrochemical Iridium Oxides.

PubMed

Saveleva, Viktoriia A; Wang, Li; Teschner, Detre; Jones, Travis; Gago, Aldo S; Friedrich, K Andreas; Zafeiratos, Spyridon; Schlögl, Robert; Savinova, Elena R

2018-06-07

Progress in the development of proton exchange membrane (PEM) water electrolysis technology requires decreasing the anode overpotential, where the sluggish multistep oxygen evolution reaction (OER) occurs. This calls for an understanding of the nature of the active OER sites and reaction intermediates, which are still being debated. In this work, we apply synchrotron radiation-based near-ambient pressure X-ray photoelectron and absorption spectroscopies under operando conditions in order to unveil the nature of the reaction intermediates and shed light on the OER mechanism on electrocatalysts most widely used in PEM electrolyzers-electrochemical and thermal iridium oxides. Analysis of the O K-edge and Ir 4f spectra backed by density functional calculations reveals a universal oxygen anion red-ox mechanism regardless of the nature (electrochemical or thermal) of the iridium oxide. The formation of molecular oxygen is considered to occur through a chemical step from the electrophilic O I- species, which itself is formed in an electrochemical step.

Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences

PubMed Central

Sheinman, Michael; Ramisch, Anna; Massip, Florian; Arndt, Peter F.

2016-01-01

Since the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of human texts, such as Zipf’s law. Despite recent efforts, the understanding of this phenomenon is still lacking. Here we find that selfish DNA elements, such as those belonging to the Alu family of repeats, dominate the power-law tail. Interestingly, for the Alu elements the power-law exponent increases with the length of the considered subsequences. Motivated by these observations, we develop a model of selfish DNA expansion. The predictions of this model qualitatively and quantitatively agree with the empirical observations. This allows us to estimate parameters for the process of selfish DNA spreading in a genome during its evolution. The obtained results shed light on how evolution of selfish DNA elements shapes non-trivial statistical properties of genomes. PMID:27488939

A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds

DOE PAGES

Knoll, Fabien; Chiappe, Luis M.; Sanchez, Sophie; ...

2018-03-05

Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages ofmore » development. Finally, comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.« less

A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Knoll, Fabien; Chiappe, Luis M.; Sanchez, Sophie

Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages ofmore » development. Finally, comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.« less

Critical roles for a genetic code alteration in the evolution of the genus Candida.

PubMed

Silva, Raquel M; Paredes, João A; Moura, Gabriela R; Manadas, Bruno; Lima-Costa, Tatiana; Rocha, Rita; Miranda, Isabel; Gomes, Ana C; Koerkamp, Marian J G; Perrot, Michel; Holstege, Frank C P; Boucherie, Hélian; Santos, Manuel A S

2007-10-31

During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross-protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation.

The role of hyperparasitism in microbial pathogen ecology and evolution.

PubMed

Parratt, Steven R; Laine, Anna-Liisa

2016-08-01

Many micro-organisms employ a parasitic lifestyle and, through their antagonistic interactions with host populations, have major impacts on human, agricultural and natural ecosystems. Most pathogens are likely to host parasites of their own, that is, hyperparasites, but how nested chains of parasites impact on disease dynamics is grossly neglected in the ecological and evolutionary literature. In this minireview we argue that the diversity and dynamics of micro-hyperparasites are an important component of natural host-pathogen systems. We use the current literature from a handful of key systems to show that observed patterns of pathogen virulence and disease dynamics may well be influenced by hyperparasites. Exploring these factors will shed light on many aspects of microbial ecology and disease biology, including resistance-virulence evolution, apparent competition, epidemiology and ecosystem stability. Considering the importance of hyperparasites in natural populations will have applied consequences for the field of biological control and therapeutic science, where hyperparastism is employed as a control mechanism but not necessarily ecologically understood.

Consistent individual differences in human social learning strategies.

PubMed

Molleman, Lucas; van den Berg, Pieter; Weissing, Franz J

2014-04-04

Social learning has allowed humans to build up extensive cultural repertoires, enabling them to adapt to a wide variety of environmental and social conditions. However, it is unclear which social learning strategies people use, especially in social contexts where their payoffs depend on the behaviour of others. Here we show experimentally that individuals differ in their social learning strategies and that they tend to employ the same learning strategy irrespective of the interaction context. Payoff-based learners focus on their peers' success, while decision-based learners disregard payoffs and exclusively focus on their peers' past behaviour. These individual differences may be of considerable importance for cultural evolution. By means of a simple model, we demonstrate that groups harbouring individuals with different learning strategies may be faster in adopting technological innovations and can be more efficient through successful role differentiation. Our study highlights the importance of individual variation for human interactions and sheds new light on the dynamics of cultural evolution.

Extremophiles in Household Water Heaters

NASA Astrophysics Data System (ADS)

Wilpiszeski, R.; House, C. H.

2016-12-01

A significant fraction of Earth's microbial diversity comes from species living in extreme environments, but natural extreme environments can be difficult to access. Manmade systems like household water heaters serve as an effective proxy for thermophilic environments that are otherwise difficult to sample directly. As such, we are investigating the biogeography, taxonomic distribution, and evolution of thermophiles growing in domestic water heaters. Citizen scientists collected hot tap water culture- and filter- samples from 101 homes across the United States. We recovered a single species of thermophilic heterotroph from culture samples inoculated from water heaters across the United States, Thermus scotoductus. Whole-genome sequencing was conducted to better understand the distribution and evolution of this single species. We have also sequenced hyper-variable regions of the 16S rRNA gene from whole-community filter samples to identify the broad diversity and distribution of microbial cells captured from each water heater. These results shed light on the processes that shape thermophilic populations and genomes at a spatial resolution that is difficult to access in naturally occurring extreme ecosystems.

Cholesterol suppresses membrane leakage by decreasing water penetrability.

PubMed

Bu, Bing; Crowe, Michael; Diao, Jiajie; Ji, Baohua; Li, Dechang

2018-06-13

Membrane fusion is a fundamental biological process that lies at the heart of enveloped virus infection, synaptic signaling, intracellular vesicle trafficking, gamete fertilization, and cell-cell fusion. Membrane fusion is initiated as two apposed membranes merge to a single bilayer called a hemifusion diaphragm. It is believed that the contents of the two fusing membranes are released through a fusion pore formed at the hemifusion diaphragm, and yet another possible pathway has been proposed in which an undefined pore may form outside the hemifusion diaphragm at the apposed membranes, leading to the so-called leaky fusion. Here, we performed all-atom molecular dynamics simulations to study the evolution of the hemifusion diaphragm structure with various lipid compositions. We found that the lipid cholesterol decreased water penetrability to inhibit leakage pore formation. Biochemical leakage experiments support these simulation results. This study may shed light on the underlying mechanism of the evolution pathways of the hemifusion structure, especially the understanding of content leakage during membrane fusion.

Microstructural Evolutions During Reversion Annealing of Cold-Rolled AISI 316 Austenitic Stainless Steel

NASA Astrophysics Data System (ADS)

Naghizadeh, Meysam; Mirzadeh, Hamed

2018-06-01

Microstructural evolutions during reversion annealing of a plastically deformed AISI 316 stainless steel were investigated and three distinct stages were identified: the reversion of strain-induced martensite to austenite, the primary recrystallization of the retained austenite, and the grain growth process. It was found that the slow kinetics of recrystallization at lower annealing temperatures inhibit the formation of an equiaxed microstructure and might effectively impair the usefulness of this thermomechanical treatment for the objective of grain refinement. By comparing the behavior of AISI 316 and 304 alloys, it was found that the mentioned slow kinetics is related to the retardation effect of solute Mo in the former alloy. At high reversion annealing temperature, however, an equiaxed austenitic microstructure was achieved quickly in AISI 316 stainless steel due to the temperature dependency of retardation effect of molybdenum, which allowed the process of recrystallization to happen easily. Conclusively, this work can shed some light on the issues of this efficient grain refining approach for microstructural control of austenitic stainless steels.

Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws

PubMed Central

Šmajs, David; Norris, Steven J.; Weinstock, George M.

2013-01-01

Pathogenic uncultivable treponemes, similar to syphilis-causing Treponema pallidum subspecies pallidum, include T. pallidum ssp. pertenue, T. pallidum ssp. endemicum and Treponema carateum, which cause yaws, bejel and pinta, respectively. Genetic analyses of these pathogens revealed striking similarity among these bacteria and also a high degree of similarity to the rabbit pathogen, T. paraluiscuniculi, a treponeme not infectious to humans. Genome comparisons between pallidum and non-pallidum treponemes revealed genes with potential involvement in human infectivity, whereas comparisons between pallidum and pertenue treponemes identified genes possibly involved in the high invasivity of syphilis treponemes. Genetic variability within syphilis strains is considered as the basis of syphilis molecular epidemiology with potential to detect more virulent strains, whereas genetic variability within a single strain is related to its ability to elude the immune system of the host. Genome analyses also shed light on treponemal evolution and on chromosomal targets for molecular diagnostics of treponemal infections. PMID:22198325

Three legacies of humanitarianism in China.

PubMed

Hirono, Miwa

2013-10-01

The rise of China has altered the context of the international humanitarian community of donors and aid agencies. China is becoming one of the key actors in this grouping, undertaking infrastructure projects in areas in which paramount humanitarian challenges exist. The literature discusses how the Chinese approach differs from that of Western donors, but it does not pay much attention to why China concentrates on its state-centric and infrastructure-based approach. This paper seeks to shed some light on this subject by examining the historical evolution of the concept of humanitarianism in China. This evolution has produced three legacies: (i) the ideal of a well-ordered state; (ii) anti-Western sentiment; and (iii) the notion of comprehensive development based on a human-oriented approach. China's policies and discourses on assistance in humanitarian crises today rest on these three legacies. Traditional donors would be well advised to consider carefully the implications of the Chinese understanding of humanitarianism when engaging with the country. © 2013 The Author(s). Disasters © Overseas Development Institute, 2013.

Trade-offs between light interception and leaf water shedding: a comparison of shade- and sun-adapted species in a subtropical rainforest.

PubMed

Meng, Fengqun; Cao, Rui; Yang, Dongmei; Niklas, Karl J; Sun, Shucun

2014-01-01

Species in high-rainfall regions have two major alternative approaches to quickly drain off water, i.e., increasing leaf inclination angles relative to the horizontal plane, or developing long leaf drip tips. We hypothesized that shade-adapted species will have more pronounced leaf drip tips but not greater inclination angles (which can reduce the ability to intercept light) compared to sun-adapted species and that length of leaf drip tips will be negatively correlated with photosynthetic capacity [characterized by light-saturated net photosynthetic rates (Amax), associated light compensation points (LCP), and light saturation points (LSP)]. We tested this hypothesis by measuring morphological and physiological traits that are associated with light-interception and water shedding for seven shade-adapted shrub species, ten sun-adapted understory shrub species, and 15 sun-adapted tree species in a subtropical Chinese rainforest, where mean annual precipitation is around 1,600 mm. Shade-adapted understory species had lower LMA, Amax, LSP, and LCP compared to understory or canopy sun-adapted species; their leaf and twig inclination angles were significantly smaller and leaf drip tips were significantly longer than those in sun-adapted species. This suggests that shade-adapted understory species tend to develop pronounced leaf drip tips but not large leaf inclination angles to shed water. The length of leaf drip tips was negatively correlated with leaf inclination angles and photosynthetic capacity. These relationships were consistent between ordinary regression and phylogenetic generalized least squares analyses. Our study illustrates the trade-offs between light interception and leaf water shedding and indicates that length of leaf drip tips can be used as an indicator of adaptation to shady conditions and overall photosynthetic performance of shrub species in subtropical rainforests.

Genomic analysis of expressed sequence tags in American black bear Ursus americanus

PubMed Central

2010-01-01

Background Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Results Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. Conclusion We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes. PMID:20338065

Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport.

PubMed

Eu, Byung Chan

2008-09-07

In the traditional theories of irreversible thermodynamics and fluid mechanics, the specific volume and molar volume have been interchangeably used for pure fluids, but in this work we show that they should be distinguished from each other and given distinctive statistical mechanical representations. In this paper, we present a general formula for the statistical mechanical representation of molecular domain (volume or space) by using the Voronoi volume and its mean value that may be regarded as molar domain (volume) and also the statistical mechanical representation of volume flux. By using their statistical mechanical formulas, the evolution equations of volume transport are derived from the generalized Boltzmann equation of fluids. Approximate solutions of the evolution equations of volume transport provides kinetic theory formulas for the molecular domain, the constitutive equations for molar domain (volume) and volume flux, and the dissipation of energy associated with volume transport. Together with the constitutive equation for the mean velocity of the fluid obtained in a previous paper, the evolution equations for volume transport not only shed a fresh light on, and insight into, irreversible phenomena in fluids but also can be applied to study fluid flow problems in a manner hitherto unavailable in fluid dynamics and irreversible thermodynamics. Their roles in the generalized hydrodynamics will be considered in the sequel.

Genomic analysis of expressed sequence tags in American black bear Ursus americanus.

PubMed

Zhao, Sen; Shao, Chunxuan; Goropashnaya, Anna V; Stewart, Nathan C; Xu, Yichi; Tøien, Øivind; Barnes, Brian M; Fedorov, Vadim B; Yan, Jun

2010-03-26

Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus). Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes. We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes.

Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence

PubMed Central

Clerc, Melanie; Ebert, Dieter; Hall, Matthew D.

2015-01-01

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence. PMID:25761710

New insights into the phylogeny of the TMBIM superfamily across the three of life: Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants.

PubMed

Gamboa-Tuz, Samuel D; Pereira-Santana, Alejandro; Zhao, Tao; Schranz, M Eric; Castano, Enrique; Rodriguez-Zapata, Luis C

2018-04-25

The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes. However, no research has focused on the evolution of this superfamily in plants. We identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. Then, we used orthology and synteny network analyses to further investigate the evolution and expansion of the BI and LFG families in 48 plants from diverse taxa. Plant BI family forms a single monophyletic group; however, monocot BI sequences transposed to another genomic context during evolution. Plant LFG family, which expanded trough whole genome and tandem duplications, is subdivided in LFG I, LFG IIA, and LFG IIB major phylogenetic groups, and retains synteny in angiosperms. Moreover, two orthologous groups (OGs) are shared between bryophytes and seed plants. Other several lineage-specific OGs are present in plants. This work clarifies the phylogenetic classification of the TMBIM superfamily across the three domains of life. Furthermore, it sheds new light on the evolution of the BI and LFG families in plants providing a benchmark for future research. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Predicting the emergence of H3N2 influenza viruses reveals contrasted modes of evolution of HA and NA antigens.

PubMed

Sandie, Reatha; Aris-Brosou, Stéphane

2014-01-01

Vaccine design for rapidly changing viruses is based on empirical surveillance of strains circulating in a given season to assess those that will most likely spread during the next season. The choice of which strains to include in the vaccine is critical, as an erroneous decision can lead to a nonimmunized human population that will then be at risk in the face of an epidemic or, worse, a pandemic. Here, we present the first steps toward a very general phylogenetic approach to predict the emergence of novel viruses. Our genomic model builds upon natural features of viral evolution such as selection and recombination / reassortment, and incorporates episodic bursts of evolution and or of recombination. As a proof-of-concept, we assess the performance of this model in a retrospective study, focusing: (i) on the emergence of an unexpected H3N2 influenza strain in 2007, and (ii) on a longitudinal design. Based on the analysis of hemagglutinin (HA) and neuraminidase (NA) genes, our results show a lack of predictive power in both experimental designs, but shed light on the mode of evolution of these two antigens: (i) supporting the lack of significance of recombination in the evolution of this influenza virus, and (ii) showing that HA evolves episodically while NA changes gradually.

Nucleosynthesis in the neighborhood of a black hole

NASA Technical Reports Server (NTRS)

Chakrabarti, Sandip K.

1986-01-01

The preliminary results from simulations of nucleosynthesis inside a thick accretion disk around a black hole are discussed as a function of the accretion rate, the viscosity parameter, and the mass of the black hole. Results for the Bondi accretion case are also presented. Taking the case of a 10-solar mass and a 10 to the 6th-solar mass central Schwarzschild hole, detailed evolution of a representative element of matter as it accretes into the hole is presented in the case when the initial abundance (at the outer edge of the disk) is the same as the solar abundance. It is suggested that such studies may eventually shed light on the composition of the outgoing jets observed in the active galaxies and SS433.

Black Hole Safari: Tracking Populations and Hunting Big Game

NASA Astrophysics Data System (ADS)

McConnell, N. J.

2013-10-01

Understanding the physical connection, or lack thereof, between the growth of galaxies and supermassive black holes is a key challenge in extragalactic astronomy. Dynamical studies of nearby galaxies are building a census of black hole masses across a broad range of galaxy types and uncovering statistical correlations between galaxy bulge properties and black hole masses. These local correlations provide a baseline for studying galaxies and black holes at higher redshifts. Recent measurements have probed the extremes of the supermassive black hole population and introduced surprises that challenge simple models of black hole and galaxy co-evolution. Future advances in the quality and quantity of dynamical black hole mass measurements will shed light upon the growth of massive galaxies and black holes in different cosmic environments.

Systems biology and the quest for correlates of protection to guide the development of an HIV vaccine.

PubMed

Kuri-Cervantes, Leticia; Fourati, Slim; Canderan, Glenda; Sekaly, Rafick-Pierre

2016-08-01

Over the last three decades, a myriad of data has been generated regarding HIV/SIV evolution, immune evasion, immune response, and pathogenesis. Much of this data can be integrated and potentially used to generate a successful vaccine. Although individual approaches have begun to shed light on mechanisms involved in vaccine-conferred protection from infection, true correlates of protection have not yet been identified. The systems biology approach helps unify datasets generated using different techniques and broaden our understanding of HIV immunopathogenesis. Moreover, systems biology is a tool that can provide correlates of protection, which can be targeted for the production of a successful HIV vaccine. Copyright © 2016. Published by Elsevier Ltd.

Modeling the unidentified infrared emission with combinations of polycyclic aromatic hydrocarbons

NASA Technical Reports Server (NTRS)

Allamandola, L. J.; Hudgins, D. M.; Sandford, S. A.

1999-01-01

The infrared emission band spectrum associated with many different interstellar objects can be modeled successfully by using combined laboratory spectra of neutral and positively charged polycyclic aromatic hydrocarbons (PAHs). These model spectra, shown here for the first time, alleviate the principal spectroscopic criticisms previously leveled at the PAH hypothesis and demonstrate that mixtures of free molecular PAHs can indeed account for the overall appearance of the widespread interstellar infrared emission spectrum. Furthermore, these models give us insight into the structures, stabilities, abundances, and ionization balance of the interstellar PAH population. These, in turn, reflect conditions in the emission zones and shed light on the microscopic processes involved in the carbon nucleation, growth, and evolution in circumstellar shells and the interstellar medium.

Formation of hydroxyapatite onto glasses of the CaO-MgO-SiO2 system with B2O3, Na2O, CaF2 and P2O5 additives.

PubMed

Agathopoulos, S; Tulyaganov, D U; Ventura, J M G; Kannan, S; Karakassides, M A; Ferreira, J M F

2006-03-01

New bioactive glasses with compositions based on the CaO-MgO-SiO(2) system and additives of B(2)O(3), P(2)O(5), Na(2)O, and CaF(2) were prepared. The in vitro mineralization behaviour was tested by immersion of powders or bulk glasses in simulated body fluid (SBF). Monitoring of ionic concentrations in SBF and scanning electron microscopy (SEM) observations at the surface of the glasses were conducted over immersion time. Raman and infrared (IR) spectroscopy shed light on the structural evolution occurring at the surface of the glasses that leads to formation of hydroxyapatite.

The positioning of sustainability within residential property marketing.

PubMed

Kriese, Ulrich; Scholz, Roland W

2011-01-01

This article investigates the evolution of sustainability positioning in residential property marketing to shed light on the specific role and responsibility of housebuilders and housing investors in urban development. To this end, an analysis is made of housing advertisements published in Basel, Switzerland, over a period of more than 100 years. The paper demonstrates how to draw successfully on advertisements to discern sustainability patterns in housing, using criteria situated along the dimensions building, location and people. Cluster analysis allows five clusters of sustainability positioning to be described—namely, good location, green building, comfort living, pre-sustainability and sustainability. Investor and builder types are differently located in these clusters. Location emerges as an issue which, to a large extent, is advertised independently from other sustainability issues.

Shifting fitness landscapes in response to altered environments

PubMed Central

Jensen, Jeffrey D.; Bolon, Daniel N. A.

2013-01-01

The role of adaptation in molecular evolution has been contentious for decades. Here, we shed light on the adaptive potential in Saccharomyces cerevisiae by presenting systematic fitness measurements for all possible point mutations in a region of Hsp90 under four environmental conditions. Under elevated salinity, we observe numerous beneficial mutations with growth advantages up to 7% relative to the wild type. All of these beneficial mutations were observed to be associated with high costs of adaptation. We thus demonstrate that an essential protein can harbor adaptive potential upon an environmental challenge, and report a remarkable fit of the data to a version of Fisher's geometric model that focuses on the fitness trade-offs between mutations in different environments. PMID:24299404

Karyological characterization of the endemic Iberian rock lizard, Iberolacerta monticola (Squamata, Lacertidae): insights into sex chromosome evolution.

PubMed

Rojo, V; Giovannotti, M; Naveira, H; Nisi Cerioni, P; González-Tizón, A M; Caputo Barucchi, V; Galán, P; Olmo, E; Martínez-Lage, A

2014-01-01

Rock lizards of the genus Iberolacerta constitute a promising model to examine the process of sex chromosome evolution, as these closely related taxa exhibit remarkable diversity in the degree of sex chromosome differentiation with no clear phylogenetic segregation, ranging from cryptic to highly heteromorphic ZW chromosomes and even multiple chromosome systems (Z1Z1Z2Z2/Z1Z2W). To gain a deeper insight into the patterns of karyotype and sex chromosome evolution, we performed a cytogenetic analysis based on conventional staining, banding techniques and fluorescence in situ hybridization in the species I. monticola, for which previous cytogenetic investigations did not detect differentiated sex chromosomes. The karyotype is composed of 2n = 36 acrocentric chromosomes. NORs and the major ribosomal genes were located in the subtelomeric region of chromosome pair 6. Hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes and interstitially in 5 chromosome pairs. C-banding showed constitutive heterochromatin at the centromeres of all chromosomes, as well as clear pericentromeric and light telomeric C-bands in several chromosome pairs. These results highlight some chromosomal markers which can be useful to identify species-specific diagnostic characters, although they may not accurately reflect the phylogenetic relationships among the taxa. In addition, C-banding revealed the presence of a heteromorphic ZW sex chromosome pair, where W is smaller than Z and almost completely heterochromatic. This finding sheds light on sex chromosome evolution in the genus Iberolacerta and suggests that further comparative cytogenetic analyses are needed to understand the processes underlying the origin, differentiation and plasticity of sex chromosome systems in lacertid lizards. © 2013 S. Karger AG, Basel.

Ferns: the missing link in shoot evolution and development.

PubMed

Plackett, Andrew R G; Di Stilio, Verónica S; Langdale, Jane A

2015-01-01

Shoot development in land plants is a remarkably complex process that gives rise to an extreme diversity of forms. Our current understanding of shoot developmental mechanisms comes almost entirely from studies of angiosperms (flowering plants), the most recently diverged plant lineage. Shoot development in angiosperms is based around a layered multicellular apical meristem that produces lateral organs and/or secondary meristems from populations of founder cells at its periphery. In contrast, non-seed plant shoots develop from either single apical initials or from a small population of morphologically distinct apical cells. Although developmental and molecular information is becoming available for non-flowering plants, such as the model moss Physcomitrella patens, making valid comparisons between highly divergent lineages is extremely challenging. As sister group to the seed plants, the monilophytes (ferns and relatives) represent an excellent phylogenetic midpoint of comparison for unlocking the evolution of shoot developmental mechanisms, and recent technical advances have finally made transgenic analysis possible in the emerging model fern Ceratopteris richardii. This review compares and contrasts our current understanding of shoot development in different land plant lineages with the aim of highlighting the potential role that the fern C. richardii could play in shedding light on the evolution of underlying genetic regulatory mechanisms.

Opinion formation in time-varying social networks: The case of the naming game

NASA Astrophysics Data System (ADS)

Maity, Suman Kalyan; Manoj, T. Venkat; Mukherjee, Animesh

2012-09-01

We study the dynamics of the naming game as an opinion formation model on time-varying social networks. This agent-based model captures the essential features of the agreement dynamics by means of a memory-based negotiation process. Our study focuses on the impact of time-varying properties of the social network of the agents on the naming game dynamics. In particular, we perform a computational exploration of this model using simulations on top of real networks. We investigate the outcomes of the dynamics on two different types of time-varying data: (1) the networks vary on a day-to-day basis and (2) the networks vary within very short intervals of time (20 sec). In the first case, we find that networks with strong community structure hinder the system from reaching global agreement; the evolution of the naming game in these networks maintains clusters of coexisting opinions indefinitely leading to metastability. In the second case, we investigate the evolution of the naming game in perfect synchronization with the time evolution of the underlying social network shedding new light on the traditional emergent properties of the game that differ largely from what has been reported in the existing literature.

Accounting for rate variation among lineages in comparative demographic analyses.

PubMed

Hope, Andrew G; Ho, Simon Y W; Malaney, Jason L; Cook, Joseph A; Talbot, Sandra L

2014-09-01

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana.

PubMed

Tong, Janette; Dolezal, Pavel; Selkrig, Joel; Crawford, Simon; Simpson, Alastair G B; Noinaj, Nicholas; Buchanan, Susan K; Gabriel, Kipros; Lithgow, Trevor

2011-05-01

The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway. Reclinomonas americana is a unicellular eukaryote with the most gene-rich mitochondrial genome known, and the large collection of membrane proteins encoded on the mitochondrial genome of R. americana includes a bacterial-type SecY protein transporter. Analysis of expressed sequence tags shows R. americana also has components of a mitochondrial protein translocase or "translocase in the inner mitochondrial membrane complex." Along with several other membrane proteins encoded on the mitochondrial genome Cox11, an assembly factor for cytochrome c oxidase retains sequence features suggesting that it is assembled by the SecY complex in R. americana. Despite this, protein import studies show that the RaCox11 protein is suited for import into mitochondria and functional complementation if the gene is transferred into the nucleus of yeast. Reclinomonas americana provides direct evidence that bacterial protein transport pathways were retained, alongside the evolving mitochondrial protein import machinery, shedding new light on the process of mitochondrial evolution.

Two-Fold Anisotropy Governs Morphological Evolution and Stress Generation in Sodiated Black Phosphorus for Sodium Ion Batteries.

PubMed

Chen, Tianwu; Zhao, Peng; Guo, Xu; Zhang, Sulin

2017-04-12

Phosphorus represents a promising anode material for sodium ion batteries owing to its extremely high theoretical capacity. Recent in situ transmission electron microscopy studies evidenced anisotropic swelling in sodiated black phosphorus, which may find an origin from the two intrinsic anisotropic properties inherent to the layered structure of black phosphorus: sodium diffusional directionality and insertion strain anisotropy. To understand the morphological evolution and stress generation in sodiated black phosphorus, we develop a chemo-mechanical model by incorporating the intrinsic anisotropic properties into the large elasto-plastic deformation. Our modeling results reveal that the apparent morphological evolution in sodiated black phosphorus is critically controlled by the coupled effect of the two intrinsic anisotropic properties. In particular, sodium diffusional directionality generates sharp interphases along the [010] and [001] directions, which constrain anisotropic development of the insertion strain. The coupled effect renders distinctive stress-generation and fracture mechanisms when sodiation starts from different crystal facets. In addition to providing a powerful modeling framework for sodiation and lithiation of layered structures, our findings shed significant light on the sodiation-induced chemo-mechanical degradation of black phosphorus as a promising anode for the next-generation sodium ion batteries.

Comparative phylogeography of oceanic archipelagos: Hotspots for inferences of evolutionary process

PubMed Central

Shaw, Kerry L.; Gillespie, Rosemary G.

2016-01-01

Remote island archipelagos offer superb opportunities to study the evolution of community assembly because of their relatively young and simple communities where speciation contributes to the origin and evolution of community structure. There is great potential for common phylogeographic patterns among remote archipelagos that originate through hotspot volcanism, particularly when the islands formed are spatially isolated and linearly arranged. The progression rule is characterized by a phylogeographic concordance between island age and lineage age in a species radiation. Progression is most likely to arise when a species radiation begins on an older island before the emergence of younger islands of a hotspot archipelago. In the simplest form of progression, colonization of younger islands as they emerge and offer appropriate habitat, is coincident with cladogenesis. In this paper, we review recent discoveries of the progression rule on seven hotspot archipelagos. We then discuss advantages that progression offers to the study of community assembly, and insights that community dynamics may offer toward understanding the evolution of progression. We describe results from two compelling cases of progression where the mosaic genome may offer insights into contrasting demographic histories that shed light on mechanisms of speciation and progression on remote archipelagos. PMID:27432948

Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game

PubMed Central

Sasaki, Tatsuya; Okada, Isamu

2015-01-01

It is well known that in contrast to the Prisoner’s Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness. PMID:25868940

Cheating is evolutionarily assimilated with cooperation in the continuous snowdrift game.

PubMed

Sasaki, Tatsuya; Okada, Isamu

2015-05-01

It is well known that in contrast to the Prisoner's Dilemma, the snowdrift game can lead to a stable coexistence of cooperators and cheaters. Recent theoretical evidence on the snowdrift game suggests that gradual evolution for individuals choosing to contribute in continuous degrees can result in the social diversification to a 100% contribution and 0% contribution through so-called evolutionary branching. Until now, however, game-theoretical studies have shed little light on the evolutionary dynamics and consequences of the loss of diversity in strategy. Here, we analyze continuous snowdrift games with quadratic payoff functions in dimorphic populations. Subsequently, conditions are clarified under which gradual evolution can lead a population consisting of those with 100% contribution and those with 0% contribution to merge into one species with an intermediate contribution level. The key finding is that the continuous snowdrift game is more likely to lead to assimilation of different cooperation levels rather than maintenance of diversity. Importantly, this implies that allowing the gradual evolution of cooperative behavior can facilitate social inequity aversion in joint ventures that otherwise could cause conflicts that are based on commonly accepted notions of fairness. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Qualitative psychotherapy research: the journey so far and future directions.

PubMed

Levitt, Heidi M

2015-03-01

This article documents the evolution of qualitative psychotherapy research over the past 3 decades. Clients' and therapists' accounts of their experiences in psychotherapy provide a window into the psychotherapy relationship and its mechanisms of change. A sizable body of literature has been generated that uses qualitative methods to collect and analyze these accounts and to shed light on the psychotherapy process. It notes changes in the field such as growing numbers of dissertations and publications using qualitative methods as well as a strengthening emphasis on qualitative research within graduate education and research funding bodies. Future recommendations include developing principles for practice from qualitative methods and conducting qualitative meta-analyses. Other recommendations include forming journal review policies that support the publication of qualitative research and that focus on coherence in adapting methods to meet research goals, in light of a study's characteristics and epistemological framework, rather than focusing on sets of procedures. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

Autonomous Onboard Science Data Analysis for Comet Missions

NASA Technical Reports Server (NTRS)

Thompson, David R.; Tran, Daniel Q.; McLaren, David; Chien, Steve A.; Bergman, Larry; Castano, Rebecca; Doyle, Richard; Estlin, Tara; Lenda, Matthew

2012-01-01

Coming years will bring several comet rendezvous missions. The Rosetta spacecraft arrives at Comet 67P/Churyumov-Gerasimenko in 2014. Subsequent rendezvous might include a mission such as the proposed Comet Hopper with multiple surface landings, as well as Comet Nucleus Sample Return (CNSR) and Coma Rendezvous and Sample Return (CRSR). These encounters will begin to shed light on a population that, despite several previous flybys, remains mysterious and poorly understood. Scientists still have little direct knowledge of interactions between the nucleus and coma, their variation across different comets or their evolution over time. Activity may change on short timescales so it is challenging to characterize with scripted data acquisition. Here we investigate automatic onboard image analysis that could act faster than round-trip light time to capture unexpected outbursts and plume activity. We describe one edge-based method for detect comet nuclei and plumes, and test the approach on an existing catalog of comet images. Finally, we quantify benefits to specific measurement objectives by simulating a basic plume monitoring campaign.

Galaxy evolution in groups. NGC 3447/NGC 3447A: the odd couple in LGG 225

NASA Astrophysics Data System (ADS)

Mazzei, P.; Marino, A.; Rampazzo, R.; Plana, H.; Rosado, M.; Arias, L.

2018-02-01

Context. Local Group (LG) analogs (LGAs) are galaxy associations dominated by a few bright spirals reminiscent of the LG. The NGC 3447/NGC 3447A system is a member of the LGG 225 group, a nearby LGA. This system is considered a physical pair composed of an intermediate-luminosity late-type spiral, NGC 3447 itself, and an irregular companion, NGC 3447A, linked by a faint, short filament of matter. A ring-like structure in the NGC 3447 outskirts has been emphasised by Galaxy Evolution Explorer (GALEX) observations. Aims: This work aims to contribute to the study of galaxy evolution in low-density environments, a favourable habitat to highly effective encounters, shedding light on the evolution of the NGC 3447/NGC 3447A system. Methods: We performed a multi-λ analysis of the surface photometry of this system to derive its spectral energy distribution and structural properties using ultraviolet (UV), Swift UVOT, and optical Sloan Digital Sky Survey (SDSS) images complemented with available far-IR observations. We also characterised the velocity field of the pair using two-dimensional Hα kinematical observations of the system obtained with PUMA Fabry-Perot interferometer at the 2.1 m telescope of San Pedro Mártir (Mexico). All these data are used to constrain smooth particle hydrodynamic simulations with chemo-photometric implementation to shed light on the evolution of this system. Results: The luminosity profiles, from UV to optical wavelengths, are all consistent with the presence of a disc extending and including NGC 3447A. The overall velocity field does not emphasise any significant rotation pattern, rather a small velocity gradient between NGC 3447 and NGC 3447A. Our simulation, detached from a large grid explored to best-fit the global properties of the system, suggests that this arises from an encounter between two halos of equal mass. Conclusions: NGC 3447 and NGC 3447A belong to the same halo, NGC 3447A being a substructure of the same disk including NGC 3447. The halo gravitational instability, enhanced by the encounter, fuels a long-lived instability in this dark-matter-dominated disk, driving the observed morphology. The NGC 3447/NGC 3447A system may warn of a new class of "false pairs" and the potential danger of a misunderstanding of such objects in pair surveys that could produce a severe underestimate of the total mass of a system. The reduced images and datacubes are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/610/A8

7. Outhouse and shed, view west northwest, south and east ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. Outhouse and shed, view west northwest, south and east sides - Ram Island Light Station, Ram Island, south of Ocean Point & just north of Fisherman Island, marking south side of Fisherman Island Passage, Ocean Point, Lincoln County, ME

7. Shed and keeper' house with helicopter pad in foreground, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

7. Shed and keeper' house with helicopter pad in foreground, view east, southwest and northwest sides - Goat Island Light Station, Goat Island, next to entrance to Cape Porpoise Harbor, just south of Trott Island, Cape Porpoise, York County, ME

Shedding Light on Learning.

ERIC Educational Resources Information Center

Graves, Ben E.

1985-01-01

Summarizes findings of an Alberta light/color study that looked at mood, noise levels, IQ test scores, blood pressure, and absences under fluorescent or full-spectrum light in two color schemes in four elementary schools with 700 students. (MLF)

National Security And Institutional Pathologies: A Path Dependent Analysis Of U.S. Interventions In Iran, Guatemala, Cuba, And Iraq

DTIC Science & Technology

2016-09-01

The period of investigation for the expanded case study centers on the Eisenhower administration, but also addresses factors that occurred immediately...Understanding how institutional path dependent factors converged in each of these cases may shed light on how to prevent such foreign policy missteps in the...converged in each of these cases may shed light on how to prevent such foreign policy missteps in the future. vi THIS PAGE INTENTIONALLY LEFT BLANK

PHAROS: Shedding Light on the Near-Earth Asteroid Apophis

NASA Technical Reports Server (NTRS)

Sharma, Jonathan; Lafleur, Jarret; Barron, Kreston; Townley, Jonathan; Shah, Nilesh; Apa, Jillian

2007-01-01

The Pharos mission to asteroid Apophis provides the first major opportunity to enhance orbital state and scientific knowledge of the most threatening Earth-crossing asteroid that has ever been tracked. Pharos aims to accomplish concrete and feasible orbit determination and scientific objectives while achieving balance among mission cost, nsk,and schedule. Similar to its ancient Egyptian namesake, Pharos acts as a beacon shedding light not only on the physical characteristics of Apophis, but also on its state as it travels through the solar system.

Shedding Some Light.

ERIC Educational Resources Information Center

Whitney, Tim

1998-01-01

Discusses the basics of designing natural and artificial light in an indoor athletic facility. Also examines individual lighting requirements of typical rooms such as weight and fitness rooms, aerobics and multipurpose rooms, gymnasiums, field houses, pools, and racquetball and squash courts. (GR)

The phenomenon of dynamic stall. [vortex shedding phenomenon on oscillating airfoils

NASA Technical Reports Server (NTRS)

Mccroskey, W. J.

1981-01-01

The general features of dynamic stall on oscillating airfoils are explained in terms of the vortex shedding phenomenon, and the important differences between static stall, light dynamic stall, and deep stall are described. An overview of experimentation and prediction techniques is given.

Retinal transcriptome sequencing sheds light on the adaptation to nocturnal and diurnal lifestyles in raptors.

PubMed

Wu, Yonghua; Hadly, Elizabeth A; Teng, Wenjia; Hao, Yuyang; Liang, Wei; Liu, Yu; Wang, Haitao

2016-09-20

Owls (Strigiformes) represent a fascinating group of birds that are the ecological night-time counterparts to diurnal raptors (Accipitriformes). The nocturnality of owls, unusual within birds, has favored an exceptional visual system that is highly tuned for hunting at night, yet the molecular basis for this adaptation is lacking. Here, using a comparative evolutionary analysis of 120 vision genes obtained by retinal transcriptome sequencing, we found strong positive selection for low-light vision genes in owls, which contributes to their remarkable nocturnal vision. Not surprisingly, we detected gene loss of the violet/ultraviolet-sensitive opsin (SWS1) in all owls we studied, but two other color vision genes, the red-sensitive LWS and the blue-sensitive SWS2, were found to be under strong positive selection, which may be linked to the spectral tunings of these genes toward maximizing photon absorption in crepuscular conditions. We also detected the only other positively selected genes associated with motion detection in falcons and positively selected genes associated with bright-light vision and eye protection in other diurnal raptors (Accipitriformes). Our results suggest the adaptive evolution of vision genes reflect differentiated activity time and distinct hunting behaviors.

Initial sequence and comparative analysis of the cat genome

PubMed Central

Pontius, Joan U.; Mullikin, James C.; Smith, Douglas R.; Lindblad-Toh, Kerstin; Gnerre, Sante; Clamp, Michele; Chang, Jean; Stephens, Robert; Neelam, Beena; Volfovsky, Natalia; Schäffer, Alejandro A.; Agarwala, Richa; Narfström, Kristina; Murphy, William J.; Giger, Urs; Roca, Alfred L.; Antunes, Agostinho; Menotti-Raymond, Marilyn; Yuhki, Naoya; Pecon-Slattery, Jill; Johnson, Warren E.; Bourque, Guillaume; Tesler, Glenn; O’Brien, Stephen J.

2007-01-01

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence. PMID:17975172

Retinal transcriptome sequencing sheds light on the adaptation to nocturnal and diurnal lifestyles in raptors

PubMed Central

Wu, Yonghua; Hadly, Elizabeth A.; Teng, Wenjia; Hao, Yuyang; Liang, Wei; Liu, Yu; Wang, Haitao

2016-01-01

Owls (Strigiformes) represent a fascinating group of birds that are the ecological night-time counterparts to diurnal raptors (Accipitriformes). The nocturnality of owls, unusual within birds, has favored an exceptional visual system that is highly tuned for hunting at night, yet the molecular basis for this adaptation is lacking. Here, using a comparative evolutionary analysis of 120 vision genes obtained by retinal transcriptome sequencing, we found strong positive selection for low-light vision genes in owls, which contributes to their remarkable nocturnal vision. Not surprisingly, we detected gene loss of the violet/ultraviolet-sensitive opsin (SWS1) in all owls we studied, but two other color vision genes, the red-sensitive LWS and the blue-sensitive SWS2, were found to be under strong positive selection, which may be linked to the spectral tunings of these genes toward maximizing photon absorption in crepuscular conditions. We also detected the only other positively selected genes associated with motion detection in falcons and positively selected genes associated with bright-light vision and eye protection in other diurnal raptors (Accipitriformes). Our results suggest the adaptive evolution of vision genes reflect differentiated activity time and distinct hunting behaviors. PMID:27645106

Sequence Determines Degree of Knottedness in a Coarse-Grained Protein Model

NASA Astrophysics Data System (ADS)

Wüst, Thomas; Reith, Daniel; Virnau, Peter

2015-01-01

Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar lattice protein model. By employing large-scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.

Wind Generated Rogue Waves in an Annular Wave Flume.

PubMed

Toffoli, A; Proment, D; Salman, H; Monbaliu, J; Frascoli, F; Dafilis, M; Stramignoni, E; Forza, R; Manfrin, M; Onorato, M

2017-04-07

We investigate experimentally the statistical properties of a wind-generated wave field and the spontaneous formation of rogue waves in an annular flume. Unlike many experiments on rogue waves where waves are mechanically generated, here the wave field is forced naturally by wind as it is in the ocean. What is unique about the present experiment is that the annular geometry of the tank makes waves propagating circularly in an unlimited-fetch condition. Within this peculiar framework, we discuss the temporal evolution of the statistical properties of the surface elevation. We show that rogue waves and heavy-tail statistics may develop naturally during the growth of the waves just before the wave height reaches a stationary condition. Our results shed new light on the formation of rogue waves in a natural environment.

Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine

PubMed Central

Kumar, Avishek; Butler, Brandon M.; Kumar, Sudhir; Ozkan, S. Banu

2016-01-01

Summary Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. PMID:26684487

Poincaré recurrences of DNA sequences

NASA Astrophysics Data System (ADS)

Frahm, K. M.; Shepelyansky, D. L.

2012-01-01

We analyze the statistical properties of Poincaré recurrences of Homo sapiens, mammalian, and other DNA sequences taken from the Ensembl Genome data base with up to 15 billion base pairs. We show that the probability of Poincaré recurrences decays in an algebraic way with the Poincaré exponent β≈4 even if the oscillatory dependence is well pronounced. The correlations between recurrences decay with an exponent ν≈0.6 that leads to an anomalous superdiffusive walk. However, for Homo sapiens sequences, with the largest available statistics, the diffusion coefficient converges to a finite value on distances larger than one million base pairs. We argue that the approach based on Poncaré recurrences determines new proximity features between different species and sheds a new light on their evolution history.

Intermittent Lagrangian velocities and accelerations in three-dimensional porous medium flow.

PubMed

Holzner, M; Morales, V L; Willmann, M; Dentz, M

2015-07-01

Intermittency of Lagrangian velocity and acceleration is a key to understanding transport in complex systems ranging from fluid turbulence to flow in porous media. High-resolution optical particle tracking in a three-dimensional (3D) porous medium provides detailed 3D information on Lagrangian velocities and accelerations. We find sharp transitions close to pore throats, and low flow variability in the pore bodies, which gives rise to stretched exponential Lagrangian velocity and acceleration distributions characterized by a sharp peak at low velocity, superlinear evolution of particle dispersion, and double-peak behavior in the propagators. The velocity distribution is quantified in terms of pore geometry and flow connectivity, which forms the basis for a continuous-time random-walk model that sheds light on the observed Lagrangian flow and transport behaviors.

Molecular Regulation of Lumen Morphogenesis Review

PubMed Central

Datta, Anirban; Bryant, David M.; Mostov, Keith E.

2013-01-01

The asymmetric polarization of cells allows specialized functions to be performed at discrete subcellular locales. Spatiotemporal coordination of polarization between groups of cells allowed the evolution of metazoa. For instance, coordinated apical-basal polarization of epithelial and endothelial cells allows transport of nutrients and metabolites across cell barriers and tissue microenvironments. The defining feature of such tissues is the presence of a central, interconnected luminal network. Although tubular networks are present in seemingly different organ systems, such as the kidney, lung, and blood vessels, common underlying principles govern their formation. Recent studies using in vivo and in vitro models of lumen formation have shed new light on the molecular networks regulating this fundamental process. We here discuss progress in understanding common design principles underpinning de novo lumen formation and expansion. PMID:21300279

More than just orphans: are taxonomically-restricted genes important in evolution?

PubMed

Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

2009-09-01

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

Gout in Duke Federico of Montefeltro (1422-1482): a new pearl of the Italian Renaissance.

PubMed

Fornaciari, Antonio; Giuffra, Valentina; Armocida, Emanuele; Caramella, Davide; Rühli, Frank J; Galassi, Francesco Maria

2018-01-01

The article examines the truthfulness of historical accounts claiming that Renaissance Duke Federico of Montefeltro (1422-1482) suffered from gout. By direct paleopathological assessment of the skeletal remains and by the philological investigation of historical and documental sources, primarily a 1461 handwritten letter by the Duke himself to his personal physician, a description of the symptoms and Renaissance therapy is offered and a final diagnosis of gout is formulated. The Duke's handwritten letter offers a rare testimony of ancient clinical self-diagnostics and Renaissance living-experience of gout. Moreover, the article also shows how an alliance between historical, documental and paleopathological methods can greatly increase the precision of retrospective diagnoses, thus helping to shed clearer light onto the antiquity and evolution of diseases.

A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopoda.

PubMed

Villegente, Matthieu; Marmey, Philippe; Job, Claudette; Galland, Marc; Cueff, Gwendal; Godin, Béatrice; Rajjou, Loïc; Balliau, Thierry; Zivy, Michel; Fogliani, Bruno; Sarramegna-Burtet, Valérie; Job, Dominique

2017-07-28

Desiccation tolerance allows plant seeds to remain viable in a dry state for years and even centuries. To reveal potential evolutionary processes of this trait, we have conducted a shotgun proteomic analysis of isolated embryo and endosperm from mature seeds of Amborella trichopoda , an understory shrub endemic to New Caledonia that is considered to be the basal extant angiosperm. The present analysis led to the characterization of 415 and 69 proteins from the isolated embryo and endosperm tissues, respectively. The role of these proteins is discussed in terms of protein evolution and physiological properties of the rudimentary, underdeveloped, Amborella embryos, notably considering that the acquisition of desiccation tolerance corresponds to the final developmental stage of mature seeds possessing large embryos.

A Combination of Histological, Physiological, and Proteomic Approaches Shed Light on Seed Desiccation Tolerance of the Basal Angiosperm Amborella trichopoda

PubMed Central

Villegente, Matthieu; Marmey, Philippe; Job, Claudette; Galland, Marc; Cueff, Gwendal; Godin, Béatrice; Rajjou, Loïc; Balliau, Thierry; Zivy, Michel; Sarramegna-Burtet, Valérie; Job, Dominique

2017-01-01

Desiccation tolerance allows plant seeds to remain viable in a dry state for years and even centuries. To reveal potential evolutionary processes of this trait, we have conducted a shotgun proteomic analysis of isolated embryo and endosperm from mature seeds of Amborella trichopoda, an understory shrub endemic to New Caledonia that is considered to be the basal extant angiosperm. The present analysis led to the characterization of 415 and 69 proteins from the isolated embryo and endosperm tissues, respectively. The role of these proteins is discussed in terms of protein evolution and physiological properties of the rudimentary, underdeveloped, Amborella embryos, notably considering that the acquisition of desiccation tolerance corresponds to the final developmental stage of mature seeds possessing large embryos. PMID:28788068

Planet Formation in Binary Star Systems

NASA Astrophysics Data System (ADS)

Martin, Rebecca

About half of observed exoplanets are estimated to be in binary systems. Understanding planet formation and evolution in binaries is therefore essential for explaining observed exoplanet properties. Recently, we discovered that a highly misaligned circumstellar disk in a binary system can undergo global Kozai-Lidov (KL) oscillations of the disk inclination and eccentricity. These oscillations likely have a significant impact on the formation and orbital evolution of planets in binary star systems. Planet formation by core accretion cannot operate during KL oscillations of the disk. First, we propose to consider the process of disk mass transfer between the binary members. Secondly, we will investigate the possibility of planet formation by disk fragmentation. Disk self gravity can weaken or suppress the oscillations during the early disk evolution when the disk mass is relatively high for a narrow range of parameters. Thirdly, we will investigate the evolution of a planet whose orbit is initially aligned with respect to the disk, but misaligned with respect to the orbit of the binary. We will study how these processes relate to observations of star-spin and planet orbit misalignment and to observations of planets that appear to be undergoing KL oscillations. Finally, we will analyze the evolution of misaligned multi-planet systems. This theoretical work will involve a combination of analytic and numerical techniques. The aim of this research is to shed some light on the formation of planets in binary star systems and to contribute to NASA's goal of understanding of the origins of exoplanetary systems.

The Apostasia genome and the evolution of orchids.

PubMed

Zhang, Guo-Qiang; Liu, Ke-Wei; Li, Zhen; Lohaus, Rolf; Hsiao, Yu-Yun; Niu, Shan-Ce; Wang, Jie-Yu; Lin, Yao-Cheng; Xu, Qing; Chen, Li-Jun; Yoshida, Kouki; Fujiwara, Sumire; Wang, Zhi-Wen; Zhang, Yong-Qiang; Mitsuda, Nobutaka; Wang, Meina; Liu, Guo-Hui; Pecoraro, Lorenzo; Huang, Hui-Xia; Xiao, Xin-Ju; Lin, Min; Wu, Xin-Yi; Wu, Wan-Lin; Chen, You-Yi; Chang, Song-Bin; Sakamoto, Shingo; Ohme-Takagi, Masaru; Yagi, Masafumi; Zeng, Si-Jin; Shen, Ching-Yu; Yeh, Chuan-Ming; Luo, Yi-Bo; Tsai, Wen-Chieh; Van de Peer, Yves; Liu, Zhong-Jian

2017-09-21

Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.

Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence.

PubMed

Clerc, Melanie; Ebert, Dieter; Hall, Matthew D

2015-04-07

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Sensory exploitation and cultural transmission: the late emergence of iconic representations in human evolution.

PubMed

Verpooten, Jan; Nelissen, Mark

2010-09-01

Iconic representations (i.e., figurative imagery and realistic art) only started to appear consistently some 45,000 years ago, although humans have been anatomically modern since 200,000-160,000 years ago. What explains this? Some authors have suggested a neurocognitive change took place, leading to a creative explosion, although this has been contested. Here, we examine the hypothesis that demographic changes caused cultural "cumulative adaptive evolution" and as such the emergence of modern symbolic behavior. This approach usefully explains the evolution of utilitarian skills and tools, and the creation of symbols to identify groups. However, it does not equally effectively explain the evolution of behaviors that may not be directly adaptive, such as the production of iconic representations like figurines and rock art. In order to shed light on their emergence, we propose to combine the above-mentioned cultural hypothesis with the concept of sensory exploitation. The concept essentially states that behavioral traits (in this case iconic art production) which exploit pre-existing sensory sensitivities will evolve if not hindered by costs (i.e., natural selection). In this view, iconic art traditions are evolved by piggy-backing on cumulative adaptive evolution. Since it is to date uncertain whether art has served any adaptive function in human evolution, parsimony demands paying more attention to the primary and a functional mechanism of sensory exploitation as opposed to mechanisms of models based exclusively on secondary benefits (such as Miller's, for instance, in which art is proposed to evolve as a sexual display of fitness).

Probing Novel Microstructural Evolution Mechanisms in Aluminum Alloys Using 4D Nanoscale Characterization

DOE PAGES

Kaira, C. Shashank; De Andrade, V.; Singh, Sudhanshu S.; ...

2017-09-14

Dispersions of nanoscale precipitates in metallic alloys have been known to play a key role in strengthening, by increasing their strain hardenability and providing resistance to deformation. Although these phenomena have been extensively investigated in the last century, the traditional approaches employed in the past have not rendered an authoritative microstructural understanding in such materials. The effect of the precipitates’ inherent complex morphology and their 3D spatial distribution on evolution and deformation behavior have often been precluded. This study reports, for the first time, implementation of synchrotron-based hard X-ray nanotomography in Al–Cu alloys to measure kinetics of different nanoscale phasesmore » in 3D, and reveals insights behind some of the observed novel phase transformation reactions. The experimental results of the present study reconcile with coarsening models from the Lifshitz–Slyozov–Wagner theory to an unprecedented extent, thereby establishing a new paradigm for thermodynamic analysis of precipitate assemblies. Lastly, this study sheds light on the possibilities for establishing new theories for dislocation–particle interactions, based on the limitations of using the Orowan equation in estimating precipitation strengthening.« less

Alloplastic temporomandibular joint replacement systems: a systematic review of their history.

PubMed

De Meurechy, N; Mommaerts, M Y

2018-06-01

This systematic review provides an overview of the historical evolution of the prosthetic temporomandibular joint and addresses the challenges and complications faced by engineers and surgeons, in an effort to shed light on why only a few systems remain available. A better understanding of the history of temporomandibular joint prostheses might also provide insights into the origin of the negative public opinion of the prosthesis, which is based on outdated information. A computerized search using the PubMed Central, ScienceDirect, Wiley Online, Ovid, and Cochrane Library databases was performed following the PRISMA guidelines. Out of 7122 articles identified, 41 met the inclusion criteria for this systematic review. Although several historical reviews have been published previously, none has covered such an extensive time period or has described all designs. Furthermore, besides providing a historical overview, this review discusses the rationale behind the evolution in design and biomaterials, which have largely contributed to the outcomes of the prosthetic systems. Copyright © 2018 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

A Cross-disciplinary Framework for the Description of Contextually Mediated Change

NASA Astrophysics Data System (ADS)

Gabora, Liane; Aerts, Diederik

We present a mathematical framework (referred to as Context-driven Actualization of Potential, or CAP) for describing how entities change over time under the influence of a context. The approach facilitates comparison of change of state of entities studied in different disciplines. Processes are seen to differ according to the degree of nondeterminism, and the degree to which they are sensitive to, internalize, and depend upon a particular context. Our analysis suggests that the dynamical evolution of a quantum entity described by the Schrödinger equation is not fundamentally different from change provoked by a measurement often referred to as collapse but a limiting case, with only one way to collapse. The biological transition to coded replication is seen as a means of preserving structure in the face of context, and sexual replication as a means of increasing potentiality thus enhancing diversity through interaction with context. The framework sheds light on concepts like selection and fitness, reveals how exceptional Darwinian evolution is as a means of 'change of state', and clarifies in what sense culture (and the creative process underlying it) are Darwinian.

Probing Novel Microstructural Evolution Mechanisms in Aluminum Alloys Using 4D Nanoscale Characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaira, C. Shashank; De Andrade, V.; Singh, Sudhanshu S.

Dispersions of nanoscale precipitates in metallic alloys have been known to play a key role in strengthening, by increasing their strain hardenability and providing resistance to deformation. Although these phenomena have been extensively investigated in the last century, the traditional approaches employed in the past have not rendered an authoritative microstructural understanding in such materials. The effect of the precipitates’ inherent complex morphology and their 3D spatial distribution on evolution and deformation behavior have often been precluded. This study reports, for the first time, implementation of synchrotron-based hard X-ray nanotomography in Al–Cu alloys to measure kinetics of different nanoscale phasesmore » in 3D, and reveals insights behind some of the observed novel phase transformation reactions. The experimental results of the present study reconcile with coarsening models from the Lifshitz–Slyozov–Wagner theory to an unprecedented extent, thereby establishing a new paradigm for thermodynamic analysis of precipitate assemblies. Lastly, this study sheds light on the possibilities for establishing new theories for dislocation–particle interactions, based on the limitations of using the Orowan equation in estimating precipitation strengthening.« less

How the initial level of visibility and limited resource affect the evolution of cooperation

NASA Astrophysics Data System (ADS)

Han, Dun; Li, Dandan; Sun, Mei

2016-06-01

This work sheds important light on how the initial level of visibility and limited resource might affect the evolution of the players’ strategies under different network structure. We perform the prisoner’s dilemma game in the lattice network and the scale-free network, the simulation results indicate that the average density of death in lattice network decreases with the increases of the initial proportion of visibility. However, the contrary phenomenon is observed in the scale-free network. Further results reflect that the individuals’ payoff in lattice network is significantly larger than the one in the scale-free network. In the lattice network, the visibility individuals could earn much more than the invisibility one. However, the difference is not apparent in the scale-free network. We also find that a high Successful-Defection-Payoff (SDB) and a rich natural environment have relatively larger deleterious cooperation effects. A high SDB is beneficial to raising the level of visibility in the heterogeneous network, however, that has adverse visibility consequences in homogeneous network. Our result reveals that players are more likely to cooperate voluntarily under homogeneous network structure.

Examples of equilibrium and non-equilibrium behavior in evolutionary systems

NASA Astrophysics Data System (ADS)

Soulier, Arne

With this thesis, we want to shed some light into the darkness of our understanding of simply defined statistical mechanics systems and the surprisingly complex dynamical behavior they exhibit. We will do so by presenting in turn one equilibrium and then one non-equilibrium system with evolutionary dynamics. In part 1, we will present the seceder-model, a newly developed system that cannot equilibrate. We will then study several properties of the system and obtain an idea of the richness of the dynamics of the seceder model, which is particular impressive given the minimal amount of modeling necessary in its setup. In part 2, we will present extensions to the directed polymer in random media problem on a hypercube and its connection to the Eigen model of evolution. Our main interest will be the influence of time-dependent and time-independent changes in the fitness landscape viewed by an evolving population. This part contains the equilibrium dynamics. The stochastic models and the topic of evolution and non-equilibrium in general will allow us to point out similarities to the various lines of thought in game theory.

Form, function and environments of the early angiosperms: merging extant phylogeny and ecophysiology with fossils.

PubMed

Feild, Taylor S; Arens, Nan Crystal

2005-05-01

The flowering plants--angiosperms--appeared during the Early Cretaceous period and within 10-30 Myr dominated the species composition of many floras worldwide. Emerging insights into the phylogenetics of development and discoveries of early angiosperm fossils are shedding increased light on the patterns and processes of early angiosperm evolution. However, we also need to integrate ecology, in particular how early angiosperms established a roothold in pre-existing Mesozoic plant communities. These events were critical in guiding subsequent waves of angiosperm diversification during the Aptian-Albian. Previous pictures of the early flowering plant ecology have been diverse, ranging from large tropical rainforest trees, weedy drought-adapted and colonizing shrubs, disturbance- and sun-loving rhizomatous herbs, and, more recently, aquatic herbs; however, none of these images were tethered to a robust hypothesis of angiosperm phylogeny. Here, we synthesize our current understanding of early angiosperm ecology, focusing on patterns of functional ecology, by merging recent molecular phylogenetic studies and functional studies on extant 'basal angiosperms' with the picture of early angiosperm evolution drawn by the fossil record.

Elastic Anomaly and Polyamorphic Transition in (La, Ce)-based Bulk Metallic Glass under Pressure

DOE PAGES

Qi, Xintong; Zou, Yongtao; Wang, Xuebing; ...

2017-04-07

In this paper, we discovered that in association with the polyamorphism of La 32Ce 32Al 16Ni 5Cu 15 bulk metallic glass, the acoustic velocities, measured up to 12.3 GPa using ultrasonic interferometry, exhibit velocity minima at 1.8 GPa for P wave and 3.2 GPa for S wave. The low and high density amorphous states are distinguished by their distinct pressure derivatives of the bulk and shear moduli. The elasticity, permanent densification, and polyamorphic transition are interpreted by the topological rearrangement of solute-centered clusters in medium-range order (MRO) mediated by the 4f electron delocalization of Ce under pressure. The precisely measuredmore » acoustic wave travel times which were used to derive the velocities and densities provided unprecedented data to document the evolution of the bulk and shear elastic moduli associated with a polyamorphic transition in La 32Ce 32Al 16Ni 5Cu 15 bulk metallic glass and can shed new light on the mechanisms of polyamorphism and structural evolution in metallic glasses under pressure.« less

The Difference Se Makes: A Bio-Inspired Dppf-Supported Nickel Selenolate Complex Boosts Dihydrogen Evolution with High Oxygen Tolerance.

PubMed

Pan, Zhong-Hua; Tao, Yun-Wen; He, Quan-Feng; Wu, Qiao-Yu; Cheng, Li-Ping; Wei, Zhan-Hua; Wu, Ji-Huai; Lin, Jin-Qing; Sun, Di; Zhang, Qi-Chun; Tian, Dan; Luo, Geng-Geng

2018-06-12

Inspired by the metal active sites of [NiFeSe]-hydrogenases, a dppf-supported nickel(II) selenolate complex (dppf=1,1'-bis(diphenylphosphino)ferrocene) shows high catalytic activity for electrochemical proton reduction with a remarkable enzyme-like H 2 evolution turnover frequency (TOF) of 7838 s -1 under an Ar atmosphere, which markedly surpasses the activity of a dppf-supported nickel(II) thiolate analogue with a low TOF of 600 s -1 . A combined study of electrochemical experiments and DFT calculations shed light on the catalytic process, suggesting that selenium atom as a bio-inspired proton relay plays a key role in proton exchange and enhancing catalytic activity of H 2 production. For the first time, this type of Ni selenolate-containing electrocatalyst displays a high degree of O 2 and H 2 tolerance. Our results should encourage the development of the design of highly efficient oxygen-tolerant Ni selenolate molecular catalysts. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris).

PubMed

Zhang, Wenping; Zhang, Zhihe; Shen, Fujun; Hou, Rong; Lv, Xiaoping; Yue, Bisong

2006-08-01

Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.

Oxygen radicals shaping evolution: why fatty acid catabolism leads to peroxisomes while neurons do without it: FADH₂/NADH flux ratios determining mitochondrial radical formation were crucial for the eukaryotic invention of peroxisomes and catabolic tissue differentiation.

PubMed

Speijer, Dave

2011-02-01

Oxygen radical formation in mitochondria is a highly important, but incompletely understood, attribute of eukaryotic cells. I propose a kinetic model in which the ratio between electrons entering the respiratory chain via FADH₂ or NADH is a major determinant in radical formation. During the breakdown of glucose, this ratio is low; during fatty acid breakdown, this ratio is much higher. The longer the fatty acid, the higher the ratio and the higher the level of radical formation. This means that very long chain fatty acids should be broken down without generation of FADH₂ for mitochondria. This is accomplished in peroxisomes, thus explaining their role and evolution. The model explains many recent observations regarding radical formation by the respiratory chain. It also sheds light on the reasons for the lack of neuronal fatty acid (beta-) oxidation and for beneficial aspects of unsaturated fatty acids. Last but not least, it has very important implications for all models describing eukaryotic origins.

Evolution of High-Temperature Superconductivity from a Low-T_{c} Phase Tuned by Carrier Concentration in FeSe Thin Flakes.

PubMed

Lei, B; Cui, J H; Xiang, Z J; Shang, C; Wang, N Z; Ye, G J; Luo, X G; Wu, T; Sun, Z; Chen, X H

2016-02-19

We report the evolution of superconductivity in an FeSe thin flake with systematically regulated carrier concentrations by the liquid-gating technique. With electron doping tuned by the gate voltage, high-temperature superconductivity with an onset at 48 K can be achieved in an FeSe thin flake with T_{c} less than 10 K. This is the first time such high temperature superconductivity in FeSe is achieved without either an epitaxial interface or external pressure, and it definitely proves that the simple electron-doping process is able to induce high-temperature superconductivity with T_{c}^{onset} as high as 48 K in bulk FeSe. Intriguingly, our data also indicate that the superconductivity is suddenly changed from a low-T_{c} phase to a high-T_{c} phase with a Lifshitz transition at a certain carrier concentration. These results help to build a unified picture to understand the high-temperature superconductivity among all FeSe-derived superconductors and shed light on the further pursuit of a higher T_{c} in these materials.

Neighbourhood reaction in the evolution of cooperation.

PubMed

Yang, Guoli; Zhang, Weiming; Xiu, Baoxin

2015-05-07

Combining evolutionary games with adaptive networks, an entangled model between strategy evolution and structure adaptation is researched in this paper. We consider a large population of cooperators C and defectors D placed in the networks, playing the repeated prisoner׳s dilemma (PD) games. Because of the conflicts between social welfare and personal rationality, both strategy and structure are allowed to change. In this paper, the dynamics of strategy originates form the partner imitation based on social learning and the dynamics of structure is driven by the active linking and neighbourhood reaction. Notably, the neighbourhood reaction is investigated considering the changes of interfaces between cooperators and defectors, where some neighbours may get away from the interface once the focal agent changes to different strategy. A rich landscape is demonstrated by changing various embedding parameters, which sheds light upon that reacting promptly to the shifted neighbour will promote the prevalence of cooperation. Our model encapsulates the dynamics of strategy, reaction and structure into the evolutionary games, which manifests some intriguing principles in the competition between two groups in natural populations, artificial systems and even human societies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Competition between Homophily and Information Entropy Maximization in Social Networks

PubMed Central

Zhao, Jichang; Liang, Xiao; Xu, Ke

2015-01-01

In social networks, it is conventionally thought that two individuals with more overlapped friends tend to establish a new friendship, which could be stated as homophily breeding new connections. While the recent hypothesis of maximum information entropy is presented as the possible origin of effective navigation in small-world networks. We find there exists a competition between information entropy maximization and homophily in local structure through both theoretical and experimental analysis. This competition suggests that a newly built relationship between two individuals with more common friends would lead to less information entropy gain for them. We demonstrate that in the evolution of the social network, both of the two assumptions coexist. The rule of maximum information entropy produces weak ties in the network, while the law of homophily makes the network highly clustered locally and the individuals would obtain strong and trust ties. A toy model is also presented to demonstrate the competition and evaluate the roles of different rules in the evolution of real networks. Our findings could shed light on the social network modeling from a new perspective. PMID:26334994

Mutual influences between the main olfactory and vomeronasal systems in development and evolution

PubMed Central

Suárez, Rodrigo; García-González, Diego; de Castro, Fernando

2012-01-01

The sense of smell plays a crucial role in the sensory world of animals. Two chemosensory systems have been traditionally thought to play-independent roles in mammalian olfaction. According to this, the main olfactory system (MOS) specializes in the detection of environmental odorants, while the vomeronasal system (VNS) senses pheromones and semiochemicals produced by individuals of the same or different species. Although both systems differ in their anatomy and function, recent evidence suggests they act synergistically in the perception of scents. These interactions include similar responses to some ligands, overlap of telencephalic connections and mutual influences in the regulation of olfactory-guided behavior. In the present work, we propose the idea that the relationships between systems observed at the organismic level result from a constant interaction during development and reflects a common history of ecological adaptations in evolution. We review the literature to illustrate examples of developmental and evolutionary processes that evidence these interactions and propose that future research integrating both systems may shed new light on the mechanisms of olfaction. PMID:23269914

Analysis of the African coelacanth genome sheds light on tetrapod evolution

PubMed Central

Amemiya, Chris T.; Alföldi, Jessica; Lee, Alison P.; Fan, Shaohua; Philippe, Hervé; MacCallum, Iain; Braasch, Ingo; Manousaki, Tereza; Schneider, Igor; Rohner, Nicolas; Organ, Chris; Chalopin, Domitille; Smith, Jeramiah J.; Robinson, Mark; Dorrington, Rosemary A.; Gerdol, Marco; Aken, Bronwen; Biscotti, Maria Assunta; Barucca, Marco; Baurain, Denis; Berlin, Aaron M.; Blatch, Gregory L.; Buonocore, Francesco; Burmester, Thorsten; Campbell, Michael S.; Canapa, Adriana; Cannon, John P.; Christoffels, Alan; De Moro, Gianluca; Edkins, Adrienne L.; Fan, Lin; Fausto, Anna Maria; Feiner, Nathalie; Forconi, Mariko; Gamieldien, Junaid; Gnerre, Sante; Gnirke, Andreas; Goldstone, Jared V.; Haerty, Wilfried; Hahn, Mark E.; Hesse, Uljana; Hoffmann, Steve; Johnson, Jeremy; Karchner, Sibel I.; Kuraku, Shigehiro; Lara, Marcia; Levin, Joshua Z.; Litman, Gary W.; Mauceli, Evan; Miyake, Tsutomu; Mueller, M. Gail; Nelson, David R.; Nitsche, Anne; Olmo, Ettore; Ota, Tatsuya; Pallavicini, Alberto; Panji, Sumir; Picone, Barbara; Ponting, Chris P.; Prohaska, Sonja J.; Przybylski, Dariusz; Saha, Nil Ratan; Ravi, Vydianathan; Ribeiro, Filipe J.; Sauka-Spengler, Tatjana; Scapigliati, Giuseppe; Searle, Stephen M. J.; Sharpe, Ted; Simakov, Oleg; Stadler, Peter F.; Stegeman, John J.; Sumiyama, Kenta; Tabbaa, Diana; Tafer, Hakim; Turner-Maier, Jason; van Heusden, Peter; White, Simon; Williams, Louise; Yandell, Mark; Brinkmann, Henner; Volff, Jean-Nicolas; Tabin, Clifford J.; Shubin, Neil; Schartl, Manfred; Jaffe, David; Postlethwait, John H.; Venkatesh, Byrappa; Di Palma, Federica; Lander, Eric S.; Meyer, Axel; Lindblad-Toh, Kerstin

2013-01-01

It was a zoological sensation when a living specimen of the coelacanth was first discovered in 1938, as this lineage of lobe-finned fish was thought to have gone extinct 70 million years ago. The modern coelacanth looks remarkably similar to many of its ancient relatives, and its evolutionary proximity to our own fish ancestors provides a glimpse of the fish that first walked on land. Here we report the genome sequence of the African coelacanth, Latimeria chalumnae. Through a phylogenomic analysis, we conclude that the lungfish, and not the coelacanth, is the closest living relative of tetrapods. Coelacanth protein-coding genes are significantly more slowly evolving than those of tetrapods, unlike other genomic features . Analyses of changes in genes and regulatory elements during the vertebrate adaptation to land highlight genes involved in immunity, nitrogen excretion and the development of fins, tail, ear, eye, brain, and olfaction. Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues demonstrate the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution. PMID:23598338

Experimental investigation of door dynamic opening caused by impinging shock wave

NASA Astrophysics Data System (ADS)

Biamino, L.; Jourdan, G.; Mariani, C.; Igra, O.; Massol, A.; Houas, L.

2011-02-01

To prevent damage caused by accidental overpressure inside a closed duct (e.g. jet engine) safety valves are introduced. The present study experimentally investigates the dynamic opening of such valves by employing a door at the end of a shock tube driven section. The door is hung on an axis and is free to rotate, thereby opening the tube. The evolved flow and wave pattern due to a collision of an incident shock wave with the door, causing the door opening, is studied by employing a high speed schlieren system and recording pressures at different places inside the tube as well as on the rotating door. Analyzing this data sheds light on the air flow evolution and the behavior of the opening door. In the present work, emphasis is given to understanding the complex, unsteady flow developed behind the transmitted shock wave as it diffracts over the opening door. It is shown that both the door inertia and the shock wave strength influence the opening dynamic evolution, but not in the proportions that might be expected.

The evolution of menstruation: A new model for genetic assimilation

PubMed Central

Emera, D.; Romero, R.; Wagner, G.

2012-01-01

Why do humans menstruate while most mammals do not? Here, we present our answer to this long-debated question, arguing that (i) menstruation occurs as a mechanistic consequence of hormone-induced differentiation of the endometrium (referred to as spontaneous decidualization, or SD); (ii) SD evolved because of maternal-fetal conflict; and (iii) SD evolved by genetic assimilation of the decidualization reaction, which is induced by the fetus in non-menstruating species. The idea that menstruation occurs as a consequence of SD has been proposed in the past, but here we present a novel hypothesis on how SD evolved. We argue that decidualization became genetically stabilized in menstruating lineages, allowing females to prepare for pregnancy without any signal from the fetus. We present three models for the evolution of SD by genetic assimilation, based on recent advances in our understanding of the mechanisms of endometrial differentiation and implantation. Testing these models will ultimately shed light on the evolutionary significance of menstruation, as well as on the etiology of human reproductive disorders like endometriosis and recurrent pregnancy loss. PMID:22057551

Pressure-induced phase transformation, reversible amorphization, and anomalous visible light response in organolead bromide perovskite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Yonggang; Lu, Xujie; Yang, Wenge

Hydrostatic pressure, as an alternative of chemical pressure to tune the crystal structure and physical properties, is a significant technique for novel function material design and fundamental research. In this article, we report the phase stability and visible light response of the organolead bromide perovskite, CH 3NH 3PbBr 3 (MAPbBr 3), under hydrostatic pressure up to 34 GPa at room temperature: Two phase transformations below 2 GPa (from Pm3¯m to Im3¯, then to Pnma) and a reversible amorphization starting from about 2 GPa were observed, which could be attributed to the tilting of PbBr 6 octahedra and destroying of long-rangemore » ordering of MA cations, respectively. The visible light response of MAPbBr 3 to pressure was studied by in situ photoluminescence, electric resistance, photocurrent measurements and first-principle simulations. The anomalous band gap evolution during compression with red-shift followed by blue-shift is explained by the competition between compression effect and pressure-induced amorphization. Along with the amorphization process accomplished around 25 GPa, the resistance increased by 5 orders of magnitude while the system still maintains its semiconductor characteristics and considerable response to the visible light irradiation. Lastly, our results not only show that hydrostatic pressure may provide an applicable tool for the organohalide perovskites based photovoltaic device functioning as switcher or controller, but also shed light on the exploration of more amorphous organometal composites as potential light absorber.« less

Pressure-Induced Phase Transformation, Reversible Amorphization, and Anomalous Visible Light Response in Organolead Bromide Perovskite.

PubMed

Wang, Yonggang; Lü, Xujie; Yang, Wenge; Wen, Ting; Yang, Liuxiang; Ren, Xiangting; Wang, Lin; Lin, Zheshuai; Zhao, Yusheng

2015-09-02

Hydrostatic pressure, as an alternative of chemical pressure to tune the crystal structure and physical properties, is a significant technique for novel function material design and fundamental research. In this article, we report the phase stability and visible light response of the organolead bromide perovskite, CH3NH3PbBr3 (MAPbBr3), under hydrostatic pressure up to 34 GPa at room temperature. Two phase transformations below 2 GPa (from Pm3̅m to Im3̅, then to Pnma) and a reversible amorphization starting from about 2 GPa were observed, which could be attributed to the tilting of PbBr6 octahedra and destroying of long-range ordering of MA cations, respectively. The visible light response of MAPbBr3 to pressure was studied by in situ photoluminescence, electric resistance, photocurrent measurements and first-principle simulations. The anomalous band gap evolution during compression with red-shift followed by blue-shift is explained by the competition between compression effect and pressure-induced amorphization. Along with the amorphization process accomplished around 25 GPa, the resistance increased by 5 orders of magnitude while the system still maintains its semiconductor characteristics and considerable response to the visible light irradiation. Our results not only show that hydrostatic pressure may provide an applicable tool for the organohalide perovskites based photovoltaic device functioning as switcher or controller, but also shed light on the exploration of more amorphous organometal composites as potential light absorber.

Pressure-induced phase transformation, reversible amorphization, and anomalous visible light response in organolead bromide perovskite

DOE PAGES

Wang, Yonggang; Lu, Xujie; Yang, Wenge; ...

2015-08-18

Hydrostatic pressure, as an alternative of chemical pressure to tune the crystal structure and physical properties, is a significant technique for novel function material design and fundamental research. In this article, we report the phase stability and visible light response of the organolead bromide perovskite, CH 3NH 3PbBr 3 (MAPbBr 3), under hydrostatic pressure up to 34 GPa at room temperature: Two phase transformations below 2 GPa (from Pm3¯m to Im3¯, then to Pnma) and a reversible amorphization starting from about 2 GPa were observed, which could be attributed to the tilting of PbBr 6 octahedra and destroying of long-rangemore » ordering of MA cations, respectively. The visible light response of MAPbBr 3 to pressure was studied by in situ photoluminescence, electric resistance, photocurrent measurements and first-principle simulations. The anomalous band gap evolution during compression with red-shift followed by blue-shift is explained by the competition between compression effect and pressure-induced amorphization. Along with the amorphization process accomplished around 25 GPa, the resistance increased by 5 orders of magnitude while the system still maintains its semiconductor characteristics and considerable response to the visible light irradiation. Lastly, our results not only show that hydrostatic pressure may provide an applicable tool for the organohalide perovskites based photovoltaic device functioning as switcher or controller, but also shed light on the exploration of more amorphous organometal composites as potential light absorber.« less

Anatomy of a Shooting Star

NASA Technical Reports Server (NTRS)

2007-01-01

[figure removed for brevity, see original site] Annotated Version

A close-up view of a star racing through space faster than a speeding bullet can be seen in this image from NASA's Galaxy Evolution Explorer. The star, called Mira (pronounced My-rah), is traveling at 130 kilometers per second, or 291,000 miles per hour. As it hurls along, it sheds material that will be recycled into new stars, planets and possibly even life.

In this image, Mira is moving from left to right. It is visible as the pinkish dot in the bulb shape at right. The yellow dot below is a foreground star. Mira is traveling so fast that it's creating a bow shock, or build-up of gas, in front of it, as can be seen here at right.

Like a boat traveling through water, a bow shock forms ahead of the star in the direction of its motion. Gas in the bow shock is heated and then mixes with the cool hydrogen gas in the wind that is blowing off Mira. This heated hydrogen gas then flows around behind the star, forming a wake.

Why is the wake of material glowing? When the hydrogen gas is heated, it transitions into a higher-energy state, which then loses energy by emitting ultraviolet light - a process called fluorescence. The Galaxy Evolution Explorer has special instruments that can detect this ultraviolet light.

A similar fluorescence process is responsible for the Northern Lights -- a glowing, green aurora that can be seen from northern latitudes. However, in that case nitrogen and oxygen gas are fluorescing with visible light.

Streams and a loop of material can also be seen coming off Mira. Astronomers are still investigating what these streams are, but they suspect that they are denser parts of Mira's wind perhaps flowing out of the star's poles.

This image consists of data captured by both the far- and near-ultraviolet detectors on the Galaxy Evolution Explorer between November 18 and December 15, 2006. It has a total exposure time of about 3 hours.

Ferns: the missing link in shoot evolution and development

PubMed Central

Plackett, Andrew R. G.; Di Stilio, Verónica S.; Langdale, Jane A.

2015-01-01

Shoot development in land plants is a remarkably complex process that gives rise to an extreme diversity of forms. Our current understanding of shoot developmental mechanisms comes almost entirely from studies of angiosperms (flowering plants), the most recently diverged plant lineage. Shoot development in angiosperms is based around a layered multicellular apical meristem that produces lateral organs and/or secondary meristems from populations of founder cells at its periphery. In contrast, non-seed plant shoots develop from either single apical initials or from a small population of morphologically distinct apical cells. Although developmental and molecular information is becoming available for non-flowering plants, such as the model moss Physcomitrella patens, making valid comparisons between highly divergent lineages is extremely challenging. As sister group to the seed plants, the monilophytes (ferns and relatives) represent an excellent phylogenetic midpoint of comparison for unlocking the evolution of shoot developmental mechanisms, and recent technical advances have finally made transgenic analysis possible in the emerging model fern Ceratopteris richardii. This review compares and contrasts our current understanding of shoot development in different land plant lineages with the aim of highlighting the potential role that the fern C. richardii could play in shedding light on the evolution of underlying genetic regulatory mechanisms. PMID:26594222

Gonadotropic and Physiological Functions of Juvenile Hormone in Bumblebee (Bombus terrestris) Workers

PubMed Central

Shpigler, Hagai; Amsalem, Etya; Huang, Zachary Y.; Cohen, Mira; Siegel, Adam J.; Hefetz, Abraham; Bloch, Guy

2014-01-01

The evolution of advanced sociality in bees is associated with apparent modifications in juvenile hormone (JH) signaling. By contrast to most insects in which JH is a gonadotropin regulating female fertility, in the highly eusocial honey bee (Apis mellifera) JH has lost its gonadotrophic function in adult females, and instead regulates age-related division of labor among worker bees. In order to shed light on the evolution of JH signaling in bees we performed allatectomy and replacement therapies to manipulate JH levels in workers of the "primitively eusocial" bumblebee Bombus terrestris. Allatectomized worker bees showed remarkable reduction in ovarian development, egg laying, Vitellogenin and Krüppel homolog 1 fat body transcript levels, hemolymph Vitellogenin protein abundance, wax secretion, and egg-cell construction. These effects were reverted, at least partially, by treating allatectomized bees with JH-III, the natural JH of bees. Allatectomy also affected the amount of ester component in Dufour's gland secretion, which is thought to convey a social signal relating to worker fertility. These findings provide a strong support for the hypothesis that in contrast to honey bees, JH is a gonadotropin in bumblebees and lend credence to the hypothesis that the evolution of advanced eusociality in honey bees was associated with major modifications in JH signaling. PMID:24959888

A New Snake Skull from the Paleocene of Bolivia Sheds Light on the Evolution of Macrostomatans

PubMed Central

Scanferla, Agustín; Zaher, Hussam; Novas, Fernando E.; de Muizon, Christian; Céspedes, Ricardo

2013-01-01

Macrostomatan snakes, one of the most diverse extant clades of squamates, display an impressive arsenal of cranial features to consume a vast array of preys. In the absence of indisputable fossil representatives of this clade with well-preserved skulls, the mode and timing of these extraordinary morphological novelties remain obscure. Here, we report the discovery of Kataria anisodonta n. gen. n. sp., a macrostomatan snake recovered in the Early Palaeocene locality of Tiupampa, Bolivia. The holotype consists of a partial, minute skull that exhibits a combination of booid and caenophidian characters, being the presence of an anisodont dentition and diastema in the maxilla the most distinctive trait. Phylogenetic analysis places Kataria basal to the Caenophidia+Tropidophiidae, and represents along with bolyeriids a distinctive clade of derived macrostomatans. The discovery of Kataria highlights the morphological diversity in the maxilla among derived macrostomatans, demonstrating the relevance of maxillary transformations in the evolution of this clade. Kataria represents the oldest macrostomatan skull recovered, revealing that the diversification of macrostomatans was well under way in early Tertiary times. This record also reinforces the importance of Gondwanan territories in the history of snakes, not only in the origin of the entire group but also in the evolution of ingroup clades. PMID:23469206

Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments.

PubMed

Sankar, Sathish; Upadhyay, Mohita; Ramamurthy, Mageshbabu; Vadivel, Kumaran; Sagadevan, Kalaiselvan; Nandagopal, Balaji; Vivekanandan, Perumal; Sridharan, Gopalan

2015-01-01

Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments. A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments. All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution. There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.

PubMed

Cheng, Feixiong; Liu, Chuang; Lin, Chen-Ching; Zhao, Junfei; Jia, Peilin; Li, Wen-Hsiung; Zhao, Zhongming

2015-09-01

Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation) alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1). The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics.

Environmental influences on the evolution of body size in Ammonoids

NASA Astrophysics Data System (ADS)

Hines, S.; Khong, C.; Pelagio, M.; Seixas, G.; Payne, J.

2012-12-01

A major debate in evolutionary biology and paleobiology focuses on the relative importance of ecological interactions between species versus changes in the physical environment in governing large-scale evolutionary patterns. Body size is among the most important traits of any organism, and so identifying the factors that influence size evolution can shed light on both the causes and consequences of many major evolutionary trends. However, the extent to which body size evolution over time can be explained by changes in the physical versus ecological context remains unknown. In this study, we examined body size evolution in ammonoids, an extinct group of marine cephalopods. We collected a representative body size for each genus from illustrated specimens in the Treatise on Invertebrate Paleontology. We then examined relative statistical support for six models of size evolution: random walk, directional trend, stasis, and environmental control by oxygen availability, temperature, and global sea level. No model is unambiguously supported over all others. Unbiased random walk was the best supported model (34%) and environmental control by atmospheric pO2 was the second best supported model (22%). Stasis received the least support (<<1%). Because we find pO2 to be inversely correlated with ammonoid size, we suspect that the observed correlation does not reflect a direct causal relationship. Overall, our results suggest that no single, simple model can be used to characterize the evolution of ammonoid size over the entire history of this clade. We speculate that controls on ammonoid size evolution varied through geological time, both due to long-term shifts in the ecological structure of marine communities and short-term perturbations associated with major extinction events.

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

PubMed Central

Lin, Chen-Ching; Zhao, Junfei; Jia, Peilin; Li, Wen-Hsiung; Zhao, Zhongming

2015-01-01

Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation) alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1). The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics. PMID:26352260

Modelling Marek's Disease Virus (MDV) infection: parameter estimates for mortality rate and infectiousness

PubMed Central

2011-01-01

Background Marek's disease virus (MDV) is an economically important oncogenic herpesvirus of poultry. Since the 1960s, increasingly virulent strains have caused continued poultry industry production losses worldwide. To understand the mechanisms of this virulence evolution and to evaluate the epidemiological consequences of putative control strategies, it is imperative to understand how virulence is defined and how this correlates with host mortality and infectiousness during MDV infection. We present a mathematical approach to quantify key epidemiological parameters. Host lifespan, virus latent periods and host viral shedding rates were estimated for unvaccinated and vaccinated birds, infected with one of three MDV strains. The strains had previously been pathotyped to assign virulence scores according to pathogenicity of strains in hosts. Results Our analyses show that strains of higher virulence have a higher viral shedding rate, and more rapidly kill hosts. Vaccination enhances host life expectancy but does not significantly reduce the shedding rate of the virus. While the primary latent period of the virus does not vary with challenge strain nor vaccine treatment of host, the time until the maximum viral shedding rate is increased with vaccination. Conclusions Our approach provides the tools necessary for a formal analysis of the evolution of virulence in MDV, and potentially simpler and cheaper approaches to comparing the virulence of MDV strains. PMID:22078942

Fabrication of efficient TiO2-RGO heterojunction composites for hydrogen generation via water-splitting: Comparison between RGO, Au and Pt reduction sites

NASA Astrophysics Data System (ADS)

El-Bery, Haitham M.; Matsushita, Yoshihisa; Abdel-moneim, Ahmed

2017-11-01

A facile one-step synthesis approach of M/TiO2/RGO (M = Au or Pt) ternary composite by hydrothermal treatment for hydrogen generation via water-splitting was investigated. Photocurrent response measurements revealed that TiO2 (P25) nanoparticles anchored on the reduced graphene oxide (RGO) surface exhibited a p-n heterojunction interface by changing the photocurrent direction with the applied bias from reverse to forward potential. H2 evolution rate of TiO2/RGO (5 wt.%) composite was substantially enhanced by 12-fold in comparison to bare TiO2 under simulated solar light irradiation. Cyclic volatmmetry measurements manifested, that the optimized 0.3 wt.% of platinum metal loaded on TiO2/RGO composite was the most active catalytic reduction sites for hydrogen generation reaction with an initial hydrogen rate of 670 μmol h-1. This study sheds the light on the tunable semiconductor type of TiO2/RGO composite fabricated by solution mixing pathway and its merits to improve the photocatalytic activity.

Adaptive Covariation between the Coat and Movement Proteins of Prunus Necrotic Ringspot Virus

PubMed Central

Codoñer, Francisco M.; Fares, Mario A.; Elena, Santiago F.

2006-01-01

The relative functional and/or structural importance of different amino acid sites in a protein can be assessed by evaluating the selective constraints to which they have been subjected during the course of evolution. Here we explore such constraints at the linear and three-dimensional levels for the movement protein (MP) and coat protein (CP) encoded by RNA 3 of prunus necrotic ringspot ilarvirus (PNRSV). By a maximum-parsimony approach, the nucleotide sequences from 46 isolates of PNRSV varying in symptomatology, host tree, and geographic origin have been analyzed and sites under different selective pressures have been identified in both proteins. We have also performed covariation analyses to explore whether changes in certain amino acid sites condition subsequent variation in other sites of the same protein or the other protein. These covariation analyses shed light on which particular amino acids should be involved in the physical and functional interaction between MP and CP. Finally, we discuss these findings in the light of what is already known about the implication of certain sites and domains in structure and protein-protein and RNA-protein interactions. PMID:16731922

Adaptive covariation between the coat and movement proteins of prunus necrotic ringspot virus.

PubMed

Codoñer, Francisco M; Fares, Mario A; Elena, Santiago F

2006-06-01

The relative functional and/or structural importance of different amino acid sites in a protein can be assessed by evaluating the selective constraints to which they have been subjected during the course of evolution. Here we explore such constraints at the linear and three-dimensional levels for the movement protein (MP) and coat protein (CP) encoded by RNA 3 of prunus necrotic ringspot ilarvirus (PNRSV). By a maximum-parsimony approach, the nucleotide sequences from 46 isolates of PNRSV varying in symptomatology, host tree, and geographic origin have been analyzed and sites under different selective pressures have been identified in both proteins. We have also performed covariation analyses to explore whether changes in certain amino acid sites condition subsequent variation in other sites of the same protein or the other protein. These covariation analyses shed light on which particular amino acids should be involved in the physical and functional interaction between MP and CP. Finally, we discuss these findings in the light of what is already known about the implication of certain sites and domains in structure and protein-protein and RNA-protein interactions.

Molecular and phylogenetic analyses reveal mammalian-like clockwork in the honey bee (Apis mellifera) and shed new light on the molecular evolution of the circadian clock.

PubMed

Rubin, Elad B; Shemesh, Yair; Cohen, Mira; Elgavish, Sharona; Robertson, Hugh M; Bloch, Guy

2006-11-01

The circadian clock of the honey bee is implicated in ecologically relevant complex behaviors. These include time sensing, time-compensated sun-compass navigation, and social behaviors such as coordination of activity, dance language communication, and division of labor. The molecular underpinnings of the bee circadian clock are largely unknown. We show that clock gene structure and expression pattern in the honey bee are more similar to the mouse than to Drosophila. The honey bee genome does not encode an ortholog of Drosophila Timeless (Tim1), has only the mammalian type Cryptochrome (Cry-m), and has a single ortholog for each of the other canonical "clock genes." In foragers that typically have strong circadian rhythms, brain mRNA levels of amCry, but not amTim as in Drosophila, consistently oscillate with strong amplitude and a phase similar to amPeriod (amPer) under both light-dark and constant darkness illumination regimes. In contrast to Drosophila, the honey bee amCYC protein contains a transactivation domain and its brain transcript levels oscillate at virtually an anti-phase to amPer, as it does in the mouse. Phylogenetic analyses indicate that the basal insect lineage had both the mammalian and Drosophila types of Cry and Tim. Our results suggest that during evolution, Drosophila diverged from the ancestral insect clock and specialized in using a set of clock gene orthologs that was lost by both mammals and bees, which in turn converged and specialized in the other set. These findings illustrate a previously unappreciated diversity of insect clockwork and raise critical questions concerning the evolution and functional significance of species-specific variation in molecular clockwork.

Brain scaling in mammalian evolution as a consequence of concerted and mosaic changes in numbers of neurons and average neuronal cell size

PubMed Central

Herculano-Houzel, Suzana; Manger, Paul R.; Kaas, Jon H.

2014-01-01

Enough species have now been subject to systematic quantitative analysis of the relationship between the morphology and cellular composition of their brain that patterns begin to emerge and shed light on the evolutionary path that led to mammalian brain diversity. Based on an analysis of the shared and clade-specific characteristics of 41 modern mammalian species in 6 clades, and in light of the phylogenetic relationships among them, here we propose that ancestral mammal brains were composed and scaled in their cellular composition like modern afrotherian and glire brains: with an addition of neurons that is accompanied by a decrease in neuronal density and very little modification in glial cell density, implying a significant increase in average neuronal cell size in larger brains, and the allocation of approximately 2 neurons in the cerebral cortex and 8 neurons in the cerebellum for every neuron allocated to the rest of brain. We also propose that in some clades the scaling of different brain structures has diverged away from the common ancestral layout through clade-specific (or clade-defining) changes in how average neuronal cell mass relates to numbers of neurons in each structure, and how numbers of neurons are differentially allocated to each structure relative to the number of neurons in the rest of brain. Thus, the evolutionary expansion of mammalian brains has involved both concerted and mosaic patterns of scaling across structures. This is, to our knowledge, the first mechanistic model that explains the generation of brains large and small in mammalian evolution, and it opens up new horizons for seeking the cellular pathways and genes involved in brain evolution. PMID:25157220

In search of late time evolution self-similar scaling laws of Rayleigh-Taylor and Richtmyer-Meshkov hydrodynamic instabilities - recent theorical advance and NIF Discovery-Science experiments

NASA Astrophysics Data System (ADS)

Shvarts, Dov

2017-10-01

Hydrodynamic instabilities, and the mixing that they cause, are of crucial importance in describing many phenomena, from very large scales such as stellar explosions (supernovae) to very small scales, such as inertial confinement fusion (ICF) implosions. Such mixing causes the ejection of stellar core material in supernovae, and impedes attempts at ICF ignition. The Rayleigh-Taylor instability (RTI) occurs at an accelerated interface between two fluids with the lower density accelerating the higher density fluid. The Richtmyer-Meshkov (RM) instability occurs when a shock wave passes an interface between the two fluids of different density. In the RTI, buoyancy causes ``bubbles'' of the light fluid to rise through (penetrate) the denser fluid, while ``spikes'' of the heavy fluid sink through (penetrate) the lighter fluid. With realistic multi-mode initial conditions, in the deep nonlinear regime, the mixing zone width, H, and its internal structure, progress through an inverse cascade of spatial scales, reaching an asymptotic self-similar evolution: hRT =αRT Agt2 for RT and hRM =αRM tθ for RM. While this characteristic behavior has been known for years, the self-similar parameters αRT and θRM and their dependence on dimensionality and density ratio have continued to be intensively studied and a relatively wide distribution of those values have emerged. This talk will describe recent theoretical advances in the description of this turbulent mixing evolution that sheds light on the spread in αRT and θRM. Results of new and specially designed experiments, done by scientists from several laboratories, were performed recently using NIF, the only facility that is powerful enough to reach the self-similar regime, for quantitative testing of this theoretical advance, will be presented.

Systematics of hot giant electric dipole resonance widths

NASA Astrophysics Data System (ADS)

Schiller, A.; Thoennessen, M.; McAlpine, K. M.

2007-05-01

Giant Electric Dipole Resonance (GDR) parameters for γ decay to excited states with finite spin and temperature have been compiled by two of the authors ( nucl-ex/0605004). Over 100 original works have been reviewed and from some 70 of them, more than 300 sets of hot GDR parameters for different isotopes, excitation energies, and spin regions have been extracted. All parameter sets have been brought onto a common footing by calculating the equivalent Lorentzian parameters. Together with a complementary compilation by Samuel S. Dietrich and Barry L. Berman [At. Data Nucl. Data Tables 38, 199-338, (1988)] on ground-state photo-neutron and photo-absorption cross sections and their Lorentzian parameters, it is now possible by means of a comparison of the two data sets to shed light on the evolution of GDR parameters with temperature and spin.

Compilation of giant electric dipole resonances built on excited states

NASA Astrophysics Data System (ADS)

Schiller, A.; Thoennessen, M.

2007-07-01

Giant Electric Dipole Resonance (GDR) parameters for γ decay to excited states with finite spin and temperature are compiled. Over 100 original works have been reviewed and from some 70 of them, about 350 sets of hot GDR parameters for different isotopes, excitation energies, and spin regions have been extracted. All parameter sets have been brought onto a common footing by calculating the equivalent Lorentzian parameters. The current compilation is complementary to an earlier compilation by Samuel S. Dietrich and Barry L. Berman (At. Data Nucl. Data Tables 38 (1988) 199-338) on ground-state photo-neutron and photo-absorption cross sections and their Lorentzian parameters. A comparison of the two may help shed light on the evolution of GDR parameters with temperature and spin. The present compilation is current as of July 2006.

Stability properties of solitary waves for fractional KdV and BBM equations

NASA Astrophysics Data System (ADS)

Angulo Pava, Jaime

2018-03-01

This paper sheds new light on the stability properties of solitary wave solutions associated with Korteweg-de Vries-type models when the dispersion is very low. Using a compact, analytic approach and asymptotic perturbation theory, we establish sufficient conditions for the existence of exponentially growing solutions to the linearized problem and so a criterium of spectral instability of solitary waves is obtained for both models. Moreover, the nonlinear stability and spectral instability of the ground state solutions for both models is obtained for some specific regimen of parameters. Via a Lyapunov strategy and a variational analysis, we obtain the stability of the blow-up of solitary waves for the critical fractional KdV equation. The arguments presented in this investigation show promise for use in the study of the instability of traveling wave solutions of other nonlinear evolution equations.

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.

PubMed

Kumar, Avishek; Butler, Brandon M; Kumar, Sudhir; Ozkan, S Banu

2015-12-01

Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Strange, Expanding World of Animal Hepaciviruses

PubMed Central

Hartlage, Alex S.; Cullen, John M.; Kapoor, Amit

2017-01-01

Hepaciviruses and pegiviruses constitute two closely related sister genera of the family Flaviviridae. In the past five years, the known phylogenetic diversity of the hepacivirus genera has absolutely exploded. What was once an isolated infection in humans (and possibly other primates) has now expanded to include horses, rodents, bats, colobus monkeys, cows, and, most recently, catsharks, shedding new light on the genetic diversity and host range of hepaciviruses. Interestingly, despite the identification of these many animal and primate hepaciviruses, the equine hepaciviruses remain the closest genetic relatives of the human hepaciviruses, providing an intriguing clue to the zoonotic source of hepatitis C virus. This review summarizes the significance of these studies and discusses current thinking about the origin and evolution of the animal hepaciviruses as well as their potential usage as surrogate models for the study of hepatitis C virus. PMID:27741408

Fatigue mechanism verified using photovoltaic properties of Pb(Zr0.52Ti0.48)O3 thin films

NASA Astrophysics Data System (ADS)

Wu, Ming; Li, Wei; Li, Junning; Wang, Shaolan; Li, Yaqi; Peng, Biaolin; Huang, Haitao; Lou, Xiaojie

2017-03-01

The photovoltaic effect and its evolution during electrical fatigue in Pb(Zr0.52Ti0.48)O3 (PZT) thin films have been investigated. It is found that the photovoltaic effect of the as-grown PZT thin film is highly affected by the asymmetric Schottky barriers, which can be tuned by applying an external electric field. During fatigue processes, both open-circuit voltage (Voc) and short-circuit current (Jsc) decrease considerably with the increase of the number of electrical cycles. This phenomenon could be ascribed to the degradation of the interfacial layer between the thin film and the electrode induced by highly energetic charge carriers injected from the electrode during bipolar cycling. Our work sheds light on the physical mechanism of both ferroelectric photovoltaics and polarization fatigue in thin-film ferroelectrics.

Skill complementarity enhances heterophily in collaboration networks

PubMed Central

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Tan, Qun-Zhao; Podobnik, Boris; Zhou, Wei-Xing; Stanley, H. Eugene

2016-01-01

Much empirical evidence shows that individuals usually exhibit significant homophily in social networks. We demonstrate, however, skill complementarity enhances heterophily in the formation of collaboration networks, where people prefer to forge social ties with people who have professions different from their own. We construct a model to quantify the heterophily by assuming that individuals choose collaborators to maximize utility. Using a huge database of online societies, we find evidence of heterophily in collaboration networks. The results of model calibration confirm the presence of heterophily. Both empirical analysis and model calibration show that the heterophilous feature is persistent along the evolution of online societies. Furthermore, the degree of skill complementarity is positively correlated with their production output. Our work sheds new light on the scientific research utility of virtual worlds for studying human behaviors in complex socioeconomic systems. PMID:26743687

The cophylogeny of populations and cultures: reconstructing the evolution of Iranian tribal craft traditions using trees and jungles

PubMed Central

Tehrani, Jamshid J.; Collard, Mark; Shennan, Stephen J.

2010-01-01

Phylogenetic approaches to culture have shed new light on the role played by population dispersals in the spread and diversification of cultural traditions. However, the fact that cultural inheritance is based on separate mechanisms from genetic inheritance means that socially transmitted traditions have the potential to diverge from population histories. Here, we suggest that associations between these two systems can be reconstructed using techniques developed to study cospeciation between hosts and parasites and related problems in biology. Relationships among the latter are patterned by four main processes: co-divergence, intra-host speciation (duplication), intra-host extinction (sorting) and horizontal transfers. We show that patterns of cultural inheritance are structured by analogous processes, and then demonstrate the applicability of the host–parasite model to culture using empirical data on Iranian tribal populations. PMID:21041211

The interaction of light and gravity on the transmission of Echinostoma caproni (Digenea: Echinostomatidae) cercariae to the second intermediate host, Biomphalaria glabrata (Gastropoda: Pulmonata).

PubMed

Platt, Thomas R; Greenlee, Hali; Zelmer, Derek A

2010-04-01

The current experiments were designed to assess the interaction of light and gravity on the transmission of Echinostoma caproni cercariae to the second intermediate host, Biomphalaria glabrata. Transmission chambers were constructed of clear polyvinyl chloride pipe covered with a black sleeve to exclude light. Snails were constrained within the chamber to prevent movement, while permitting the cercariae to swim freely. A trial consisted of 2 infected B. glabrata shedding E. caproni cercariae placed at the center of the chamber with 5 uninfected B. glabrata placed 10 cm above and below the shedding snails as sentinels. Three experiments, consisting of 12 trials each, were conducted under the following lighting conditions, i.e., above and below the transmission chamber, and in complete darkness. In all 3 experiments, the proportion of metacercariae was significantly higher in snails at the top of the chamber. The results suggest that a negative geotaxis is the primary factor in the initial dispersal of E. caproni cercariae. Coupling negative geotaxis and positive phototaxis (light from above) resulted in a significantly higher proportion of metacercariae in sentinel snails at the top of the transmission chamber when corrected for cercarial density. There was no significant difference in the proportion of metacercariae in snails at the top or bottom of the transmission chamber with light at the bottom of the chamber or in complete darkness. Cercariae of E. caproni only respond to light in context, i.e., from above, and ignore the light stimulus when it comes from an unexpected location (bottom of the water column). Significantly greater numbers of cercariae were released from shedding snails when light was present, suggesting that emergence of cercariae from B. glabrata is dependent on light regardless of the position of the light source.

SHEDDING LIGHT ON CORALS HEALTH: INTERACTIONS OF CLIMATE CHANGE AND SOLAR RADIATION WITH BLEACHING

EPA Science Inventory

Coral bleaching and declines in coral reef health in recent years have been attributed in part to processes driven by UV and/or visible light. For coral assemblages, exposure to UV light is often an unavoidable consequence of having access to visible (photosynthetically active) ...

33 CFR 165.810 - Mississippi River, LA-regulated navigation area.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (c) Movement of vessels in vicinity of Algiers Point, New Orleans Harbor: (1) Control lights. When... green lights designated and located as follows: Governor Nicholls Light located on the left descending bank on the wharf shed at the upstream end of Esplanade Avenue Wharf, New Orleans, approximately 94.3...

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

PubMed Central

2011-01-01

Background We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. Results The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Conclusions Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution. PMID:21854559

The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees.

PubMed

Brand, Philipp; Ramírez, Santiago R

2017-08-01

Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ∼80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be driven mostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.

PubMed

Renfree, Marilyn B; Papenfuss, Anthony T; Deakin, Janine E; Lindsay, James; Heider, Thomas; Belov, Katherine; Rens, Willem; Waters, Paul D; Pharo, Elizabeth A; Shaw, Geoff; Wong, Emily S W; Lefèvre, Christophe M; Nicholas, Kevin R; Kuroki, Yoko; Wakefield, Matthew J; Zenger, Kyall R; Wang, Chenwei; Ferguson-Smith, Malcolm; Nicholas, Frank W; Hickford, Danielle; Yu, Hongshi; Short, Kirsty R; Siddle, Hannah V; Frankenberg, Stephen R; Chew, Keng Yih; Menzies, Brandon R; Stringer, Jessica M; Suzuki, Shunsuke; Hore, Timothy A; Delbridge, Margaret L; Patel, Hardip R; Mohammadi, Amir; Schneider, Nanette Y; Hu, Yanqiu; O'Hara, William; Al Nadaf, Shafagh; Wu, Chen; Feng, Zhi-Ping; Cocks, Benjamin G; Wang, Jianghui; Flicek, Paul; Searle, Stephen M J; Fairley, Susan; Beal, Kathryn; Herrero, Javier; Carone, Dawn M; Suzuki, Yutaka; Sugano, Sumio; Toyoda, Atsushi; Sakaki, Yoshiyuki; Kondo, Shinji; Nishida, Yuichiro; Tatsumoto, Shoji; Mandiou, Ion; Hsu, Arthur; McColl, Kaighin A; Lansdell, Benjamin; Weinstock, George; Kuczek, Elizabeth; McGrath, Annette; Wilson, Peter; Men, Artem; Hazar-Rethinam, Mehlika; Hall, Allison; Davis, John; Wood, David; Williams, Sarah; Sundaravadanam, Yogi; Muzny, Donna M; Jhangiani, Shalini N; Lewis, Lora R; Morgan, Margaret B; Okwuonu, Geoffrey O; Ruiz, San Juana; Santibanez, Jireh; Nazareth, Lynne; Cree, Andrew; Fowler, Gerald; Kovar, Christie L; Dinh, Huyen H; Joshi, Vandita; Jing, Chyn; Lara, Fremiet; Thornton, Rebecca; Chen, Lei; Deng, Jixin; Liu, Yue; Shen, Joshua Y; Song, Xing-Zhi; Edson, Janette; Troon, Carmen; Thomas, Daniel; Stephens, Amber; Yapa, Lankesha; Levchenko, Tanya; Gibbs, Richard A; Cooper, Desmond W; Speed, Terence P; Fujiyama, Asao; Graves, Jennifer A M; O'Neill, Rachel J; Pask, Andrew J; Forrest, Susan M; Worley, Kim C

2011-08-29

We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.

Shedding Some Light on Fluorescent Bulbs.

ERIC Educational Resources Information Center

Guilbert, Nicholas R.

1996-01-01

Explores some of the principles behind the working of fluorescent bulbs using a specially prepared fluorescent bulb with the white inner fluorescent coating applied along only half its length. Discusses the spectrum, the bulb plasma, and light production. (JRH)

Bayesian phylogeny of sucrose transporters: ancient origins, differential expansion and convergent evolution in monocots and dicots

PubMed Central

Peng, Duo; Gu, Xi; Xue, Liang-Jiao; Leebens-Mack, James H.; Tsai, Chung-Jui

2014-01-01

Sucrose transporters (SUTs) are essential for the export and efficient movement of sucrose from source leaves to sink organs in plants. The angiosperm SUT family was previously classified into three or four distinct groups, Types I, II (subgroup IIB), and III, with dicot-specific Type I and monocot-specific Type IIB functioning in phloem loading. To shed light on the underlying drivers of SUT evolution, Bayesian phylogenetic inference was undertaken using 41 sequenced plant genomes, including seven basal lineages at key evolutionary junctures. Our analysis supports four phylogenetically and structurally distinct SUT subfamilies, originating from two ancient groups (AG1 and AG2) that diverged early during terrestrial colonization. In both AG1 and AG2, multiple intron acquisition events in the progenitor vascular plant established the gene structures of modern SUTs. Tonoplastic Type III and plasmalemmal Type II represent evolutionarily conserved descendants of AG1 and AG2, respectively. Type I and Type IIB were previously thought to evolve after the dicot-monocot split. We show, however, that divergence of Type I from Type III SUT predated basal angiosperms, likely associated with evolution of vascular cambium and phloem transport. Type I SUT was subsequently lost in monocots along with vascular cambium, and independent evolution of Type IIB coincided with modified monocot vasculature. Both Type I and Type IIB underwent lineage-specific expansion. In multiple unrelated taxa, the newly-derived SUTs exhibit biased expression in reproductive tissues, suggesting a functional link between phloem loading and reproductive fitness. Convergent evolution of Type I and Type IIB for SUT function in phloem loading and reproductive organs supports the idea that differential vascular development in dicots and monocots is a strong driver for SUT family evolution in angiosperms. PMID:25429293

The Evolutionary Dynamics of the Odorant Receptor Gene Family in Corbiculate Bees

PubMed Central

Ramírez, Santiago R.

2017-01-01

Abstract Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ∼80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be driven mostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects. PMID:28854688

Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals.

PubMed

Zhang, Zhigang; Xu, Dongming; Wang, Li; Hao, Junjun; Wang, Jinfeng; Zhou, Xin; Wang, Weiwei; Qiu, Qiang; Huang, Xiaodan; Zhou, Jianwei; Long, Ruijun; Zhao, Fangqing; Shi, Peng

2016-07-25

Studies of genetic adaptation, a central focus of evolutionary biology, most often focus on the host's genome and only rarely on its co-evolved microbiome. The Qinghai-Tibetan Plateau (QTP) offers one of the most extreme environments for the survival of human and other mammalian species. Yaks (Bos grunniens) and Tibetan sheep (T-sheep) (Ovis aries) have adaptations for living in this harsh high-altitude environment, where nomadic Tibetan people keep them primarily for food and livelihood [1]. Adaptive evolution affects energy-metabolism-related genes in a way that helps these ruminants live at high altitude [2, 3]. Herein, we report convergent evolution of rumen microbiomes for energy harvesting persistence in two typical high-altitude ruminants, yaks and T-sheep. Both ruminants yield significantly lower levels of methane and higher yields of volatile fatty acids (VFAs) than their low-altitude relatives, cattle (Bos taurus) and ordinary sheep (Ovis aries). Ultra-deep metagenomic sequencing reveals significant enrichment in VFA-yielding pathways of rumen microbial genes in high-altitude ruminants, whereas methanogenesis pathways show enrichment in the cattle metagenome. Analyses of RNA transcriptomes reveal significant upregulation in 36 genes associated with VFA transport and absorption in the ruminal epithelium of high-altitude ruminants. Our study provides novel insights into the contributions of microbiomes to adaptive evolution in mammals and sheds light on the biological control of greenhouse gas emissions from livestock enteric fermentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

On the capabilities and limitations of high altitude pseudo-satellites

NASA Astrophysics Data System (ADS)

Gonzalo, Jesús; López, Deibi; Domínguez, Diego; García, Adrián; Escapa, Alberto

2018-04-01

The idea of self-sustaining air vehicles that excited engineers in the seventies has nowadays become a reality as proved by several initiatives worldwide. High altitude platforms, or Pseudo-satellites (HAPS), are unmanned vehicles that take advantage of weak stratospheric winds and solar energy to operate without interfering with current commercial aviation and with enough endurance to provide long-term services as satellites do. Target applications are communications, Earth observation, positioning and science among others. This paper reviews the major characteristics of stratospheric flight, where airplanes and airships will compete for best performance. The careful analysis of involved technologies and their trends allow budget models to shed light on the capabilities and limitations of each solution. Aerodynamics and aerostatics, structures and materials, propulsion, energy management, thermal control, flight management and ground infrastructures are the critical elements revisited to assess current status and expected short-term evolutions. Stratospheric airplanes require very light wing loading, which has been demonstrated to be feasible but currently limits their payload mass to few tenths of kilograms. On the other hand, airships need to be large and operationally complex but their potential to hover carrying hundreds of kilograms with reasonable power supply make them true pseudo-satellites with enormous commercial interest. This paper provides useful information on the relative importance of the technology evolutions, as well as on the selection of the proper platform for each application or set of payload requirements. The authors envisage prompt availability of both types of HAPS, aerodynamic and aerostatic, providing unprecedented services.

Mira Soars Through the Sky

NASA Technical Reports Server (NTRS)

2007-01-01

[figure removed for brevity, see original site] [figure removed for brevity, see original site] Figure 1Figure 2

New ultraviolet images from NASA's Galaxy Evolution Explorer shows a speeding star that is leaving an enormous trail of 'seeds' for new solar systems. The star, named Mira (pronounced my-rah) after the latin word for 'wonderful,' is shedding material that will be recycled into new stars, planets and possibly even life as it hurls through our galaxy.

In figure 1, the upper panel shows Mira's full, comet-like tail as seen only in shorter, or 'far' ultraviolet wavelengths, while the lower panel is a combined view showing both far and longer, or 'near' ultraviolet wavelengths. The close-up picture at bottom gives a better look at Mira itself, which appears as a pinkish dot, and is moving from left to right in this view. Shed material appears in light blue. The dots in the picture are stars and distant galaxies. The large blue dot on the left side of the upper panel, and the large yellow dot in the lower panel, are both stars that are closer to us than Mira.

The Galaxy Evolution Explorer discovered the strange tail during part of its routine survey of the entire sky at ultraviolet wavelengths. When astronomers first saw the picture, they were shocked because Mira has been studied for over 400 years yet nothing like this has ever been documented before.

Mira's comet-like tail stretches a startling 13 light-years across the sky. For comparison, the nearest star to our sun, Proxima Centauri, is only about 4 light-years away. Mira's tail also tells a tale of its history -- the material making it up has been slowly blown off over time, with the oldest material at the end of the tail being released about 30,000 years ago (figure 2).

Mira is a highly evolved, 'red giant' star near the end of its life. Technically, it is called an asymptotic giant branch star. It is red in color and bloated; for example, if a red giant were to replace our sun, it would engulf everything out to the orbit of Mars. Our sun will mature into a red giant in about 5 billion years.

Like other red giants, Mira will lose a large fraction of its mass in the form of gas and dust. In fact, Mira ejects the equivalent of the Earth's mass every 10 years. It has released enough material over the past 30,000 years to seed at least 3,000 Earth-sized planets or 9 Jupiter-sized ones.

While most stars travel along together around the disk of our Milky Way, Mira is charging through it. Because Mira is not moving with the 'pack,' it is moving much faster relative to the ambient gas in our section of the Milky Way. It is zipping along at 130 kilometers per second, or 291,000 miles per hour, relative to this gas.

Mira's breakneck speed together with its outflow of material are responsible for its unique glowing tail. Images from the Galaxy Evolution Explorer show a large build-up of gas, or bow shock, in front of the star, similar to water piling up in front of a speeding boat. Scientists now know that hot gas in this bow shock mixes with the cooler, hydrogen gas being shed from Mira, causing it to heat up as it swirls back into a turbulent wake. As the hydrogen gas loses energy, it fluoresces with ultraviolet light, which the Galaxy Evolution Explorer can detect.

Mira, also known as Mira A, is not alone in its travels through space. It has a distant companion star called Mira B that is thought to be the burnt-out, dead core of a star, called a white dwarf. Mira A and B circle around each other slowly, making one orbit about every 500 years. Astronomers believe that Mira B has no effect on Mira's tail.

Mira is also what's called a pulsating variable star. It dims and brightens by a factor of 1,500 every 332 days, and will become bright enough to see with the naked eye in mid-November 2007. Because it was the first variable star with a regular period ever discovered, other stars of this type are often referred to as 'Miras.'

Mira is located 350 light-years from Earth in the constellation Cetus, otherwise known as the whale. Coincidentally, Mira and its 'whale of a tail' can be found in the tail of the whale constellation.

These images were between November 18 and December 15, 2006.

Spectrum Project

NASA Image and Video Library

2017-10-16

Inside the Spectrum prototype unit, organisms in a Petri plate are exposed to blue excitation lighting. The device works by exposing organisms to different colors of fluorescent light while a camera records what's happening with time-lapse photography. Results from the Spectrum project will shed light on which living things are best suited for long-duration flights into deep space.

Spectrum Project

NASA Image and Video Library

2017-10-16

Inside the Spectrum prototype unit, organisms in a Petri plate are exposed to different colors of lighting. The device works by exposing organisms to different colors of fluorescent light while a camera records what's happening with time-lapse photography. Results from the Spectrum project will shed light on which living things are best suited for long-duration flights into deep space.

Stimulus Control: The Sought or Unsought Influence of the Objects We Tend to

ERIC Educational Resources Information Center

Morsella, Ezequiel; Larson, Lindsay R. L.; Zarolia, Pareezad; Bargh, John A.

2011-01-01

Does the mere presence of the things we have tended to influence our actions systematically, in ways that escape our awareness? For example, while entering a tool shed, does perceiving objects that we once tended to (e.g., tools, musical instruments) influence how we then execute a simple action (e.g., flicking the shed's light switch)? Ancient…

UVC Sheds New Light on School Mold Problems.

ERIC Educational Resources Information Center

Freeman, James

2002-01-01

Describes how the LaPorte Independent School District in Texas turned to ultraviolent light devices installed within the HVAC system to combat mold and fungus after conventional approaches failed. Describes the additional benefits of energy savings from the system. (EV)

Quantum trajectories for time-dependent adiabatic master equations

NASA Astrophysics Data System (ADS)

Yip, Ka Wa; Albash, Tameem; Lidar, Daniel A.

2018-02-01

We describe a quantum trajectories technique for the unraveling of the quantum adiabatic master equation in Lindblad form. By evolving a complex state vector of dimension N instead of a complex density matrix of dimension N2, simulations of larger system sizes become feasible. The cost of running many trajectories, which is required to recover the master equation evolution, can be minimized by running the trajectories in parallel, making this method suitable for high performance computing clusters. In general, the trajectories method can provide up to a factor N advantage over directly solving the master equation. In special cases where only the expectation values of certain observables are desired, an advantage of up to a factor N2 is possible. We test the method by demonstrating agreement with direct solution of the quantum adiabatic master equation for 8-qubit quantum annealing examples. We also apply the quantum trajectories method to a 16-qubit example originally introduced to demonstrate the role of tunneling in quantum annealing, which is significantly more time consuming to solve directly using the master equation. The quantum trajectories method provides insight into individual quantum jump trajectories and their statistics, thus shedding light on open system quantum adiabatic evolution beyond the master equation.

Changes in predator community structure shifts the efficacy of two warning signals in Arctiid moths.

PubMed

Nokelainen, Ossi; Valkonen, Janne; Lindstedt, Carita; Mappes, Johanna

2014-05-01

Polymorphism in warning coloration is puzzling because positive frequency-dependent selection by predators is expected to promote monomorphic warning signals in defended prey. We studied predation on the warning-coloured wood tiger moth (Parasemia plantaginis) by using artificial prey resembling white and yellow male colour morphs in five separate populations with different naturally occurring morph frequencies. We tested whether predation favours one of the colour morphs over the other and whether that is influenced either by local, natural colour morph frequencies or predator community composition. We found that yellow specimens were attacked less than white ones regardless of the local frequency of the morphs indicating frequency-independent selection, but predation did depend on predator community composition: yellows suffered less attacks when Paridae were abundant, whereas whites suffered less attacks when Prunellidae were abundant. Our results suggest that spatial heterogeneity in predator community composition can generate a geographical mosaic of selection facilitating the evolution of polymorphic warning signals. This is the first time this mechanism gains experimental support. Altogether, this study sheds light on the evolution of adaptive coloration in heterogeneous environments. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Evolutionary game dynamics of controlled and automatic decision-making

NASA Astrophysics Data System (ADS)

Toupo, Danielle F. P.; Strogatz, Steven H.; Cohen, Jonathan D.; Rand, David G.

2015-07-01

We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model in which agents who make decisions using either automatic or controlled processing compete with each other for survival. Agents using automatic processing act quickly and so are more likely to acquire resources, but agents using controlled processing are better planners and so make more effective use of the resources they have. Using the replicator equation, we characterize the conditions under which automatic or controlled agents dominate, when coexistence is possible and when bistability occurs. We then extend the replicator equation to consider feedback between the state of the population and the environment. Under conditions in which having a greater proportion of controlled agents either enriches the environment or enhances the competitive advantage of automatic agents, we find that limit cycles can occur, leading to persistent oscillations in the population dynamics. Critically, however, these limit cycles only emerge when feedback occurs on a sufficiently long time scale. Our results shed light on the connection between evolution and human cognition and suggest necessary conditions for the rise and fall of rationality.

Local microstructure evolution at shear bands in metallic glasses with nanoscale phase separation

PubMed Central

He, Jie; Kaban, Ivan; Mattern, Norbert; Song, Kaikai; Sun, Baoan; Zhao, Jiuzhou; Kim, Do Hyang; Eckert, Jürgen; Greer, A. Lindsay

2016-01-01

At room temperature, plastic flow of metallic glasses (MGs) is sharply localized in shear bands, which are a key feature of the plastic deformation in MGs. Despite their clear importance and decades of study, the conditions for formation of shear bands, their structural evolution and multiplication mechanism are still under debate. In this work, we investigate the local conditions at shear bands in new phase-separated bulk MGs containing glassy nanospheres and exhibiting exceptional plasticity under compression. It is found that the glassy nanospheres within the shear band dissolve through mechanical mixing driven by the sharp strain localization there, while those nearby in the matrix coarsen by Ostwald ripening due to the increased atomic mobility. The experimental evidence demonstrates that there exists an affected zone around the shear band. This zone may arise from low-strain plastic deformation in the matrix between the bands. These results suggest that measured property changes originate not only from the shear bands themselves, but also from the affected zones in the adjacent matrix. This work sheds light on direct visualization of deformation-related effects, in particular increased atomic mobility, in the region around shear bands. PMID:27181922

Magnetoresistance Behavior of Conducting Filaments in Resistive-Switching NiO with Different Resistance States.

PubMed

Zhao, Diyang; Qiao, Shuang; Luo, Yuxiang; Chen, Aitian; Zhang, Pengfei; Zheng, Ping; Sun, Zhong; Guo, Minghua; Chiang, Fu-Kuo; Wu, Jian; Luo, Jianlin; Li, Jianqi; Kokado, Satoshi; Wang, Yayu; Zhao, Yonggang

2017-03-29

The resistive switching (RS) effect in various materials has attracted much attention due to its interesting physics and potential for applications. NiO is an important system and its RS effect has been generally explained by the formation/rupture of Ni-related conducting filaments. These filaments are unique since they are formed by an electroforming process, so it is interesting to explore their magnetoresistance (MR) behavior, which can also shed light on unsolved issues such as the nature of the filaments and their evolution in the RS process, and this behavior is also important for multifunctional devices. Here, we focus on MR behavior in NiO RS films with different resistance states. Rich and interesting MR behaviors have been observed, including the normal and anomalous anisotropic magnetoresistance and tunneling magnetoresistance, which provide new insights into the nature of the filaments and their evolution in the RS process. First-principles calculation reveals the essential role of oxygen migration into the filaments during the RESET process and can account for the experimental results. Our work provides a new avenue for exploration of the conducting filaments in resistive switching materials and is significant for understanding the mechanism of RS effect and multifunctional devices.

Grooves to tubes: evolution of the venom delivery system in a Late Triassic "reptile"

NASA Astrophysics Data System (ADS)

Mitchell, Jonathan S.; Heckert, Andrew B.; Sues, Hans-Dieter

2010-12-01

Venom delivery systems occur in a wide range of extant and fossil vertebrates and are primarily based on oral adaptations. Teeth range from unmodified (Komodo dragons) to highly specialized fangs similar to hypodermic needles (protero- and solenoglyphous snakes). Developmental biologists have documented evidence for an infolding pathway of fang evolution, where the groove folds over to create the more derived condition. However, the oldest known members of venomous clades retain the same condition as their extant relatives, resulting in no fossil evidence for the transition. Based on a comparison of previously known specimens with newly discovered teeth from North Carolina, we describe a new species of the Late Triassic archosauriform Uatchitodon and provide detailed analyses that provide evidence for both venom conduction and document a complete structural series from shallow grooves to fully enclosed tubular canals. While known only from teeth, Uatchitodon is highly diagnostic in possessing compound serrations and for having two venom canals on each tooth in the dentition. Further, although not a snake, Uatchitodon sheds light on the evolutionary trajectory of venom delivery systems in amniotes and provide solid evidence for venom conduction in archosaur-line diapsids.

Follicular lymphomas and their transformation: Past and current research.

PubMed

Mendez, Miriam; Torrente, Maria; Provencio, Mariano

2017-06-01

Follicular lymphoma (FL) is the second most common type of non-Hodgkin lymphoma (NHL). Histological transformation (HT) refers to the evolution of a clinically indolent NHL to a clinically aggressive one, defined as those lymphomas in which survival is limited to a few months when untreated. Areas covered: HT is associated with rapid progression of lymphadenopathy, infiltration of extranodal sites, development of systemic symptoms, and elevated serum level of lactate dehydrogenase (LDH). It is frequently related to a poor prognosis, and the median survival after transformation is less than 2 years. Transformation to diffuse large B cell lymphoma (DLBCL) in patients with FL occurs at an annual rate of approximately 3% for the first 15 years, after which the risk of HT falls for reasons that remain unclear. Expert commentary: Although it has long been assumed that transformation reflects the emergence of an aggressive subclone of cells from the primary FL, recent studies suggest that FL transformation might also arise by divergent evolution from a more immature common progenitor cell. Studies on genomic changes and DNA sequencing have shed some light onto the process of transformation. Nowadays, we know that HT is a complex process where several molecular pathways are involved.

EUV Dimmings as a Diagnostic of CMEs and Related Phenomena

NASA Technical Reports Server (NTRS)

Thompson, Barbara J.; Mays, M. Leila; Webb, David F.; West, Matthew J.

2012-01-01

Large-scale coronal EUV dimmings, developing on timescaJes of minutes to hours in association with a flare or filament eruption, are known to exhibit a high correlation with coronal mass ejections. While most observations indicate that the decrease in emission in a dimming is due, at least in part, to a density decrease, a complete understanding requires us to examine at least four mechanisms that have been observed to cause darkened regions in the corona: 1) mass loss, 2) cooling, 3) heating, and 4) absorption/obscuration. Recent advances in automatic detection, observations with improved cadence and resolution, multi-viewpoint imaging, and spectroscopic studies have continued to shed light on dimming formation, evolution, and recovery. However, there are still some outstanding questions, including 1) Why do some CMEs show dimming and some do not? 2) What determines the location of a dimming? 3) What determines the temporal evolution of a dimming? 4) How does the post-eruption dimming connect to the ICME? 5) What is the relationship between dimmings and other CME-associated phenomena? The talk will emphasize the different formation mechanisms of dimmings and their relationship to CMEs and CME-associated phenomena.

Continuous Adaptive Population Reduction (CAPR) for Differential Evolution Optimization.

PubMed

Wong, Ieong; Liu, Wenjia; Ho, Chih-Ming; Ding, Xianting

2017-06-01

Differential evolution (DE) has been applied extensively in drug combination optimization studies in the past decade. It allows for identification of desired drug combinations with minimal experimental effort. This article proposes an adaptive population-sizing method for the DE algorithm. Our new method presents improvements in terms of efficiency and convergence over the original DE algorithm and constant stepwise population reduction-based DE algorithm, which would lead to a reduced number of cells and animals required to identify an optimal drug combination. The method continuously adjusts the reduction of the population size in accordance with the stage of the optimization process. Our adaptive scheme limits the population reduction to occur only at the exploitation stage. We believe that continuously adjusting for a more effective population size during the evolutionary process is the major reason for the significant improvement in the convergence speed of the DE algorithm. The performance of the method is evaluated through a set of unimodal and multimodal benchmark functions. In combining with self-adaptive schemes for mutation and crossover constants, this adaptive population reduction method can help shed light on the future direction of a completely parameter tune-free self-adaptive DE algorithm.

Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms.

PubMed

Beaulieu, Jeremy M; O'Meara, Brian C; Crane, Peter; Donoghue, Michael J

2015-09-01

Dating analyses based on molecular data imply that crown angiosperms existed in the Triassic, long before their undisputed appearance in the fossil record in the Early Cretaceous. Following a re-analysis of the age of angiosperms using updated sequences and fossil calibrations, we use a series of simulations to explore the possibility that the older age estimates are a consequence of (i) major shifts in the rate of sequence evolution near the base of the angiosperms and/or (ii) the representative taxon sampling strategy employed in such studies. We show that both of these factors do tend to yield substantially older age estimates. These analyses do not prove that younger age estimates based on the fossil record are correct, but they do suggest caution in accepting the older age estimates obtained using current relaxed-clock methods. Although we have focused here on the angiosperms, we suspect that these results will shed light on dating discrepancies in other major clades. ©The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

PubMed

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

Differential expression of non-coding RNAs and continuous evolution of the X chromosome in testicular transcriptome of two mouse species.

PubMed

Homolka, David; Ivanek, Robert; Forejt, Jiri; Jansa, Petr

2011-02-14

Tight regulation of testicular gene expression is a prerequisite for male reproductive success, while differentiation of gene activity in spermatogenesis is important during speciation. Thus, comparison of testicular transcriptomes between closely related species can reveal unique regulatory patterns and shed light on evolutionary constraints separating the species. Here, we compared testicular transcriptomes of two closely related mouse species, Mus musculus and Mus spretus, which diverged more than one million years ago. We analyzed testicular expression using tiling arrays overlapping Chromosomes 2, X, Y and mitochondrial genome. An excess of differentially regulated non-coding RNAs was found on Chromosome 2 including the intronic antisense RNAs, intergenic RNAs and premature forms of Piwi-interacting RNAs (piRNAs). Moreover, striking difference was found in the expression of X-linked G6pdx gene, the parental gene of the autosomal retrogene G6pd2. The prevalence of non-coding RNAs among differentially expressed transcripts indicates their role in species-specific regulation of spermatogenesis. The postmeiotic expression of G6pdx in Mus spretus points towards the continuous evolution of X-chromosome silencing and provides an example of expression change accompanying the out-of-the X-chromosomal retroposition.

Evolutionary game dynamics of controlled and automatic decision-making.

PubMed

Toupo, Danielle F P; Strogatz, Steven H; Cohen, Jonathan D; Rand, David G

2015-07-01

We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model in which agents who make decisions using either automatic or controlled processing compete with each other for survival. Agents using automatic processing act quickly and so are more likely to acquire resources, but agents using controlled processing are better planners and so make more effective use of the resources they have. Using the replicator equation, we characterize the conditions under which automatic or controlled agents dominate, when coexistence is possible and when bistability occurs. We then extend the replicator equation to consider feedback between the state of the population and the environment. Under conditions in which having a greater proportion of controlled agents either enriches the environment or enhances the competitive advantage of automatic agents, we find that limit cycles can occur, leading to persistent oscillations in the population dynamics. Critically, however, these limit cycles only emerge when feedback occurs on a sufficiently long time scale. Our results shed light on the connection between evolution and human cognition and suggest necessary conditions for the rise and fall of rationality.

Fusing enacted and expected mimicry generates a winning strategy that promotes the evolution of cooperation.

PubMed

Fischer, Ilan; Frid, Alex; Goerg, Sebastian J; Levin, Simon A; Rubenstein, Daniel I; Selten, Reinhard

2013-06-18

Although cooperation and trust are essential features for the development of prosperous populations, they also put cooperating individuals at risk for exploitation and abuse. Empirical and theoretical evidence suggests that the solution to the problem resides in the practice of mimicry and imitation, the expectation of opponent's mimicry and the reliance on similarity indices. Here we fuse the principles of enacted and expected mimicry and condition their application on two similarity indices to produce a model of mimicry and relative similarity. Testing the model in computer simulations of behavioral niches, populated with agents that enact various strategies and learning algorithms, shows how mimicry and relative similarity outperforms all the opponent strategies it was tested against, pushes noncooperative opponents toward extinction, and promotes the development of cooperative populations. The proposed model sheds light on the evolution of cooperation and provides a blueprint for intentional induction of cooperation within and among populations. It is suggested that reducing conflict intensities among human populations necessitates (i) instigation of social initiatives that increase the perception of similarity among opponents and (ii) efficient lowering of the similarity threshold of the interaction, the minimal level of similarity that makes cooperation advisable.

Is mammalian chromosomal evolution driven by regions of genome fragility?

PubMed Central

Ruiz-Herrera, Aurora; Castresana, Jose; Robinson, Terence J

2006-01-01

Background A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. Results Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. Conclusion These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity. PMID:17156441

CUSP-SHAPED STRUCTURE OF A JET OBSERVED BY IRIS AND SDO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Yuzong; Zhang, Jun, E-mail: yuzong@nao.cas.cn, E-mail: zjun@nao.cas.cn

2017-01-01

On 2014 August 29, the trigger and evolution of a cusp-shaped jet were captured in detail at 1330 Å by the Interface Region Imaging Spectrograph . At first, two neighboring mini-prominences arose in turn from the low solar atmosphere and collided with a loop-like system over them. The collisions between the loop-like system and the mini-prominences lead to the blowout, and then a cusp-shaped jet formed with a spire and an arch-base. In the spire, many brightening blobs originating from the junction between the spire and the arch-base moved upward in a rotating manner and then in a straight line inmore » the late phase of the jet. In the arch-base, dark and bright material simultaneously tracked in a fan-like structure, and the majority of the material moved along the fan's threads. At the later phase of the jet's evolution, bidirectional flows emptied the arch-base, while downflows emptied the spire, thus making the jet entirely vanish. The extremely detailed observations in this study shed new light on how magnetic reconnection alters the inner topological structure of a jet and provides a beneficial complement for understanding current jet models.« less

Three-Dimensional View of Ionized Gas Conditions in Galaxies

NASA Astrophysics Data System (ADS)

Juneau, Stephanie; NOAO Data Lab

2018-06-01

We present a 3D version of common emission line diagnostic diagrams used to identify the source of ionization in galaxies, and highlight interesting features in this new 3D space, which are associated with global galaxy properties. Namely, we combine the BPT and Mass-Excitation (MEx) diagrams, and apply it to a set of >300,000 galaxies from the SDSS survey. Among other features, we show that the usual “branch” of star-forming galaxies becomes a curved surface in the new 3D space. Understanding the underlying reasons can shed light on the nearby galaxy population but also aid our interpretation of high-redshift surveys, which indicate a strong evolution of emission line ratios. Despite efforts to explain the origin of this strong evolution, a consensus has not yet been reached. Yet, the implications are crucial to our understanding of galaxy growth across cosmic time, and in particular to assess how star forming regions differed at earlier times (gas properties? stellar properties? a combination?). We perform this analysis within the framework of the NOAO Data Lab (datalab.noao.edu) jointly with public visualization tools. The final workflow will be released publicly.

A new 3-D View of Ionized Gas Conditions in Galaxies

NASA Astrophysics Data System (ADS)

Juneau, Stephanie

2018-01-01

We present a 3D version of common emission line diagnostic diagrams used to identify the source of ionization in galaxies, and highlight interesting features in this new 3D space, which are associated with global galaxy properties. Namely, we combine the BPT and Mass-Excitation (MEx) diagrams, and apply it to a set of >300,000 galaxies from the SDSS survey. Among other features, we show that the usual “branch” of star-forming galaxies becomes a curved surface in the new 3D space. Understanding the underlying reasons can shed light on the nearby galaxy population but also aid our interpretation of high-redshift surveys, which indicate a strong evolution of emission line ratios. Despite efforts to explain the origin of this strong evolution, a consensus has not yet been reached. Yet, the implications are crucial to our understanding of galaxy growth across cosmic time, and in particular to assess how star forming regions differed at earlier times (gas properties? stellar properties? a combination?). We perform this analysis within the framework of the NOAO Data Lab (datalab.noao.edu) jointly with public visualization tools. The final workflow will be released publicly.

The evolution of menstruation: a new model for genetic assimilation: explaining molecular origins of maternal responses to fetal invasiveness.

PubMed

Emera, Deena; Romero, Roberto; Wagner, Günter

2012-01-01

Why do humans menstruate while most mammals do not? Here, we present our answer to this long-debated question, arguing that (i) menstruation occurs as a mechanistic consequence of hormone-induced differentiation of the endometrium (referred to as spontaneous decidualization, or SD); (ii) SD evolved because of maternal-fetal conflict; and (iii) SD evolved by genetic assimilation of the decidualization reaction, which is induced by the fetus in non-menstruating species. The idea that menstruation occurs as a consequence of SD has been proposed in the past, but here we present a novel hypothesis on how SD evolved. We argue that decidualization became genetically stabilized in menstruating lineages, allowing females to prepare for pregnancy without any signal from the fetus. We present three models for the evolution of SD by genetic assimilation, based on recent advances in our understanding of the mechanisms of endometrial differentiation and implantation. Testing these models will ultimately shed light on the evolutionary significance of menstruation, as well as on the etiology of human reproductive disorders like endometriosis and recurrent pregnancy loss. Copyright © 2012 WILEY Periodicals, Inc.

Homoplasious colony morphology and mito-nuclear phylogenetic discordance among Eastern Pacific octocorals.

PubMed

Ament-Velásquez, Sandra L; Breedy, Odalisca; Cortés, Jorge; Guzman, Hector M; Wörheide, Gert; Vargas, Sergio

2016-05-01

Octocorals are a diverse and ecologically important group of cnidarians. However, the phylogenetic relationships of many octocoral groups are not well understood and are based mostly on mitochondrial sequence data. In addition, the discovery and description of new gorgonian species displaying unusual or intermediate morphologies and uncertain phylogenetic affinities further complicates the study of octocoral systematics and raises questions about the role played by processes such as plasticity, crypsis, and convergence in the evolution of this group of organisms. Here, we use nuclear (i.e. 28S rDNA) and mitochondrial (mtMutS) markers and a sample of Eastern Pacific gorgonians thought to be remarkable from a morphological point of view to shed light on the morphological diversification among these organisms. Our study reveals the loss of the anastomosed colony morphology in two unrelated lineages of the seafan genus Pacifigorgia and offers strong evidence for the independent evolution of a whip-like morphology in two lineages of Eastern Pacific Leptogorgia. Additionally, our data revealed one instance of mito-nuclear discordance in the genera Leptogorgia and Eugorgia, which may be the results of incomplete lineage sorting or ancient hybridization-introgression events. Our study stresses the importance of comprehensive taxonomic sampling and the use of independent sources of evidence to address the phylogenetic relationships and clarifying the evolution of octocorals. Copyright © 2016 Elsevier Inc. All rights reserved.

Complete mitogenome of Asiatic lion resolves phylogenetic status within Panthera.

PubMed

Bagatharia, Snehal B; Joshi, Madhvi N; Pandya, Rohan V; Pandit, Aanal S; Patel, Riddhi P; Desai, Shivangi M; Sharma, Anu; Panchal, Omkar; Jasmani, Falguni P; Saxena, Akshay K

2013-08-23

The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability.

Main drivers of flood-risk dynamics along the Po River

NASA Astrophysics Data System (ADS)

Domeneghetti, Alessio; Carisi, Francesca; Castellarin, Attilio; Brath, Armando

2017-04-01

The increasing frequency with which floods damages are recorded, or reported by media, strengthen the common perception that the flood risk is dramatically increasing in Europe and other areas of the world, due to a combination of different causes, among which climate change is often described as the major factor. However, there is a growing awareness of how anthropogenic pressures, such as uncontrolled urban and industrial expansion on flood-prone areas, may strongly impact the evolution of flood-risk in a given area, increasing potential flood damages and losses. Starting from these considerations, our study aims at shedding some light on the impact and relative importance of different factors controlling the flood risk. Focusing in particular on the middle-lower portion of the River Po, we analyze the evolution of flood hazard in the last half century referring to long streamflow series for different gauging stations located along the study reach ( 450 km), while the modification of anthropogenic pressure is evaluated by referring to land-use and demographic dynamics observed from 1950s. Our study proposes simplified flood-vulnerability indices to be used for large scale flood-risk assessments and, on the basis of these indices, (1) we assess the importance of the different elements contributing to the definition of flood risk and (2) represent the evolution of flood risk in time along the middle and lower portion of the River Po.

Impact of shill intervention on the evolution of cooperation

NASA Astrophysics Data System (ADS)

Sun, Changhao; Duan, Haibin

2015-09-01

The practical significance of effective intervention in collective behavior has its roots not only in frequent migration in the modern society, but also in the actual demands of real-world applications for system efficiency improvement. Within the framework of soft control, this paper focuses on an evolutionary public goods game staged on a scale free network and explores the dependence of the evolution of cooperation on the intervention of a fraction of shills, who follow the Fixed-Cost-per-Player paradigm while the locals follow the Fixed-Cost-per-Game paradigm. We demonstrate that higher cooperation levels and better social welfare could be simultaneously induced by tuning the distribution coefficient α, where desirable outcomes are associated with large α > 0 for tense dilemmas while small α < 0 leads to satisfactory results when the enhancement factor γ increases. Moreover, we observe a transition of the composition of equilibrium cooperators from full dominance of shills to co-existence of shills and locals, and the boundary has a positive correlation with α. These results are somehow affected when we attenuate the heterogeneity of the network by relating individual fitness to payoffs averaged over its connectivity. Our findings may not only shed some light on the mechanism behind the evolution of cooperation from the perspective of external intervention, but also provide a feasible way to effectively intervene in the evolutionary outcomes of negative scenarios.

Role of maternal thyroid hormones in the developing neocortex and during human evolution

PubMed Central

Stenzel, Denise; Huttner, Wieland B.

2013-01-01

The importance of thyroid hormones during brain development has been appreciated for many decades. In humans, low levels of circulating maternal thyroid hormones, e.g., caused by maternal hypothyroidism or lack of iodine in diet, results in a wide spectrum of severe neurological defects, including neurological cretinism characterized by profound neurologic impairment and mental retardation, underlining the importance of the maternal thyroid hormone contribution. In fact, iodine intake, which is essential for thyroid hormone production in the thyroid gland, has been related to the expansion of the brain, associated with the increased cognitive capacities during human evolution. Because thyroid hormones regulate transcriptional activity of target genes via their nuclear thyroid hormone receptors (THRs), even mild and transient changes in maternal thyroid hormone levels can directly affect and alter the gene expression profile, and thus disturb fetal brain development. Here we summarize how thyroid hormones may have influenced human brain evolution through the adaptation to new habitats, concomitant with changes in diet and, therefore, iodine intake. Further, we review the current picture we gained from experimental studies in rodents on the function of maternal thyroid hormones during developmental neurogenesis. We aim to evaluate the effects of maternal thyroid hormone deficiency as well as lack of THRs and transporters on brain development and function, shedding light on the cellular behavior conducted by thyroid hormones. PMID:23882187

Complete mitogenome of asiatic lion resolves phylogenetic status within Panthera

PubMed Central

2013-01-01

Background The origin, evolution and speciation of the lion, has been subject of interest, debate and study. The present surviving lions of the genus Panthera comprise of eight sub-species inclusive of Asiatic lion Panthera leo persica of India's Gir forest. Except for the Asiatic lion, the other seven subspecies are found in different parts of Africa. There have been different opinions regarding the phylogenetic status of Panthera leo, as well as classifying lions of different geographic regions into subspecies and races. In the present study, mitogenome sequence of P. leo persica deduced, using Ion Torrent PGM to assess phylogeny and evolution which may play an increasingly important role in conservation biology. Results The mtDNA sequence of P. leo persica is 17,057 bp in length with 40.8% GC content. Annotation of mitogenome revealed total 37 genes, including 13 protein coding, 2 rRNA and 22 tRNA. Phylogenetic analysis based on whole mitogenome, suggests Panthera pardus as a neighbouring species to P. leo with species divergence at ~2.96 mya. Conclusion This work presents first report on complete mitogenome of Panthera leo persica. It sheds light on the phylogenetic and evolutionary status within and across Felidae members. The result compared and evaluated with earlier reports of Felidae shows alteration of phylogenetic status and species evolution. This study may provide information on genetic diversity and population stability. PMID:23968279

Our Way to Understand the World: Darwin's Controversial Inheritance

NASA Astrophysics Data System (ADS)

Schmidt-Salomon, Michael

Shortly after he had completed the first draft of his theory of evolution in 1844, Charles Darwin wrote to his friend Joseph Hooker, the botanist, that publishing the theory seemed to him "like confessing a murder" (Glaubrecht 2009, p. 161). Right from the beginning, Darwin was aware of the far-reaching impact his theory would have. And this was probably one of the main reasons for his postponing the publication of his ideas for such a long time. After the completion of the 230 page text in 1844, it was another 15 years (!) before his famous book On the Origin of Species was published. Since that time 150 years have passed, but the theory of evolution is as controversial as ever. Darwin's dangerous idea is still putting many traditional world views through some very hard tests. This is the central theme to which I have devoted the following thoughts. I have divided my study into three parts: I shall start by shedding some light on the conflict between Darwin's challenging idea and traditional (Christian) beliefs, a conflict that has lasted till this very day. In the second part, I want to focus on the ideological abuse of the theory of evolution. The third and final part introduces Julian Huxley's concept of 'evolutionary humanism', which links Darwin's scientific inheritance with a distinctly humanist ethic.

Urban driven phenotypic changes: empirical observations and theoretical implications for eco-evolutionary feedback

PubMed Central

Marzluff, John

2017-01-01

Emerging evidence that cities drive micro-evolution raises the question of whether rapid urbanization of Earth might impact ecosystems by causing systemic changes in functional traits that regulate urban ecosystems' productivity and stability. Intraspecific trait variation—variation in organisms' morphological, physiological or behavioural characteristics stemming from genetic variability and phenotypic plasticity—has significant implications for ecological functions such as nutrient cycling and primary productivity. While it is well established that changes in ecological conditions can drive evolutionary change in species' traits that, in turn, can alter ecosystem function, an understanding of the reciprocal and simultaneous processes associated with such interactions is only beginning to emerge. In urban settings, the potential for rapid trait change may be exacerbated by multiple selection pressures operating simultaneously. This paper reviews evidence on mechanisms linking urban development patterns to rapid phenotypic changes, and differentiates phenotypic changes for which there is evidence of micro-evolution versus phenotypic changes which may represent plasticity. Studying how humans mediate phenotypic trait changes through urbanization could shed light on fundamental concepts in ecological and evolutionary theory. It can also contribute to our understanding of eco-evolutionary feedback and provide insights for maintaining ecosystem function over the long term. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences’. PMID:27920374

Contrasting magmatic structures between small plutons and batholiths emplaced at shallow crustal level (Sierras de Córdoba, Argentina)

NASA Astrophysics Data System (ADS)

Pinotti, Lucio P.; D'Eramo, Fernando J.; Weinberg, Roberto F.; Demartis, Manuel; Tubía, José María; Coniglio, Jorge E.; Radice, Stefania; Maffini, M. Natalia; Aragón, Eugenio

2016-11-01

Processes like injection, magma flow and differentiation and influence of the regional strain field are here described and contrasted to shed light on their role in the formation of small plutons and large batholiths their magmatic structures. The final geometric and compositional arrangement of magma bodies are a complex record of their construction and internal flow history. Magma injection, flow and differentiation, as well as regional stresses, all control the internal nature of magma bodies. Large magma bodies emplaced at shallow crustal levels result from the intrusion of multiple magma batches that interact in a variety of ways, depending on internal and external dynamics, and where the early magmatic, growth-related structures are commonly overprinted by subsequent history. In contrast, small plutons emplaced in the brittle-ductile transition more likely preserve growth-related structures, having a relatively simple cooling history and limited internal magma flow. Outcrop-scale magmatic structures in both cases record a rich set of complementary information that can help elucidate their evolution. Large and small granitic bodies of the Sierra Pampeanas preserve excellent exposures of magmatic structures that formed as magmas stepped through different rheological states during pluton growth and solidification. These structures reveal not only the flow pattern inside magma chambers, but also the rheological evolution of magmas in response to temperature evolution.

The Evolution of MicroRNA Pathway Protein Components in Cnidaria

PubMed Central

Moran, Yehu; Praher, Daniela; Fredman, David; Technau, Ulrich

2013-01-01

In the last decade, it became evident that posttranscriptional regulation of gene expression by microRNAs is a central biological process in both plants and animals. Yet, our knowledge about microRNA biogenesis and utilization in animals stems mostly from the study of Bilateria. In this study, we identified genes encoding the protein components of different parts of the microRNA pathway in Cnidaria, the likely sister phylum of Bilateria. These genes originated from three cnidarian lineages (sea anemones, stony corals, and hydras) that are separated by at least 500 My from one another. We studied the expression and phylogeny of the cnidarian homologs of Drosha and Pasha (DGCR8) that compose the microprocessor, the RNAse III enzyme Dicer and its partners, the HEN1 methyltransferase, the Argonaute protein effectors, as well as members of the GW182 protein family. We further reveal that whereas the bilaterian dicer partners Loquacious/TRBP and PACT are absent from Cnidaria, this phylum contains homologs of the double-stranded RNA-binding protein HYL1, the Dicer partner found in plants. We also identified HYL1 homologs in a sponge and a ctenophore. This finding raises questions regarding the independent evolution of the microRNA pathway in plants and animals, and together with the other results shed new light on the evolution of an important regulatory pathway. PMID:24030553

The evolution of microRNA pathway protein components in Cnidaria.

PubMed

Moran, Yehu; Praher, Daniela; Fredman, David; Technau, Ulrich

2013-12-01

In the last decade, it became evident that posttranscriptional regulation of gene expression by microRNAs is a central biological process in both plants and animals. Yet, our knowledge about microRNA biogenesis and utilization in animals stems mostly from the study of Bilateria. In this study, we identified genes encoding the protein components of different parts of the microRNA pathway in Cnidaria, the likely sister phylum of Bilateria. These genes originated from three cnidarian lineages (sea anemones, stony corals, and hydras) that are separated by at least 500 My from one another. We studied the expression and phylogeny of the cnidarian homologs of Drosha and Pasha (DGCR8) that compose the microprocessor, the RNAse III enzyme Dicer and its partners, the HEN1 methyltransferase, the Argonaute protein effectors, as well as members of the GW182 protein family. We further reveal that whereas the bilaterian dicer partners Loquacious/TRBP and PACT are absent from Cnidaria, this phylum contains homologs of the double-stranded RNA-binding protein HYL1, the Dicer partner found in plants. We also identified HYL1 homologs in a sponge and a ctenophore. This finding raises questions regarding the independent evolution of the microRNA pathway in plants and animals, and together with the other results shed new light on the evolution of an important regulatory pathway.

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

PubMed

Lindblad-Toh, Kerstin; Wade, Claire M; Mikkelsen, Tarjei S; Karlsson, Elinor K; Jaffe, David B; Kamal, Michael; Clamp, Michele; Chang, Jean L; Kulbokas, Edward J; Zody, Michael C; Mauceli, Evan; Xie, Xiaohui; Breen, Matthew; Wayne, Robert K; Ostrander, Elaine A; Ponting, Chris P; Galibert, Francis; Smith, Douglas R; DeJong, Pieter J; Kirkness, Ewen; Alvarez, Pablo; Biagi, Tara; Brockman, William; Butler, Jonathan; Chin, Chee-Wye; Cook, April; Cuff, James; Daly, Mark J; DeCaprio, David; Gnerre, Sante; Grabherr, Manfred; Kellis, Manolis; Kleber, Michael; Bardeleben, Carolyne; Goodstadt, Leo; Heger, Andreas; Hitte, Christophe; Kim, Lisa; Koepfli, Klaus-Peter; Parker, Heidi G; Pollinger, John P; Searle, Stephen M J; Sutter, Nathan B; Thomas, Rachael; Webber, Caleb; Baldwin, Jennifer; Abebe, Adal; Abouelleil, Amr; Aftuck, Lynne; Ait-Zahra, Mostafa; Aldredge, Tyler; Allen, Nicole; An, Peter; Anderson, Scott; Antoine, Claudel; Arachchi, Harindra; Aslam, Ali; Ayotte, Laura; Bachantsang, Pasang; Barry, Andrew; Bayul, Tashi; Benamara, Mostafa; Berlin, Aaron; Bessette, Daniel; Blitshteyn, Berta; Bloom, Toby; Blye, Jason; Boguslavskiy, Leonid; Bonnet, Claude; Boukhgalter, Boris; Brown, Adam; Cahill, Patrick; Calixte, Nadia; Camarata, Jody; Cheshatsang, Yama; Chu, Jeffrey; Citroen, Mieke; Collymore, Alville; Cooke, Patrick; Dawoe, Tenzin; Daza, Riza; Decktor, Karin; DeGray, Stuart; Dhargay, Norbu; Dooley, Kimberly; Dooley, Kathleen; Dorje, Passang; Dorjee, Kunsang; Dorris, Lester; Duffey, Noah; Dupes, Alan; Egbiremolen, Osebhajajeme; Elong, Richard; Falk, Jill; Farina, Abderrahim; Faro, Susan; Ferguson, Diallo; Ferreira, Patricia; Fisher, Sheila; FitzGerald, Mike; Foley, Karen; Foley, Chelsea; Franke, Alicia; Friedrich, Dennis; Gage, Diane; Garber, Manuel; Gearin, Gary; Giannoukos, Georgia; Goode, Tina; Goyette, Audra; Graham, Joseph; Grandbois, Edward; Gyaltsen, Kunsang; Hafez, Nabil; Hagopian, Daniel; Hagos, Birhane; Hall, Jennifer; Healy, Claire; Hegarty, Ryan; Honan, Tracey; Horn, Andrea; Houde, Nathan; Hughes, Leanne; Hunnicutt, Leigh; Husby, M; Jester, Benjamin; Jones, Charlien; Kamat, Asha; Kanga, Ben; Kells, Cristyn; Khazanovich, Dmitry; Kieu, Alix Chinh; Kisner, Peter; Kumar, Mayank; Lance, Krista; Landers, Thomas; Lara, Marcia; Lee, William; Leger, Jean-Pierre; Lennon, Niall; Leuper, Lisa; LeVine, Sarah; Liu, Jinlei; Liu, Xiaohong; Lokyitsang, Yeshi; Lokyitsang, Tashi; Lui, Annie; Macdonald, Jan; Major, John; Marabella, Richard; Maru, Kebede; Matthews, Charles; McDonough, Susan; Mehta, Teena; Meldrim, James; Melnikov, Alexandre; Meneus, Louis; Mihalev, Atanas; Mihova, Tanya; Miller, Karen; Mittelman, Rachel; Mlenga, Valentine; Mulrain, Leonidas; Munson, Glen; Navidi, Adam; Naylor, Jerome; Nguyen, Tuyen; Nguyen, Nga; Nguyen, Cindy; Nguyen, Thu; Nicol, Robert; Norbu, Nyima; Norbu, Choe; Novod, Nathaniel; Nyima, Tenchoe; Olandt, Peter; O'Neill, Barry; O'Neill, Keith; Osman, Sahal; Oyono, Lucien; Patti, Christopher; Perrin, Danielle; Phunkhang, Pema; Pierre, Fritz; Priest, Margaret; Rachupka, Anthony; Raghuraman, Sujaa; Rameau, Rayale; Ray, Verneda; Raymond, Christina; Rege, Filip; Rise, Cecil; Rogers, Julie; Rogov, Peter; Sahalie, Julie; Settipalli, Sampath; Sharpe, Theodore; Shea, Terrance; Sheehan, Mechele; Sherpa, Ngawang; Shi, Jianying; Shih, Diana; Sloan, Jessie; Smith, Cherylyn; Sparrow, Todd; Stalker, John; Stange-Thomann, Nicole; Stavropoulos, Sharon; Stone, Catherine; Stone, Sabrina; Sykes, Sean; Tchuinga, Pierre; Tenzing, Pema; Tesfaye, Senait; Thoulutsang, Dawa; Thoulutsang, Yama; Topham, Kerri; Topping, Ira; Tsamla, Tsamla; Vassiliev, Helen; Venkataraman, Vijay; Vo, Andy; Wangchuk, Tsering; Wangdi, Tsering; Weiand, Michael; Wilkinson, Jane; Wilson, Adam; Yadav, Shailendra; Yang, Shuli; Yang, Xiaoping; Young, Geneva; Yu, Qing; Zainoun, Joanne; Zembek, Lisa; Zimmer, Andrew; Lander, Eric S

2005-12-08

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

The Emerging Field of Human Social Genomics

PubMed Central

Slavich, George M.; Cole, Steven W.

2013-01-01

Although we generally experience our bodies as being biologically stable across time and situations, an emerging field of research is demonstrating that external social conditions, especially our subjective perceptions of those conditions, can influence our most basic internal biological processes—namely, the expression of our genes. This research on human social genomics has begun to identify the types of genes that are subject to social-environmental regulation, the neural and molecular mechanisms that mediate the effects of social processes on gene expression, and the genetic polymorphisms that moderate individual differences in genomic sensitivity to social context. The molecular models resulting from this research provide new opportunities for understanding how social and genetic factors interact to shape complex behavioral phenotypes and susceptibility to disease. This research also sheds new light on the evolution of the human genome and challenges the fundamental belief that our molecular makeup is relatively stable and impermeable to social-environmental influence. PMID:23853742

Reaction kinetics in open reactors and serial transfers between closed reactors

NASA Astrophysics Data System (ADS)

Blokhuis, Alex; Lacoste, David; Gaspard, Pierre

2018-04-01

Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with a finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.

Behaviors of Zn2GeO4 under high pressure and high temperature

NASA Astrophysics Data System (ADS)

Shu-Wen, Yang; Fang, Peng; Wen-Tao, Li; Qi-Wei, Hu; Xiao-Zhi, Yan; Li, Lei; Xiao-Dong, Li; Duan-Wei, He

2016-07-01

The structural stability of Zn2GeO4 was investigated by in-situ synchrotron radiation angle dispersive x-ray diffraction. The pressure-induced amorphization is observed up to 10 GPa at room temperature. The high-pressure and high-temperature sintering experiments and the Raman spectrum measurement firstly were performed to suggest that the amorphization is caused by insufficient thermal energy and tilting Zn-O-Ge and Ge-O-Ge bond angles with increasing pressure, respectively. The calculated bulk modulus of Zn2GeO4 is 117.8 GPa from the pressure-volume data. In general, insights into the mechanical behavior and structure evolution of Zn2GeO4 will shed light on the micro-mechanism of the materials variation under high pressure and high temperature. Project supported by the Joint Fund of the National Natural Science Foundation of China and Chinese Academy of Sciences (Grant No. U1332104).

Small Cofactors May Assist Protein Emergence from RNA World: Clues from RNA-Protein Complexes

PubMed Central

Shen, Liang; Ji, Hong-Fang

2011-01-01

It is now widely accepted that at an early stage in the evolution of life an RNA world arose, in which RNAs both served as the genetic material and catalyzed diverse biochemical reactions. Then, proteins have gradually replaced RNAs because of their superior catalytic properties in catalysis over time. Therefore, it is important to investigate how primitive functional proteins emerged from RNA world, which can shed light on the evolutionary pathway of life from RNA world to the modern world. In this work, we proposed that the emergence of most primitive functional proteins are assisted by the early primitive nucleotide cofactors, while only a minority are induced directly by RNAs based on the analysis of RNA-protein complexes. Furthermore, the present findings have significant implication for exploring the composition of primitive RNA, i.e., adenine base as principal building blocks. PMID:21789260

Spectrally resolved localized states in GaAs 1– xBi x

DOE PAGES

Christian, Theresa M.; Alberi, Kirstin; Beaton, Daniel A.; ...

2017-02-01

In this study, the role of localized states and their influence on the broader band structure remains a crucial question in understanding the band structure evolution in GaAs 1-xBi x. Here in this work, we present clear spectroscopic observations of recombination at several localized states in GaAs 1-xBi x. Sharp and recognizable photoluminescence features appear in multiple samples and redshift as a function of GaBi fraction between x = 0.16% and 0.4% at a linearized rate of 34 meV per % Bi, weaker than the redshift associated with band-to-band recombination. Interpreting these results in terms of radiative recombination between localizedmore » holes and free electrons sheds light on the relative movement of the conduction band minimum and the characteristics of localized bismuth-related trap states in GaAs 1-xBi x alloys.« less

The Effect of a History-Fitness Updating Rule on Evolutionary Games

NASA Astrophysics Data System (ADS)

Du, Wen-Bo; Cao, Xian-Bin; Liu, Run-Ran; Jia, Chun-Xiao

In this paper, we introduce a history-fitness-based updating rule into the evolutionary prisoner's dilemma game (PDG) on square lattices, and study how it works on the evolution of cooperation level. Under this updating rule, the player i will firstly select player j from its direct neighbors at random and then compare their fitness which is determined by the current payoff and history fitness. If player i's fitness is larger than that of j, player i will be more likely to keep its own strategy. Numerical results show that the cooperation level is remarkably promoted by the history-fitness-based updating rule. Moreover, there exists a moderate mixing proportion of current payoff and history fitness that can induce the optimal fitness, where the highest cooperation level is obtained. Our work may shed some new light on the ubiquitous cooperative behaviors in nature and society induced by the history factor.

Optical analogues of the Newton-Schrödinger equation and boson star evolution.

PubMed

Roger, Thomas; Maitland, Calum; Wilson, Kali; Westerberg, Niclas; Vocke, David; Wright, Ewan M; Faccio, Daniele

2016-11-14

Many gravitational phenomena that lie at the core of our understanding of the Universe have not yet been directly observed. An example in this sense is the boson star that has been proposed as an alternative to some compact objects currently interpreted as being black holes. In the weak field limit, these stars are governed by the Newton-Schrodinger equation. Here we present an optical system that, under appropriate conditions, identically reproduces such equation in two dimensions. A rotating boson star is experimentally and numerically modelled by an optical beam propagating through a medium with a positive thermal nonlinearity and is shown to oscillate in time while also stable up to relatively high densities. For higher densities, instabilities lead to an apparent breakup of the star, yet coherence across the whole structure is maintained. These results show that optical analogues can be used to shed new light on inaccessible gravitational objects.

Optical analogues of the Newton–Schrödinger equation and boson star evolution

PubMed Central

Roger, Thomas; Maitland, Calum; Wilson, Kali; Westerberg, Niclas; Vocke, David; Wright, Ewan M.; Faccio, Daniele

2016-01-01

Many gravitational phenomena that lie at the core of our understanding of the Universe have not yet been directly observed. An example in this sense is the boson star that has been proposed as an alternative to some compact objects currently interpreted as being black holes. In the weak field limit, these stars are governed by the Newton–Schrodinger equation. Here we present an optical system that, under appropriate conditions, identically reproduces such equation in two dimensions. A rotating boson star is experimentally and numerically modelled by an optical beam propagating through a medium with a positive thermal nonlinearity and is shown to oscillate in time while also stable up to relatively high densities. For higher densities, instabilities lead to an apparent breakup of the star, yet coherence across the whole structure is maintained. These results show that optical analogues can be used to shed new light on inaccessible gravitational objects. PMID:27841261

Genome research elucidating environmental adaptation: Dark-fly project as a case study.

PubMed

Fuse, Naoyuki

2017-08-01

Organisms have the capacity to adapt to diverse environments, and environmental adaptation is a substantial driving force of evolution. Recent progress of genome science has addressed the genetic mechanisms underlying environmental adaptation. Whole genome sequencing has identified adaptive genes selected under particular environments. Genome editing technology enables us to directly test the role(s) of a gene in environmental adaptation. Genome science has also shed light on a unique organism, Dark-fly, which has been reared long-term in the dark. We determined the whole genome sequence of Dark-fly and reenacted environmental selections of the Dark-fly genome to identify the genes related to dark-adaptation. Here I will give an overview of current progress in genome science and summarize our study using Dark-fly, as a case study for environmental adaptation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Multisensory integration in Lepidoptera: Insights into flower-visitor interactions.

PubMed

Kinoshita, Michiyo; Stewart, Finlay J; Ômura, Hisashi

2017-04-01

As most work on flower foraging focuses on bees, studying Lepidoptera can offer fresh perspectives on how sensory capabilities shape the interaction between flowers and insects. Through a combination of innate preferences and learning, many Lepidoptera persistently visit particular flower species. Butterflies tend to rely on their highly developed sense of colour to locate rewarding flowers, while moths have evolved sophisticated olfactory systems towards the same end. However, these modalities can interact in complex ways; for instance, butterflies' colour preference can shift depending on olfactory context. The mechanisms by which such cross-modal interaction occurs are poorly understood, but the mushroom bodies appear to play a central role. Because of the diversity seen within Lepidoptera in terms of their sensory capabilities and the nature of their relationships with flowers, they represent a fruitful avenue for comparative studies to shed light on the co-evolution of flowers and flower-visiting insects. © 2017 WILEY Periodicals, Inc.

The geometric nature of weights in real complex networks

NASA Astrophysics Data System (ADS)

Allard, Antoine; Serrano, M. Ángeles; García-Pérez, Guillermo; Boguñá, Marián

2017-01-01

The topology of many real complex networks has been conjectured to be embedded in hidden metric spaces, where distances between nodes encode their likelihood of being connected. Besides of providing a natural geometrical interpretation of their complex topologies, this hypothesis yields the recipe for sustainable Internet's routing protocols, sheds light on the hierarchical organization of biochemical pathways in cells, and allows for a rich characterization of the evolution of international trade. Here we present empirical evidence that this geometric interpretation also applies to the weighted organization of real complex networks. We introduce a very general and versatile model and use it to quantify the level of coupling between their topology, their weights and an underlying metric space. Our model accurately reproduces both their topology and their weights, and our results suggest that the formation of connections and the assignment of their magnitude are ruled by different processes.

Laboratory investigations

NASA Technical Reports Server (NTRS)

Russell, Ray W.

1988-01-01

Laboratory studies related to cometary grains and the nuclei of comets can be broken down into three areas which relate to understanding the spectral properties, the formation mechanisms, and the evolution of grains and nuclei: (1) Spectral studies to be used in the interpretation of cometary spectra; (2) Sample preparation experiments which may shed light on the physical nature and history of cometary grains and nuclei by exploring the effects on grain emissivities resulting from the ways in which the samples are created; and (3) Grain processing experiments which should provide insight on the interaction of cometary grains with the environment in the immediate vicinity of the cometary nucleus as the comet travels from the Oort cloud through perihelion, and perhaps even suggestions regarding the relationship between interstellar grains and cometary matter. A summary is presented with a different view of lab experiments than is found in the literature, concentrating on measurement techniques and sample preparations especially relevant to cometary dust.

The evolution of honey bee dance communication: a mechanistic perspective.

PubMed

Barron, Andrew B; Plath, Jenny Aino

2017-12-01

Honey bee dance has been intensively studied as a communication system, and yet we still know very little about the neurobiological mechanisms supporting how dances are produced and interpreted. Here, we discuss how new information on the functions of the central complex (CX) of the insect brain might shed some light on possible neural mechanisms of dance behaviour. We summarise the features of dance communication across the species of the genus Apis We then propose that neural mechanisms of orientation and spatial processing found to be supported by the CX may function in dance communication also, and that this mechanistic link could explain some specific features of the dance form. This is purely a hypothesis, but in proposing this hypothesis, and how it might be investigated, we hope to stimulate new mechanistic analyses of dance communication. © 2017. Published by The Company of Biologists Ltd.

Love Influences Reproductive Success in Humans

PubMed Central

Sorokowski, Piotr; Sorokowska, Agnieszka; Butovskaya, Marina; Karwowski, Maciej; Groyecka, Agata; Wojciszke, Bogdan; Pawłowski, Bogusław

2017-01-01

As love seems to be universal, researchers have attempted to find its biological basis. However, no studies till date have shown its direct association with reproductive success, which is broadly known to be a good measure of fitness. Here, we show links between love, as defined by the Sternberg Triangular Theory of Love, and reproductive success among the Hadza—traditional hunter-gatherer population. We found that commitment and reproductive success were positively and consistently related in both sexes, with number of children showing negative and positive associations with intimacy and passion, respectively, only among women. Our study may shed new light on the meaning of love in humans' evolutionary past, especially in traditional hunter-gatherer societies in which individuals, not their parents, were responsible for partner choice. We suggest that passion and commitment may be the key factors that increase fitness, and therefore, that selection promoted love in human evolution. However, further studies in this area are recommended. PMID:29209243

Reverse engineering the ancient ceramic technology based on X-ray fluorescence spectromicroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sciau, Philippe; Leon, Yoanna; Goudeau, Philippe

2011-07-06

We present results of X-ray fluorescence (XRF) microprobe analyses of ancient ceramic cross-sections aiming at deciphering the different firing protocols used for their production. Micro-focused XRF elemental mapping, Fe chemical mapping and Fe K-edge X-ray absorption near edge structure spectroscopy were performed on pre-sigillata ceramics from southern Gaul, and terra Sigillata vessels from Italy and southern Gaul. Pieces from the different workshops and regions showed significant difference in the starting clay material, clay conditioning and kiln firing condition. By contrast, sherds from the same workshop exhibited more subtle differences and possible misfirings. Understanding the precise firing conditions and protocols wouldmore » allow recreation of kilns for various productions. Furthermore, evolution and modification of kiln design would shed some light on how ancient potters devised solutions to diverse technological problems they encountered.« less

A new stem turtle from the Middle Jurassic of Scotland: new insights into the evolution and palaeoecology of basal turtles.

PubMed

Anquetin, Jérémy; Barrett, Paul M; Jones, Marc E H; Moore-Fay, Scott; Evans, Susan E

2009-03-07

The discovery of a new stem turtle from the Middle Jurassic (Bathonian) deposits of the Isle of Skye, Scotland, sheds new light on the early evolutionary history of Testudinata. Eileanchelys waldmani gen. et sp. nov. is known from cranial and postcranial material of several individuals and represents the most complete Middle Jurassic turtle described to date, bridging the morphological gap between basal turtles from the Late Triassic-Early Jurassic and crown-group turtles that diversify during the Late Jurassic. A phylogenetic analysis places the new taxon within the stem group of Testudines (crown-group turtles) and suggests a sister-group relationship between E. waldmani and Heckerochelys romani from the Middle Jurassic of Russia. Moreover, E. waldmani also demonstrates that stem turtles were ecologically diverse, as it may represent the earliest known aquatic turtle.

A Gray-purple Mass on the Floor of the Mouth: Gigantic Mucogingival Pyogenic Granuloma in a Teenage Patient.

PubMed

Brunet-LLobet, Lluís; Miranda-Rius, Jaume; Lahor-Soler, Eduard; Mrina, Ombeni; Nadal, Alfons

2014-01-01

Pyogenic granuloma is defined as a benign neoplasm of vascular phenotype. This case describes the clinical and histopathological features of a gigantic mucogingival pyogenic granuloma, in a 14-year-old healthy black boy. This exophytic gray-purple mass, related to a toothpick injury, had more than twelve-month evolution on the anterior mandible involving lingual area besides to the floor of the mouth pressing the right salivary duct. Conservative excision was performed, followed by uncomplicated healing with no recurrence in two years. The histopathological examination reported a pyogenic granuloma (lobular capillary haemangioma). The authors provide a discussion of the presurgical differential diagnosis of the lesion. This case report presents an extremely uncommon location of a gigantic pyogenic granuloma, involving mucogingival complex and affecting the salivary outflow. This clinical manuscript may shed light on the controversies about possible mechanisms inducing oral pyogenic granuloma.

A Gray-purple Mass on the Floor of the Mouth: Gigantic Mucogingival Pyogenic Granuloma in a Teenage Patient

PubMed Central

Brunet-LLobet, Lluís; Miranda-Rius, Jaume; Lahor-Soler, Eduard; Mrina, Ombeni; Nadal, Alfons

2014-01-01

Pyogenic granuloma is defined as a benign neoplasm of vascular phenotype. This case describes the clinical and histopathological features of a gigantic mucogingival pyogenic granuloma, in a 14-year-old healthy black boy. This exophytic gray-purple mass, related to a toothpick injury, had more than twelve-month evolution on the anterior mandible involving lingual area besides to the floor of the mouth pressing the right salivary duct. Conservative excision was performed, followed by uncomplicated healing with no recurrence in two years. The histopathological examination reported a pyogenic granuloma (lobular capillary haemangioma). The authors provide a discussion of the presurgical differential diagnosis of the lesion. This case report presents an extremely uncommon location of a gigantic pyogenic granuloma, involving mucogingival complex and affecting the salivary outflow. This clinical manuscript may shed light on the controversies about possible mechanisms inducing oral pyogenic granuloma. PMID:24987485

Laboratory Studies of Anomalous Entrainment in Cumulus Cloud Flows

NASA Astrophysics Data System (ADS)

Diwan, Sourabh S.; Narasimha, Roddam; Bhat, G. S.; Sreenivas, K. R.

2011-12-01

Entrainment in cumulus clouds has been a subject of investigation for the last sixty years, and continues to be a central issue in current research. The development of a laboratory facility that can simulate cumulus cloud evolution enables us to shed light on the problem. The apparatus for the purpose is based on a physical model of cloud flow as a plume with off-source diabatic heating that is dynamically similar to the effect of latent-heat release in natural clouds. We present a critical review of the experimental data so far obtained in such facilities on the variation of the entrainment coefficient in steady diabatic jets and plumes. Although there are some unexplained differences among different data sets, the dominant trend of the results compares favourably with recent numerical simulations on steady-state deep convection, and helps explain certain puzzles in the fluid dynamics of clouds.

Optical analogues of the Newton-Schrödinger equation and boson star evolution

NASA Astrophysics Data System (ADS)

Roger, Thomas; Maitland, Calum; Wilson, Kali; Westerberg, Niclas; Vocke, David; Wright, Ewan M.; Faccio, Daniele

2016-11-01

Many gravitational phenomena that lie at the core of our understanding of the Universe have not yet been directly observed. An example in this sense is the boson star that has been proposed as an alternative to some compact objects currently interpreted as being black holes. In the weak field limit, these stars are governed by the Newton-Schrodinger equation. Here we present an optical system that, under appropriate conditions, identically reproduces such equation in two dimensions. A rotating boson star is experimentally and numerically modelled by an optical beam propagating through a medium with a positive thermal nonlinearity and is shown to oscillate in time while also stable up to relatively high densities. For higher densities, instabilities lead to an apparent breakup of the star, yet coherence across the whole structure is maintained. These results show that optical analogues can be used to shed new light on inaccessible gravitational objects.

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

PubMed Central

Kay, Gemma L.; Sergeant, Martin J.; Giuffra, Valentina; Bandiera, Pasquale; Milanese, Marco; Bramanti, Barbara

2014-01-01

ABSTRACT Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical material. We sequenced the metagenome of a calcified nodule from the skeleton of a 14th-century middle-aged male excavated from the medieval Sardinian settlement of Geridu. We obtained 6.5-fold coverage of a Brucella melitensis genome. Sequence reads from this genome showed signatures typical of ancient or aged DNA. Despite the relatively low coverage, we were able to use information from single-nucleotide polymorphisms to place the medieval pathogen genome within a clade of B. melitensis strains that included the well-studied Ether strain and two other recent Italian isolates. We confirmed this placement using information from deletions and IS711 insertions. We conclude that metagenomics stands ready to document past and present infections, shedding light on the emergence, evolution, and spread of microbial pathogens. PMID:25028426

Glycols modulate terminator stem stability and ligand-dependency of a glycine riboswitch.

PubMed

Hamachi, Kokoro; Hayashi, Hikari; Shimamura, Miyuki; Yamaji, Yuiha; Kaneko, Ai; Fujisawa, Aruma; Umehara, Takuya; Tamura, Koji

2013-08-01

The Bacillus subtilis glycine riboswitch comprises tandem glycine-binding aptamers and a putative terminator stem followed by the gcvT operon. Gene expression is regulated via the sensing of glycine. However, we found that the riboswitch behaves in a "glycine-independent" manner in the presence of polyethylene glycol (PEG) and ethylene glycol. The effect is related to the formation of a terminator stem within the expression platform under such conditions. The results revealed that increasing PEG stabilized the structure of the terminator stem. By contrast, the addition of ethylene glycol destabilized the terminator stem. PEG and ethylene glycol have opposite effects on transcription as well as on stable terminator stem formation. The glycine-independency of the riboswitch and the effects of such glycols might shed light on the evolution of riboswitches. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

[What gene and chromosomes say about the origin and evolution of insects and other arthropods].

PubMed

Lukhtanov, V A; Kuznetsova, V G

2010-09-01

At the turn of the 21st century, the use of molecular and molecular cytogenetic methods led to revolutionary advances in systematics of insects and other arthropods. Analysis of nuclear and mitochondrial genes, as well as investigation of structural rearrangements in the mitochondrial chromosome convincingly supported the Pancrustacea hypothesis, according to which insects originated directly from crustaceans, whereas myriapods are not closely related to them. The presence of the specific telomeric motif TTAGG confirmed the monophyletic origin of arthropods (Arthropoda) and the assignment of tongue worms (Pentastomida) to this type. Several different types of telomeric sequences have been found within the class of insects. Investigation of the molecular organization of these sequences may shed light on the relationships between the orders Diptera, Siphonaptera, and Mecoptera and on the origin of such enigmatic groups as the orders Strepsiptera, Zoraptera and suborder Coleorrhyncha.

Energy development and environment: What about solar energy in a long term perspective?

NASA Astrophysics Data System (ADS)

Dessus, Benjamin; Pharabod, Francois

After decades of strong growth, the next century might be that in which the world population is stabilized around 11 billion inhabitants. Next century's main concerns include the development hoped for the probable consequences of an increase of the greenhouse effect due to main induced emissions, and the risks posed by possible dissemination of nuclear energy to all the regions of the globe. In order to shed some light on these questions, we propose an energy scenario, based on an analysis of evolution of demographics, energy needs, renewable and fossil reserves, environmental issues, technological possibilities and regional imbalances. This scenario shows that solar energy could contribute significantly in the long term energy mix. We discuss the respective advantages and drawbacks of the different solar technologies: solar power satellites, ground solar power plants and decentralized applications, as they to the needs that must be satisfied.

Toward understanding the evolution of vertebrate gene regulatory networks: comparative genomics and epigenomic approaches.

PubMed

Martinez-Morales, Juan R

2016-07-01

Vertebrates, as most animal phyla, originated >500 million years ago during the Cambrian explosion, and progressively radiated into the extant classes. Inferring the evolutionary history of the group requires understanding the architecture of the developmental programs that constrain the vertebrate anatomy. Here, I review recent comparative genomic and epigenomic studies, based on ChIP-seq and chromatin accessibility, which focus on the identification of functionally equivalent cis-regulatory modules among species. This pioneer work, primarily centered in the mammalian lineage, has set the groundwork for further studies in representative vertebrate and chordate species. Mapping of active regulatory regions across lineages will shed new light on the evolutionary forces stabilizing ancestral developmental programs, as well as allowing their variation to sustain morphological adaptations on the inherited vertebrate body plan. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The Evolutionary Innovation of Nutritional Symbioses in Leaf-Cutter Ants

PubMed Central

Aylward, Frank O.; Currie, Cameron R.; Suen, Garret

2012-01-01

Fungus-growing ants gain access to nutrients stored in plant biomass through their association with a mutualistic fungus they grow for food. This 50 million-year-old obligate mutualism likely facilitated some of these species becoming dominant Neotropical herbivores that can achieve immense colony sizes. Recent culture-independent investigations have shed light on the conversion of plant biomass into nutrients within ant fungus gardens, revealing that this process involves both the fungal cultivar and a symbiotic community of bacteria including Enterobacter, Klebsiella, and Pantoea species. Moreover, the genome sequences of the leaf-cutter ants Atta cephalotes and Acromyrmex echinatior have provided key insights into how this symbiosis has shaped the evolution of these ants at a genetic level. Here we summarize the findings of recent research on the microbial community dynamics within fungus-growing ant fungus gardens and discuss their implications for this ancient symbiosis. PMID:26467948

A new stem turtle from the Middle Jurassic of Scotland: new insights into the evolution and palaeoecology of basal turtles

PubMed Central

Anquetin, Jérémy; Barrett, Paul M.; Jones, Marc E.H.; Moore-Fay, Scott; Evans, Susan E.

2008-01-01

The discovery of a new stem turtle from the Middle Jurassic (Bathonian) deposits of the Isle of Skye, Scotland, sheds new light on the early evolutionary history of Testudinata. Eileanchelys waldmani gen. et sp. nov. is known from cranial and postcranial material of several individuals and represents the most complete Middle Jurassic turtle described to date, bridging the morphological gap between basal turtles from the Late Triassic–Early Jurassic and crown-group turtles that diversify during the Late Jurassic. A phylogenetic analysis places the new taxon within the stem group of Testudines (crown-group turtles) and suggests a sister-group relationship between E. waldmani and Heckerochelys romani from the Middle Jurassic of Russia. Moreover, E. waldmani also demonstrates that stem turtles were ecologically diverse, as it may represent the earliest known aquatic turtle. PMID:19019789

parasitised feathered dinosaurs as revealed by Cretaceous amber assemblages.

PubMed

Peñalver, Enrique; Arillo, Antonio; Delclòs, Xavier; Peris, David; Grimaldi, David A; Anderson, Scott R; Nascimbene, Paul C; Pérez-de la Fuente, Ricardo

2017-12-12

Ticks are currently among the most prevalent blood-feeding ectoparasites, but their feeding habits and hosts in deep time have long remained speculative. Here, we report direct and indirect evidence in 99 million-year-old Cretaceous amber showing that hard ticks and ticks of the extinct new family Deinocrotonidae fed on blood from feathered dinosaurs, non-avialan or avialan excluding crown-group birds. A †Cornupalpatum burmanicum hard tick is entangled in a pennaceous feather. Two deinocrotonids described as †Deinocroton draculi gen. et sp. nov. have specialised setae from dermestid beetle larvae (hastisetae) attached to their bodies, likely indicating cohabitation in a feathered dinosaur nest. A third conspecific specimen is blood-engorged, its anatomical features suggesting that deinocrotonids fed rapidly to engorgement and had multiple gonotrophic cycles. These findings provide insight into early tick evolution and ecology, and shed light on poorly known arthropod-vertebrate interactions and potential disease transmission during the Mesozoic.

Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

NASA Astrophysics Data System (ADS)

Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

2017-09-01

Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

Entomopathogenic bacteria use multiple mechanisms for bioactive peptide library design

NASA Astrophysics Data System (ADS)

Cai, Xiaofeng; Nowak, Sarah; Wesche, Frank; Bischoff, Iris; Kaiser, Marcel; Fürst, Robert; Bode, Helge. B.

2017-04-01

The production of natural product compound libraries has been observed in nature for different organisms such as bacteria, fungi and plants; however, little is known about the mechanisms generating such chemically diverse libraries. Here we report mechanisms leading to the biosynthesis of the chemically diverse rhabdopeptide/xenortide peptides (RXPs). They are exclusively present in entomopathogenic bacteria of the genera Photorhabdus and Xenorhabdus that live in symbiosis with nematodes delivering them to insect prey, which is killed and utilized for nutrition by both nematodes and bacteria. Chemical diversity of the biologically active RXPs results from a combination of iterative and flexible use of monomodular nonribosomal peptide synthetases including substrate promiscuity, enzyme cross-talk and enzyme stoichiometry as shown by in vivo and in vitro experiments. Together, this highlights several of nature's methods for diversification, or evolution, of natural products and sheds light on the biosynthesis of the bioactive RXPs.

Intragenomic spread of plastid-targeting presequences in the coccolithophore Emiliania huxleyi.

PubMed

Burki, Fabien; Hirakawa, Yoshihisa; Keeling, Patrick J

2012-09-01

Nucleus-encoded plastid-targeted proteins of photosynthetic organisms are generally equipped with an N-terminal presequence required for crossing the plastid membranes. The acquisition of these presequences played a fundamental role in the establishment of plastids. Here, we report a unique case of two non-homologous proteins possessing completely identical presequences consisting of a bipartite plastid-targeting signal in the coccolithophore Emiliania huxleyi. We further show that this presequence is highly conserved in five additional proteins that did not originally function in plastids, representing de novo plastid acquisitions. These are among the most recent cases of presequence spreading from gene to gene and shed light on important evolutionary processes that have been usually erased by the ancient history of plastid evolution. We propose a mechanism of acquisition involving genomic duplications and gene replacement through non-homologous recombination that may have played a more general role for equipping proteins with targeting information.

Alberi Validates New Theory, Sheds Light on Semiconductors | News | NREL

Science.gov Websites

the discovery when they found that light can suppress native defect formation during semiconductor growth. When Alberi and Scarpulla began discussing the concept of how light can affect semiconductor that pieces easily fit together, so are the atoms in the crystal. But when an atom appears in a crystal

Experimentally infected domestic ducks show efficient transmission of Indonesian H5N1 highly pathogenic avian influenza virus, but lack persistent viral shedding.

PubMed

Wibawa, Hendra; Bingham, John; Nuradji, Harimurti; Lowther, Sue; Payne, Jean; Harper, Jenni; Junaidi, Akhmad; Middleton, Deborah; Meers, Joanne

2014-01-01

Ducks are important maintenance hosts for avian influenza, including H5N1 highly pathogenic avian influenza viruses. A previous study indicated that persistence of H5N1 viruses in ducks after the development of humoral immunity may drive viral evolution following immune selection. As H5N1 HPAI is endemic in Indonesia, this mechanism may be important in understanding H5N1 evolution in that region. To determine the capability of domestic ducks to maintain prolonged shedding of Indonesian clade 2.1 H5N1 virus, two groups of Pekin ducks were inoculated through the eyes, nostrils and oropharynx and viral shedding and transmission investigated. Inoculated ducks (n = 15), which were mostly asymptomatic, shed infectious virus from the oral route from 1 to 8 days post inoculation, and from the cloacal route from 2-8 dpi. Viral ribonucleic acid was detected from 1-15 days post inoculation from the oral route and 1-24 days post inoculation from the cloacal route (cycle threshold <40). Most ducks seroconverted in a range of serological tests by 15 days post inoculation. Virus was efficiently transmitted during acute infection (5 inoculation-infected to all 5 contact ducks). However, no evidence for transmission, as determined by seroconversion and viral shedding, was found between an inoculation-infected group (n = 10) and contact ducks (n = 9) when the two groups only had contact after 10 days post inoculation. Clinical disease was more frequent and more severe in contact-infected (2 of 5) than inoculation-infected ducks (1 of 15). We conclude that Indonesian clade 2.1 H5N1 highly pathogenic avian influenza virus does not persist in individual ducks after acute infection.

A Real Shooting Star

NASA Technical Reports Server (NTRS)

2007-01-01

[figure removed for brevity, see original site] Click on the image for movie of A Real Shooting Star

This artist's animation illustrates a star flying through our galaxy at supersonic speeds, leaving a 13-light-year-long trail of glowing material in its wake. The star, named Mira (pronounced my-rah) after the latin word for 'wonderful,' sheds material that will be recycled into new stars, planets and possibly even life. NASA's Galaxy Evolution Explorer discovered the long trail of material behind Mira during its survey of the entire sky in ultraviolet light.

The animation begins by showing a close-up of Mira -- a red-giant star near the end of its life. Red giants are red in color and extremely bloated; for example, if a red giant were to replace our sun, it would engulf everything out to the orbit of Mars. They constantly blow off gas and dust in the form of stellar winds, supplying the galaxy with molecules, such as oxygen and carbon, that will make their way into new solar systems. Our sun will mature into a red giant in about 5 billion years.

As the animation pulls out, we can see the enormous trail of material deposited behind Mira as it hurls along between the stars. Like a boat traveling through water, a bow shock, or build up of gas, forms ahead of the star in the direction of its motion. Gas in the bow shock is heated and then mixes with the cool hydrogen gas in the wind that is blowing off Mira. This heated hydrogen gas then flows around behind the star, forming a turbulent wake.

Why does the trailing hydrogen gas glow in ultraviolet light? When it is heated, it transitions into a higher-energy state, which then loses energy by emitting ultraviolet light - a process known as fluorescence.

Finally, the artist's rendering gives way to the actual ultraviolet image taken by the Galaxy Evolution Explorer

Mira is located 350 light-years from Earth in the constellation Cetus, otherwise known as the whale. Coincidentally, Mira and its 'whale of a tail' can be found in the tail of the whale constellation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Juneau, Stéphanie; Bournaud, Frédéric; Daddi, Emanuele

Emission line diagnostic diagrams probing the ionization sources in galaxies, such as the Baldwin-Phillips-Terlevich (BPT) diagram, have been used extensively to distinguish active galactic nuclei (AGN) from purely star-forming galaxies. However, they remain poorly understood at higher redshifts. We shed light on this issue with an empirical approach based on a z ∼ 0 reference sample built from ∼300,000 Sloan Digital Sky Survey galaxies, from which we mimic selection effects due to typical emission line detection limits at higher redshift. We combine this low-redshift reference sample with a simple prescription for luminosity evolution of the global galaxy population to predictmore » the loci of high-redshift galaxies on the BPT and Mass-Excitation (MEx) diagnostic diagrams. The predicted bivariate distributions agree remarkably well with direct observations of galaxies out to z ∼ 1.5, including the observed stellar mass-metallicity (MZ) relation evolution. As a result, we infer that high-redshift star-forming galaxies are consistent with having normal interstellar medium (ISM) properties out to z ∼ 1.5, after accounting for selection effects and line luminosity evolution. Namely, their optical line ratios and gas-phase metallicities are comparable to that of low-redshift galaxies with equivalent emission-line luminosities. In contrast, AGN narrow-line regions may show a shift toward lower metallicities at higher redshift. While a physical evolution of the ISM conditions is not ruled out for purely star-forming galaxies and may be more important starting at z ≳ 2, we find that reliably quantifying this evolution is hindered by selections effects. The recipes provided here may serve as a basis for future studies toward this goal. Code to predict the loci of galaxies on the BPT and MEx diagnostic diagrams and the MZ relation as a function of emission line luminosity limits is made publicly available.« less

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

PubMed

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Modeling elastic anisotropy in strained heteroepitaxy

NASA Astrophysics Data System (ADS)

Krishna Dixit, Gopal; Ranganathan, Madhav

2017-09-01

Using a continuum evolution equation, we model the growth and evolution of quantum dots in the heteroepitaxial Ge on Si(0 0 1) system in a molecular beam epitaxy unit. We formulate our model in terms of evolution due to deposition, and due to surface diffusion which is governed by a free energy. This free energy has contributions from surface energy, curvature, wetting effects and elastic energy due to lattice mismatch between the film and the substrate. In addition to anisotropy due to surface energy which favors facet formation, we also incorporate elastic anisotropy due to an underlying crystal lattice. The complicated elastic problem of the film-substrate system subjected to boundary conditions at the free surface, interface and the bulk substrate is solved by perturbation analysis using a small slope approximation. This permits an analysis of effects at different orders in the slope and sheds new light on the observed behavior. Linear stability analysis shows the early evolution of the instability towards dot formation. The elastic anisotropy causes a change in the alignment of dots in the linear regime, whereas the surface energy anisotropy changes the dot shapes at the nonlinear regime. Numerical simulation of the full nonlinear equations shows the evolution of the surface morphology. In particular, we show, for parameters of the Ge0.25 Si0.75 on Si(0 0 1), the surface energy anisotropy dominates the shapes of the quantum dots, whereas their alignment is influenced by the elastic energy anisotropy. The anisotropy in elasticity causes a further elongation of the islands whose coarsening is interrupted due to < 1 0 5 > facets on the surface.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

PubMed Central

Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics. PMID:28173504

Evolution of senescence in nature: physiological evolution in populations of garter snake with divergent life histories.

PubMed

Robert, Kylie A; Bronikowski, Anne M

2010-02-01

Evolutionary theories of aging are linked to life-history theory in that age-specific schedules of reproduction and survival determine the trajectory of age-specific mutation/selection balances across the life span and thus the rate of senescence. This is predicted to manifest at the organismal level in the evolution of energy allocation strategies of investing in somatic maintenance and robust stress responses in less hazardous environments in exchange for energy spent on growth and reproduction. Here we report experiments from long-studied populations of western terrestrial garter snakes (Thamnophis elegans) that reside in low and high extrinsic mortality environments, with evolved long and short life spans, respectively. Laboratory common-environment colonies of these two ecotypes were tested for a suite of physiological traits after control and stressed gestations. In offspring derived from control and corticosterone-treated dams, we measured resting metabolism; mitochondrial oxygen consumption, ATP and free radical production rates; and erythrocyte DNA damage and repair ability. We evaluated whether these aging biomarkers mirrored the evolution of life span and whether they were sensitive to stress. Neonates from the long-lived ecotype (1) were smaller, (2) consumed equal amounts of oxygen when corrected for body mass, (3) had DNA that damaged more readily but repaired more efficiently, and (4) had more efficient mitochondria and more efficient cellular antioxidant defenses than short-lived snakes. Many ecotype differences were enhanced in offspring derived from stress-treated dams, which supports the conclusion that nongenetic maternal effects may further impact the cellular stress defenses of offspring. Our findings reveal that physiological evolution underpins reptilian life histories and sheds light on the connectedness between stress response and aging pathways in wild-dwelling organisms.

Modeling elastic anisotropy in strained heteroepitaxy.

PubMed

Dixit, Gopal Krishna; Ranganathan, Madhav

2017-09-20

Using a continuum evolution equation, we model the growth and evolution of quantum dots in the heteroepitaxial Ge on Si(0 0 1) system in a molecular beam epitaxy unit. We formulate our model in terms of evolution due to deposition, and due to surface diffusion which is governed by a free energy. This free energy has contributions from surface energy, curvature, wetting effects and elastic energy due to lattice mismatch between the film and the substrate. In addition to anisotropy due to surface energy which favors facet formation, we also incorporate elastic anisotropy due to an underlying crystal lattice. The complicated elastic problem of the film-substrate system subjected to boundary conditions at the free surface, interface and the bulk substrate is solved by perturbation analysis using a small slope approximation. This permits an analysis of effects at different orders in the slope and sheds new light on the observed behavior. Linear stability analysis shows the early evolution of the instability towards dot formation. The elastic anisotropy causes a change in the alignment of dots in the linear regime, whereas the surface energy anisotropy changes the dot shapes at the nonlinear regime. Numerical simulation of the full nonlinear equations shows the evolution of the surface morphology. In particular, we show, for parameters of the [Formula: see text] [Formula: see text] on Si(0 0 1), the surface energy anisotropy dominates the shapes of the quantum dots, whereas their alignment is influenced by the elastic energy anisotropy. The anisotropy in elasticity causes a further elongation of the islands whose coarsening is interrupted due to [Formula: see text] facets on the surface.

Shedding Light on Engineering Design

ERIC Educational Resources Information Center

Capobianco, Brenda M.; Nyquist, Chell; Tyrie, Nancy

2013-01-01

This article describes the steps incorporated to teach an engineering design process in a fifth-grade science classroom. The engineering design-based activity was an existing scientific inquiry activity using UV light--detecting beads and purposefully creating a series of engineering design-based challenges around the investigation. The…

Shedding Light on Fiber Optics.

ERIC Educational Resources Information Center

Bunch, Robert M.

1994-01-01

Explains the principles of fiber optics as a medium for light-wave communication. Current uses of fiber systems on college campuses include voice, video, and local area network applications. A group of seven school districts in Minnesota are linked via fiber-optic cables. Other uses are discussed. (MLF)

Meteor showers in review

NASA Astrophysics Data System (ADS)

Jenniskens, Peter

2017-09-01

Recent work on meteor showers is reviewed. New data is presented on the long duration showers that wander in sun-centered ecliptic coordinates. Since the early days of meteor photography, much progress has been made in mapping visual meteor showers, using low-light video cameras instead. Now, some 820,000 meteoroid orbits have been measured by four orbit surveys during 2007-2015. Mapped in sun-centered ecliptic coordinates in 5° intervals of solar longitude, the data show a number of long duration (>15 days) meteor showers that have drifting radiants and speeds with solar longitude. 18 showers emerge from the antihelion source and follow a drift pattern towards high ecliptic latitudes. 27 Halley-type showers in the apex source move mostly towards lower ecliptic longitudes, but those at high ecliptic latitudes move backwards. Also, 5 low-speed showers appear between the toroidal ring and the apex source, moving towards the antihelion source. Most other showers do not last long, or do not move much in sun-centered ecliptic coordinates. The surveys also detected episodic showers, which mostly document the early stages of meteoroid stream formation. New data on the sporadic background have shed light on the dynamical evolution of the zodiacal cloud.

The meaning of home for ageing women living alone: An evolutionary concept analysis.

PubMed

Barry, Arro; Heale, Roberta; Pilon, Roger; Lavoie, Anne Marise

2018-05-01

The concept of home to women ageing should be visited in the light of ongoing cultural, political, temporal and disciplinary evolutions. In part, to compliment policies increasing focus on supporting older adults to age in place and a growing attention on the home as a place where healthcare is designed and provided. The following concept analysis utilises Rodgers' evolutionary method to inductively analyse literature in order to elicit the meaning and experience of home among older women who are ageing at home. Literature was collected over an 18-month period during 2014-2015 and the sample was made up of 49 articles. The analysis led to the concept of home among women ageing in communities to be defined by four attributes. These attributes are home as (i) a resource, (ii) an attachment, (iii) the precariousness of maintaining and sustaining home and (iv) a cultural expectation. This analysis of the meaning and experience of home among women ageing at home has shed light on the needs for this group of women, while highlighting the need to continue to further clarify and define the concept through research. © 2017 John Wiley & Sons Ltd.

An optical view of extragalactic gamma-ray emitters

NASA Astrophysics Data System (ADS)

Paiano, Simona; Falomo, Renato; Landoni, Marco; Treves, Aldo; Scarpa, Riccardo

2017-11-01

The Fermi Gamma-ray Observatory discovered about a thousand extragalactic sources emitting energy from 100 MeV to 100 GeV. The majority of these sources belong to the class of blazars characterized by a quasi-featureless optical spectrum (BL Lac Objects). This hampers the determination of their redshift and therefore hinders the characterization of this class of objects. To investigate the nature of these sources and to determine their redshift, we are carrying out an extensive campaign at the 10m Gran Telescopio Canarias to secure high signal-to-noise ratio optical spectra. These observations allow us to confirm the blazar nature of the targets, to find new redshifts or to set stringent limits on the redshift based on the minimum equivalent width of absorption features expected from their host galaxy, assuming it is a massive elliptical galaxy.These results are of importance for the multi-frequencies emission models of the blazars, to test their extreme physics, to shed light on their cosmic evolution and abundance in the far Universe.These gamma emitters are also of great importance for the characterization of the extragalactic background light through the absorption by the IR-optical background photons.

Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system.

PubMed

Mordhorst, Bethany R; Wilson, Miranda L; Conant, Gavin C

2016-01-01

In this review, we discuss the way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems. In the first part of the review, we contrast the rapid evolution seen in some reproductive genes with the generally conservative nature of development. We discuss directional selection and coevolution as potential drivers of rapid evolution in sperm and egg proteins. Such rapid change is very different from the highly conservative nature of later embryo development. However, it is not unique, as some regions of the sex chromosomes also show elevated rates of evolutionary change. To explain these contradictory trends, we argue that it is not reproductive functions per se that induce rapid evolution. Rather, it is the fact that biotic interactions, such as speciation events and sexual conflict, have no evolutionary endpoint and hence can drive continuous evolutionary changes. Returning to the question of sex chromosome evolution, we discuss the way that recent advances in evolutionary genomics and systems biology and, in particular, the development of a theory of gene balance provide a better understanding of the evolutionary patterns seen on these chromosomes. We end the review with a discussion of a surprising and incompletely understood phenomenon observed in early embryos: namely the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide. We argue that evolutionary insights, from both yeasts and tumor cells, help to explain the Warburg effect, and that new metabolic modeling approaches are useful in assessing the potential sources of the effect.

A 1-D evolutionary model for icy satellites, applied to Enceladus

NASA Astrophysics Data System (ADS)

Malamud, Uri; Prialnik, Dina

2016-04-01

We develop a long-term 1-D evolution model for icy satellites that couples multiple processes: water migration and differentiation, geochemical reactions and silicate phase transitions, compaction by self-gravity, and ablation. The model further considers the following energy sources and sinks: tidal heating, radiogenic heating, geochemical energy released by serpentinization or absorbed by mineral dehydration, gravitational energy and insolation, and heat transport by conduction, convection, and advection. We apply the model to Enceladus, by guessing the initial conditions that would render a structure compatible with present-day observations, assuming the initial structure to have been homogeneous. Assuming the satellite has been losing water continually along its evolution, we postulate that it was formed as a more massive, more icy and more porous satellite, and gradually transformed into its present day state due to sustained long-term tidal heating. We consider several initial compositions and evolution scenarios and follow the evolution for the age of the Solar System, testing the present day model results against the available observational constraints. Our model shows the present configuration to be differentiated into a pure icy mantle, several tens of km thick, overlying a rocky core, composed of dehydrated rock at the center and hydrated rock in the outer part. For Enceladus, it predicts a higher rock/ice mass ratio than previously assumed and a thinner ice mantle, compatible with recent estimates based on gravity field measurements. Although, obviously, the model cannot be used to explain local phenomena, it sheds light on the internal structure invoked in explanations of localized features and activities.

Genome Evolution in the Primary Endosymbiont of Whiteflies Sheds Light on Their Divergence

PubMed Central

Santos-Garcia, Diego; Vargas-Chavez, Carlos; Moya, Andrés; Latorre, Amparo; Silva, Francisco J.

2015-01-01

Whiteflies are important agricultural insect pests, whose evolutionary success is related to a long-term association with a bacterial endosymbiont, Candidatus Portiera aleyrodidarum. To completely characterize this endosymbiont clade, we sequenced the genomes of three new Portiera strains covering the two extant whitefly subfamilies. Using endosymbiont and mitochondrial sequences we estimated the divergence dates in the clade and used these values to understand the molecular evolution of the endosymbiont coding sequences. Portiera genomes were maintained almost completely stable in gene order and gene content during more than 125 Myr of evolution, except in the Bemisia tabaci lineage. The ancestor had already lost the genetic information transfer autonomy but was able to participate in the synthesis of all essential amino acids and carotenoids. The time of divergence of the B. tabaci complex was much more recent than previous estimations. The recent divergence of biotypes B (MEAM1 species) and Q (MED species) suggests that they still could be considered strains of the same species. We have estimated the rates of evolution of Portiera genes, synonymous and nonsynonymous, and have detected significant differences among-lineages, with most Portiera lineages evolving very slowly. Although the nonsynonymous rates were much smaller than the synonymous, the genomic dN/dS ratios were similar, discarding selection as the driver of among-lineage variation. We suggest variation in mutation rate and generation time as the responsible factors. In conclusion, the slow evolutionary rates of Portiera may have contributed to its long-term association with whiteflies, avoiding its replacement by a novel and more efficient endosymbiont. PMID:25716826

Signatures of the Galactic bar on stellar kinematics unveiled by APOGEE

NASA Astrophysics Data System (ADS)

Palicio, Pedro A.; Martinez-Valpuesta, Inma; Allende Prieto, Carlos; Dalla Vecchia, Claudio; Zamora, Olga; Zasowski, Gail; Fernandez-Trincado, J. G.; Masters, Karen L.; García-Hernández, D. A.; Roman-Lopes, Alexandre

2018-07-01

Bars are common galactic structures in the local universe that play an important role in the secular evolution of galaxies, including the Milky Way. In particular, the velocity distribution of individual stars in our galaxy is useful to shed light on stellar dynamics, and provides information complementary to that inferred from the integrated light of external galaxies. However, since a wide variety of models reproduce the distribution of velocity and the velocity dispersion observed in the Milky Way, we look for signatures of the bar on higher order moments of the line-of-sight velocity (V_{los}) distribution. We use two different numerical simulations - one that has developed a bar and one that remains nearly axisymmetric - to compare them with observations in the latest Apache Point Observatory Galactic Evolution Experiment data release (SDSS DR14). This comparison reveals three interesting structures that support the notion that the Milky Way is a barred galaxy. A high-skewness region found at positive longitudes constrains the orientation angle of the bar, and is incompatible with the orientation of the bar at ℓ = 0° proposed in previous studies. We also analyse the V_{los} distributions in three regions, and introduce the Hellinger distance to quantify the differences among them. Our results show a strong non-Gaussian distribution both in the data and in the barred model, confirming the qualitative conclusions drawn from the velocity maps. In contrast to earlier work, we conclude it is possible to infer the presence of the bar from the kurtosis distribution.

Timing is everything: early degradation of abscission layer is associated with increased seed shattering in U.S. weedy rice

PubMed Central

2011-01-01

Background Seed shattering, or shedding, is an important fitness trait for wild and weedy grasses. U.S. weedy rice (Oryza sativa) is a highly shattering weed, thought to have evolved from non-shattering cultivated ancestors. All U.S. weedy rice individuals examined to date contain a mutation in the sh4 locus associated with loss of shattering during rice domestication. Weedy individuals also share the shattering trait with wild rice, but not the ancestral shattering mutation at sh4; thus, how weedy rice reacquired the shattering phenotype is unknown. To establish the morphological basis of the parallel evolution of seed shattering in weedy rice and wild, we examined the abscission layer at the flower-pedicel junction in weedy individuals in comparison with wild and cultivated relatives. Results Consistent with previous work, shattering wild rice individuals possess clear, defined abscission layers at flowering, whereas non-shattering cultivated rice individuals do not. Shattering weedy rice from two separately evolved populations in the U.S. (SH and BHA) show patterns of abscission layer formation and degradation distinct from wild rice. Prior to flowering, the abscission layer has formed in all weedy individuals and by flowering it is already degrading. In contrast, wild O. rufipogon abscission layers have been shown not to degrade until after flowering has occurred. Conclusions Seed shattering in weedy rice involves the formation and degradation of an abscission layer in the flower-pedicel junction, as in wild Oryza, but is a developmentally different process from shattering in wild rice. Weedy rice abscission layers appear to break down earlier than wild abscission layers. The timing of weedy abscission layer degradation suggests that unidentified regulatory genes may play a critical role in the reacquisition of shattering in weedy rice, and sheds light on the morphological basis of parallel evolution for shattering in weedy and wild rice. PMID:21235796

Timing is everything: early degradation of abscission layer is associated with increased seed shattering in U.S. weedy rice.

PubMed

Thurber, Carrie S; Hepler, Peter K; Caicedo, Ana L

2011-01-14

Seed shattering, or shedding, is an important fitness trait for wild and weedy grasses. U.S. weedy rice (Oryza sativa) is a highly shattering weed, thought to have evolved from non-shattering cultivated ancestors. All U.S. weedy rice individuals examined to date contain a mutation in the sh4 locus associated with loss of shattering during rice domestication. Weedy individuals also share the shattering trait with wild rice, but not the ancestral shattering mutation at sh4; thus, how weedy rice reacquired the shattering phenotype is unknown. To establish the morphological basis of the parallel evolution of seed shattering in weedy rice and wild, we examined the abscission layer at the flower-pedicel junction in weedy individuals in comparison with wild and cultivated relatives. Consistent with previous work, shattering wild rice individuals possess clear, defined abscission layers at flowering, whereas non-shattering cultivated rice individuals do not. Shattering weedy rice from two separately evolved populations in the U.S. (SH and BHA) show patterns of abscission layer formation and degradation distinct from wild rice. Prior to flowering, the abscission layer has formed in all weedy individuals and by flowering it is already degrading. In contrast, wild O. rufipogon abscission layers have been shown not to degrade until after flowering has occurred. Seed shattering in weedy rice involves the formation and degradation of an abscission layer in the flower-pedicel junction, as in wild Oryza, but is a developmentally different process from shattering in wild rice. Weedy rice abscission layers appear to break down earlier than wild abscission layers. The timing of weedy abscission layer degradation suggests that unidentified regulatory genes may play a critical role in the reacquisition of shattering in weedy rice, and sheds light on the morphological basis of parallel evolution for shattering in weedy and wild rice.

Chasing Salmonella Typhimurium in free range egg production system.

PubMed

Chousalkar, Kapil; Gole, Vaibhav; Caraguel, Charles; Rault, Jean-Loup

2016-08-30

Free range production systems are becoming a major source of egg production in Australia and worldwide. This study investigated shedding and ecology of Salmonella Typhimurium and Salmonella species in a free range layer flock, wild birds and foxes in the vicinity of the free range farm in different seasons. Shedding of Salmonella was significantly higher in summer. Within the shed, overall, Salmonella prevalence was highest in dust. Corticosterone level in faeces was highest in spring and lowest in winter. There was no direct association between the Salmonella shedding (MPN/gm) and corticosterone levels in faeces. Salmonella Typhimurium MLVA types isolated from fox and wild birds were similar to MLVA types isolated from layer flock and reported during human food borne illness. Wild birds and foxes appear to play an important role in S. Typhimurium ecology and food safety. Environmental factors could play a role in evolution of S. Typhimurium in free range environment. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Supercomputing Sheds Light on the Dark Universe

DOE Office of Scientific and Technical Information (OSTI.GOV)

Habib, Salman; Heitmann, Katrin

2012-11-15

At Argonne National Laboratory, scientists are using supercomputers to shed light on one of the great mysteries in science today, the Dark Universe. With Mira, a petascale supercomputer at the Argonne Leadership Computing Facility, a team led by physicists Salman Habib and Katrin Heitmann will run the largest, most complex simulation of the universe ever attempted. By contrasting the results from Mira with state-of-the-art telescope surveys, the scientists hope to gain new insights into the distribution of matter in the universe, advancing future investigations of dark energy and dark matter into a new realm. The team's research was named amore » finalist for the 2012 Gordon Bell Prize, an award recognizing outstanding achievement in high-performance computing.« less

Photoreceptor disc shedding in the living human eye

PubMed Central

Kocaoglu, Omer P.; Liu, Zhuolin; Zhang, Furu; Kurokawa, Kazuhiro; Jonnal, Ravi S.; Miller, Donald T.

2016-01-01

Cone photoreceptors undergo a daily cycle of renewal and shedding of membranous discs in their outer segments (OS), the portion responsible for light capture. These physiological processes are fundamental to maintaining photoreceptor health, and their dysfunction is associated with numerous retinal diseases. While both processes have been extensively studied in animal models and postmortem eyes, little is known about them in the living eye, in particular human. In this study, we report discovery of the optical signature associated with disc shedding using a method based on adaptive optics optical coherence tomography (AO-OCT) in conjunction with post-processing methods to track and monitor individual cone cells in 4D. The optical signature of disc shedding is characterized by an abrupt transient loss in the cone outer segment tip (COST) reflection followed by its return that is axially displaced anteriorly. Using this signature, we measured the temporal and spatial properties of shedding events in three normal subjects. Average duration of the shedding event was 8.8 ± 13.4 minutes, and average length loss of the OS was 2.1 μm (7.0% of OS length). Prevalence of cone shedding was highest in the morning (14.3%) followed by the afternoon (5.7%) and evening (4.0%), with load distributed across the imaged patch. To the best of our knowledge these are the first images of photoreceptor disc shedding in the living retina. PMID:27895995

A dynamic history of gene duplications and losses characterizes the evolution of the SPARC family in eumetazoans.

PubMed

Bertrand, Stephanie; Fuentealba, Jaime; Aze, Antoine; Hudson, Clare; Yasuo, Hitoyoshi; Torrejon, Marcela; Escriva, Hector; Marcellini, Sylvain

2013-04-22

The vertebrates share the ability to produce a skeleton made of mineralized extracellular matrix. However, our understanding of the molecular changes that accompanied their emergence remains scarce. Here, we describe the evolutionary history of the SPARC (secreted protein acidic and rich in cysteine) family, because its vertebrate orthologues are expressed in cartilage, bones and teeth where they have been proposed to bind calcium and act as extracellular collagen chaperones, and because further duplications of specific SPARC members produced the small calcium-binding phosphoproteins (SCPP) family that is crucial for skeletal mineralization to occur. Both phylogeny and synteny conservation analyses reveal that, in the eumetazoan ancestor, a unique ancestral gene duplicated to give rise to SPARC and SPARCB described here for the first time. Independent losses have eliminated one of the two paralogues in cnidarians, protostomes and tetrapods. Hence, only non-tetrapod deuterostomes have conserved both genes. Remarkably, SPARC and SPARCB paralogues are still linked in the amphioxus genome. To shed light on the evolution of the SPARC family members in chordates, we performed a comprehensive analysis of their embryonic expression patterns in amphioxus, tunicates, teleosts, amphibians and mammals. Our results show that in the chordate lineage SPARC and SPARCB family members were recurrently recruited in a variety of unrelated tissues expressing collagen genes. We propose that one of the earliest steps of skeletal evolution involved the co-expression of SPARC paralogues with collagenous proteins.

Heterogeneous update mechanisms in evolutionary games: Mixing innovative and imitative dynamics

NASA Astrophysics Data System (ADS)

Amaral, Marco Antonio; Javarone, Marco Alberto

2018-04-01

Innovation and evolution are two processes of paramount relevance for social and biological systems. In general, the former allows the introduction of elements of novelty, while the latter is responsible for the motion of a system in its phase space. Often, these processes are strongly related, since an innovation can trigger the evolution, and the latter can provide the optimal conditions for the emergence of innovations. Both processes can be studied by using the framework of evolutionary game theory, where evolution constitutes an intrinsic mechanism. At the same time, the concept of innovation requires an opportune mathematical representation. Notably, innovation can be modeled as a strategy, or it can constitute the underlying mechanism that allows agents to change strategy. Here, we analyze the second case, investigating the behavior of a heterogeneous population, composed of imitative and innovative agents. Imitative agents change strategy only by imitating that of their neighbors, whereas innovative ones change strategy without the need for a copying source. The proposed model is analyzed by means of analytical calculations and numerical simulations in different topologies. Remarkably, results indicate that the mixing of mechanisms can be detrimental to cooperation near phase transitions. In those regions, the spatial reciprocity from imitative mechanisms is destroyed by innovative agents, leading to the downfall of cooperation. Our investigation sheds some light on the complex dynamics emerging from the heterogeneity of strategy revision methods, highlighting the role of innovation in evolutionary games.

Shedding light on the Type Ia supernova extinction puzzle: dust location found

NASA Astrophysics Data System (ADS)

Bulla, M.; Goobar, A.; Dhawan, S.

2018-06-01

The colour evolution of reddened Type Ia supernovae can place strong constraints on the location of dust and help address the question of whether the observed extinction stems from the interstellar medium or from circumstellar material surrounding the progenitor. Here we analyse BV photometry of 48 reddened Type Ia supernovae from the literature and estimate the dust location from their B - V colour evolution. We find a time-variable colour excess E(B - V) for 15 supernovae in our sample and constrain dust to distances between 0.013 and 45 pc (4 × 1016 - 1020 cm). For the remaining supernovae, we obtain a constant E(B - V) evolution and place lower limits on the dust distance from the explosion. In all the 48 supernovae, the inferred dust location is compatible with an interstellar origin for the extinction. This is corroborated by the observation that supernovae with relatively nearby dust (≲ 1 pc) are located close to the center of their host galaxy, in high-density dusty regions where interactions between the supernova radiation and interstellar clouds close by are likely to occur. For supernovae showing time-variable E(B - V), we identify a potential preference for low RV values, unusually strong sodium absorption and blue-shifted and time-variable absorption features. Within the interstellar framework, this brings evidence to a proposed scenario where cloud-cloud collisions induced by the supernova radiation pressure can shift the grain size distribution to smaller values and enhance the abundance of sodium in the gaseous phase.

The Divided Bacterial Genome: Structure, Function, and Evolution.

PubMed

diCenzo, George C; Finan, Turlough M

2017-09-01

Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella , Vibrio , and Burkholderia . The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure. Copyright © 2017 American Society for Microbiology.

Linking Seed Photosynthesis and Evolution of the Australian and Mediterranean Seagrass Genus Posidonia.

PubMed

Celdran, David; Lloret, Javier; Verduin, Jennifer; van Keulen, Mike; Marín, Arnaldo

2015-01-01

Recent findings have shown that photosynthesis in the skin of the seed of Posidonia oceanica enhances seedling growth. The seagrass genus Posidonia is found only in two distant parts of the world, the Mediterranean Sea and southern Australia. This fact led us to question whether the acquisition of this novel mechanism in the evolution of this seagrass was a pre-adaptation prior to geological isolation of the Mediterranean from Tethys Sea in the Eocene. Photosynthetic activity in seeds of Australian species of Posidonia is still unknown. This study shows oxygen production and respiration rates, and maximum PSII photochemical efficiency (Fv : Fm) in seeds of two Australian Posidonia species (P. australis and P. sinuosa), and compares these with previous results for P. oceanica. Results showed relatively high oxygen production and respiratory rates in all three species but with significant differences among them, suggesting the existence of an adaptive mechanism to compensate for the relatively high oxygen demands of the seeds. In all cases maximal photochemical efficiency of photosystem II rates reached similar values. The existence of photosynthetic activity in the seeds of all three species implicates that it was an ability probably acquired from a common ancestor during the Late Eocene, when this adaptive strategy could have helped Posidonia species to survive in nutrient-poor temperate seas. This study sheds new light on some aspects of the evolution of marine plants and represents an important contribution to global knowledge of the paleogeographic patterns of seagrass distribution.

Marine turtle mitogenome phylogenetics and evolution.

PubMed

Duchene, Sebastián; Frey, Amy; Alfaro-Núñez, Alonzo; Dutton, Peter H; Thomas P Gilbert, M; Morin, Phillip A

2012-10-01

The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae. Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all sea turtles, and reveal phylogeographic patterns within globally-distributed species. Although there was clear concordance between phylogenies and geographic origin of samples in most taxa, we found evidence of more recent dispersal events in the loggerhead and olive ridley turtles, suggesting more recent migrations (<1 Myr) in these species. Overall, our results demonstrate the complexity of sea-turtle diversity, and indicate the need for further research in phylogeography and molecular evolution. Published by Elsevier Inc.

Physical Orbit for λ Virginis and a Test of Stellar Evolution Models

NASA Astrophysics Data System (ADS)

Zhao, M.; Monnier, J. D.; Torres, G.; Boden, A. F.; Claret, A.; Millan-Gabet, R.; Pedretti, E.; Berger, J.-P.; Traub, W. A.; Schloerb, F. P.; Carleton, N. P.; Kern, P.; Lacasse, M. G.; Malbet, F.; Perraut, K.

2007-04-01

The star λ Virginis is a well-known double-lined spectroscopic Am binary with the interesting property that both stars are very similar in abundance but one is sharp-lined and the other is broad-lined. We present combined interferometric and spectroscopic studies of λ Vir. The small scale of the λ Vir orbit (~20 mas) is well resolved by the Infrared Optical Telescope Array (IOTA), allowing us to determine its elements, as well as the physical properties of the components, to high accuracy. The masses of the two stars are determined to be 1.897 and 1.721 Msolar, with 0.7% and 1.5% errors, respectively, and the two stars are found to have the same temperature of 8280+/-200 K. The accurately determined properties of λ Vir allow comparisons between observations and current stellar evolution models, and reasonable matches are found. The best-fit stellar model gives λ Vir a subsolar metallicity of Z=0.0097 and an age of 935 Myr. The orbital and physical parameters of λ Vir also allow us to study its tidal evolution timescales and status. Although atomic diffusion is currently considered to be the most plausible cause of the Am phenomenon, the issue is still being actively debated in the literature. With the present study of the properties and evolutionary status of λ Vir, this system is an ideal candidate for further detailed abundance analyses that might shed more light on the source of the chemical anomalies in these A stars.

Linking Seed Photosynthesis and Evolution of the Australian and Mediterranean Seagrass Genus Posidonia

PubMed Central

Celdran, David; Lloret, Javier; Verduin, Jennifer; van Keulen, Mike; Marín, Arnaldo

2015-01-01

Recent findings have shown that photosynthesis in the skin of the seed of Posidonia oceanica enhances seedling growth. The seagrass genus Posidonia is found only in two distant parts of the world, the Mediterranean Sea and southern Australia. This fact led us to question whether the acquisition of this novel mechanism in the evolution of this seagrass was a pre-adaptation prior to geological isolation of the Mediterranean from Tethys Sea in the Eocene. Photosynthetic activity in seeds of Australian species of Posidonia is still unknown. This study shows oxygen production and respiration rates, and maximum PSII photochemical efficiency (Fv : Fm) in seeds of two Australian Posidonia species (P. australis and P. sinuosa), and compares these with previous results for P. oceanica. Results showed relatively high oxygen production and respiratory rates in all three species but with significant differences among them, suggesting the existence of an adaptive mechanism to compensate for the relatively high oxygen demands of the seeds. In all cases maximal photochemical efficiency of photosystem II rates reached similar values. The existence of photosynthetic activity in the seeds of all three species implicates that it was an ability probably acquired from a common ancestor during the Late Eocene, when this adaptive strategy could have helped Posidonia species to survive in nutrient-poor temperate seas. This study sheds new light on some aspects of the evolution of marine plants and represents an important contribution to global knowledge of the paleogeographic patterns of seagrass distribution. PMID:26066515

Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals.

PubMed

Hecker, Nikolai; Sharma, Virag; Hiller, Michael

2017-11-01

Kallikrein related peptidase 8 (KLK8; also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we examined the evolution of KLK8 in mammals and discovered that, out of 70 placental mammals, KLK8 is exclusively lost in three independent fully-aquatic lineages, comprising dolphin, killer whale, minke whale, and manatee. In addition, while the sperm whale has an intact KLK8 reading frame, the gene evolves neutrally in this species. We suggest that the distinct functions of KLK8 likely became obsolete in the aquatic environment, leading to the subsequent loss of KLK8 in several fully-aquatic mammalian lineages. First, the cetacean and manatee skin lacks sweat glands as an adaptation to the aquatic environment, which likely made the epidermal function of KLK8 obsolete. Second, cetaceans and manatees exhibit a proportionally small hippocampus, which may have rendered the hippocampal functions of KLK8 obsolete. Together, our results shed light on the genomic changes that correlate with skin and neuroanatomical differences of aquatic mammals, and show that even pleiotropic genes can be lost during evolution if an environmental change nullifies the need for the different functions of such genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Heterogeneous update mechanisms in evolutionary games: Mixing innovative and imitative dynamics.

PubMed

Amaral, Marco Antonio; Javarone, Marco Alberto

2018-04-01

Innovation and evolution are two processes of paramount relevance for social and biological systems. In general, the former allows the introduction of elements of novelty, while the latter is responsible for the motion of a system in its phase space. Often, these processes are strongly related, since an innovation can trigger the evolution, and the latter can provide the optimal conditions for the emergence of innovations. Both processes can be studied by using the framework of evolutionary game theory, where evolution constitutes an intrinsic mechanism. At the same time, the concept of innovation requires an opportune mathematical representation. Notably, innovation can be modeled as a strategy, or it can constitute the underlying mechanism that allows agents to change strategy. Here, we analyze the second case, investigating the behavior of a heterogeneous population, composed of imitative and innovative agents. Imitative agents change strategy only by imitating that of their neighbors, whereas innovative ones change strategy without the need for a copying source. The proposed model is analyzed by means of analytical calculations and numerical simulations in different topologies. Remarkably, results indicate that the mixing of mechanisms can be detrimental to cooperation near phase transitions. In those regions, the spatial reciprocity from imitative mechanisms is destroyed by innovative agents, leading to the downfall of cooperation. Our investigation sheds some light on the complex dynamics emerging from the heterogeneity of strategy revision methods, highlighting the role of innovation in evolutionary games.

Peripheral Nerve Regeneration by Secretomes of Stem Cells from Human Exfoliated Deciduous Teeth.

PubMed

Sugimura-Wakayama, Yukiko; Katagiri, Wataru; Osugi, Masashi; Kawai, Takamasa; Ogata, Kenichi; Sakaguchi, Kohei; Hibi, Hideharu

2015-11-15

Peripheral nerve regeneration across nerve gaps is often suboptimal, with poor functional recovery. Stem cell transplantation-based regenerative therapy is a promising approach for axon regeneration and functional recovery of peripheral nerve injury; however, the mechanisms remain controversial and unclear. Recent studies suggest that transplanted stem cells promote tissue regeneration through a paracrine mechanism. We investigated the effects of conditioned media derived from stem cells from human exfoliated deciduous teeth (SHED-CM) on peripheral nerve regeneration. In vitro, SHED-CM-treated Schwann cells exhibited significantly increased proliferation, migration, and the expression of neuron-, extracellular matrix (ECM)-, and angiogenesis-related genes. SHED-CM stimulated neuritogenesis of dorsal root ganglia and increased cell viability. Similarly, SHED-CM enhanced tube formation in an angiogenesis assay. In vivo, a 10-mm rat sciatic nerve gap model was bridged by silicon conduits containing SHED-CM or serum-free Dulbecco's modified Eagle's medium. Light and electron microscopy confirmed that the number of myelinated axons and axon-to-fiber ratio (G-ratio) were significantly higher in the SHED-CM group at 12 weeks after nerve transection surgery. The sciatic functional index (SFI) and gastrocnemius (target muscle) wet weight ratio demonstrated functional recovery. Increased compound muscle action potentials and increased SFI in the SHED-CM group suggested sciatic nerve reinnervation of the target muscle and improved functional recovery. We also observed reduced muscle atrophy in the SHED-CM group. Thus, SHEDs may secrete various trophic factors that enhance peripheral nerve regeneration through multiple mechanisms. SHED-CM may therefore provide a novel therapy that creates a more desirable extracellular microenvironment for peripheral nerve regeneration.

Experimental investigation of the flowfield of an oscillating airfoil

NASA Technical Reports Server (NTRS)

Panda, J.; Zaman, K. B. M. Q.

1992-01-01

The flowfield of an airfoil oscillated periodically over a wide range of reduced frequencies, 0 less than or = k less than or = 1.6 is studied experimentally at chord Reynolds numbers of R sub c = 22,000 and 44,000. The NACA0012 airfoil is pitched sinusoidally about one quarter chord between angles of attack (alpha) of 5 and 25 degrees. Detailed flow visualization and phase averaged vorticity measurements are carried out for k = 0.2 to document the evolution and the shedding of the dynamic stall vortex (DSV). In addition to the DSV, an intense vortex of opposite sign originates from the trailing edge just when the DSV is shed. After being shed into the wake, the two together take the shape of a large 'mushroom' while being convected away from the airfoil. The unsteady circulation around the airfoil and, therefore, the time varying component of the lift is estimated in a novel way from the shed vorticity flux and is found to be in good agreement with the lift variation reported by others. The delay in the shedding of the DSV with increasing k, as observed by previous researchers, is documented for the full range of k. The DSV, for example, is shed nearly at the maximum alpha of 25 degrees at k = 0.2, but is shed at the minimum alpha of 5 degrees at k = 0.8. At low k, the flowfield appears quasi-steady and the bluff body shedding corresponding to the maximum alpha (25 degrees) dominates the unsteady fluctuations in the wake.

Experimental investigation of the flowfield of an oscillating airfoil

NASA Technical Reports Server (NTRS)

Panda, J.; Zaman, K. B. M. Q.

1992-01-01

The flow field of an airfoil oscillated periodically over a wide range of reduced frequencies, 0 less than k less than 1.6, is studied experimentally at chord Reynolds numbers of R sub c = 22,000 and 44,000. The NACA0012 airfoil is pitched sinusoidally about one quarter chord between alpha of 5 deg and 25 deg. Detailed flow visualization and phase averaged vorticity measurements are carried out for k = 0.2 to document the evolution and the shedding of the dynamic stall vortex (DSV). In addition to the DSV, an intense vortex of opposite sign originates from the trailing edge just when the DSV is shed. After being shed into the wake, the two together take the shape of a large 'mushroom' while being convected away from the airfoil. The unsteady circulation around the airfoil and, therefore, the time varying component of the lift is estimated in a novel way from the shed vorticity flux and is found to be in good agreement with the lift variation reported by others. The delay in the shedding of the DSV with increasing k, as observed by previous researchers, is documented for the full range of k. The DSV, for example, is shed nearly at the maximum alpha of 25 deg at k = 0.2, but is shed at the minimum alpha of 5 deg at k = 0.8. At low k, the flowfield appears quasi-steady and the bluff body shedding corresponding to the maximum alpha (25 deg) dominates the unsteady fluctuations in the wake.

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

PubMed Central

2012-01-01

Background Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. Results To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Conclusions Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants. PMID:23102090

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers.

PubMed

Pavy, Nathalie; Pelgas, Betty; Laroche, Jérôme; Rigault, Philippe; Isabel, Nathalie; Bousquet, Jean

2012-10-26

Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants.

Russia as a Returning Donor--Four Roles in Development Assistance to Education

ERIC Educational Resources Information Center

Piattoeva, Nelli; Takala, Tuomas

2015-01-01

This article analyses the role of Russia in development assistance to education in light of the changing architecture of development assistance--the variety of positions identified with both "new" and "old" donor countries. We shed light on Russia's aims and agenda in the field of development assistance in general and…

The application of improved NeuroEvolution of Augmenting Topologies neural network in Marcellus Shale lithofacies prediction

NASA Astrophysics Data System (ADS)

Wang, Guochang; Cheng, Guojian; Carr, Timothy R.

2013-04-01

The organic-rich Marcellus Shale was deposited in a foreland basin during Middle Devonian. In terms of mineral composition and organic matter richness, we define seven mudrock lithofacies: three organic-rich lithofacies and four organic-poor lithofacies. The 3D lithofacies model is very helpful to determine geologic and engineering sweet spots, and consequently useful for designing horizontal well trajectories and stimulation strategies. The NeuroEvolution of Augmenting Topologies (NEAT) is relatively new idea in the design of neural networks, and shed light on classification (i.e., Marcellus Shale lithofacies prediction). We have successfully enhanced the capability and efficiency of NEAT in three aspects. First, we introduced two new attributes of node gene, the node location and recurrent connection (RCC), to increase the calculation efficiency. Second, we evolved the population size from an initial small value to big, instead of using the constant value, which saves time and computer memory, especially for complex learning tasks. Third, in multiclass pattern recognition problems, we combined feature selection of input variables and modular neural network to automatically select input variables and optimize network topology for each binary classifier. These improvements were tested and verified by true if an odd number of its arguments are true and false otherwise (XOR) experiments, and were powerful for classification.

Assortativity and leadership emerge from anti-preferential attachment in heterogeneous networks.

PubMed

Sendiña-Nadal, I; Danziger, M M; Wang, Z; Havlin, S; Boccaletti, S

2016-02-18

Real-world networks have distinct topologies, with marked deviations from purely random networks. Many of them exhibit degree-assortativity, with nodes of similar degree more likely to link to one another. Though microscopic mechanisms have been suggested for the emergence of other topological features, assortativity has proven elusive. Assortativity can be artificially implanted in a network via degree-preserving link permutations, however this destroys the graph's hierarchical clustering and does not correspond to any microscopic mechanism. Here, we propose the first generative model which creates heterogeneous networks with scale-free-like properties in degree and clustering distributions and tunable realistic assortativity. Two distinct populations of nodes are incrementally added to an initial network by selecting a subgraph to connect to at random. One population (the followers) follows preferential attachment, while the other population (the potential leaders) connects via anti-preferential attachment: they link to lower degree nodes when added to the network. By selecting the lower degree nodes, the potential leader nodes maintain high visibility during the growth process, eventually growing into hubs. The evolution of links in Facebook empirically validates the connection between the initial anti-preferential attachment and long term high degree. In this way, our work sheds new light on the structure and evolution of social networks.

The origins and evolutionary history of human non-coding RNA regulatory networks.

PubMed

Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.

How just a few makes a lot: Speciation via reticulation and apomixis on example of European brambles (Rubus subgen. Rubus, Rosaceae).

PubMed

Sochor, Michal; Vašut, Radim J; Sharbel, Timothy F; Trávníček, Bohumil

2015-08-01

New species are generated by many means, among which hybridization plays an important role. Interspecific hybrids can form isolated evolutionary units, especially when mechanisms increasing viability and fertility, like polyploidy and apomixis, are involved. A good model system to study reticulate evolution in plants is Rubus subgen. Rubus (brambles, blackberries), which only in Europe includes 748 accepted species, out of which only four are sexual diploids and all others are polyploid apomicts. We employed two molecular markers (ITS and cpDNA) to shed light on the evolutionary history of European bramble flora and main processes generating such high species diversity. We distinguished just six ancestral diploids (including two extinct ones) for both markers, which gave rise to all European polyploid accessions, and revealed an extreme reticulation in bramble evolution. We furthermore detected hybridogenous origins and identified putative parents for several taxa (e.g. ser. Nessenses), while in other groups (e.g. ser. Discolores) we could also infer the direction of hybridization. By comparing different cp haplotypes having clear geographic patterns, we hypothesize that the origin of European brambles can be attributed to both Holocene species range expansion and Pleistocene climate fluctuations. Copyright © 2015 Elsevier Inc. All rights reserved.

Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls

PubMed Central

Leininger, Elizabeth C.; Kelley, Darcy B.

2013-01-01

Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the calling brain and vocal organ (larynx) in two species that independently evolved simplified calls. We find that each species uses distinct neural and neuromuscular strategies to produce the simplified calls. Isolated  Xenopus borealis brains produce fictive vocal patterns that match temporal patterns of actual male calls; the larynx converts nerve activity faithfully into muscle contractions and single clicks. In contrast, fictive patterns from isolated Xenopus boumbaensis brains are short bursts of nerve activity; the isolated larynx requires stimulus bursts to produce a single click of sound. Thus, unlike X. borealis, the output of the X. boumbaensis hindbrain vocal pattern generator is an ancestral burst-type pattern, transformed by the larynx into single clicks. Temporally simple advertisement calls in genetically distant species of Xenopus have thus arisen independently via reconfigurations of central and peripheral vocal neuroeffectors. PMID:23407829

Assortativity and leadership emerge from anti-preferential attachment in heterogeneous networks

NASA Astrophysics Data System (ADS)

Sendiña-Nadal, I.; Danziger, M. M.; Wang, Z.; Havlin, S.; Boccaletti, S.

2016-02-01

Real-world networks have distinct topologies, with marked deviations from purely random networks. Many of them exhibit degree-assortativity, with nodes of similar degree more likely to link to one another. Though microscopic mechanisms have been suggested for the emergence of other topological features, assortativity has proven elusive. Assortativity can be artificially implanted in a network via degree-preserving link permutations, however this destroys the graph’s hierarchical clustering and does not correspond to any microscopic mechanism. Here, we propose the first generative model which creates heterogeneous networks with scale-free-like properties in degree and clustering distributions and tunable realistic assortativity. Two distinct populations of nodes are incrementally added to an initial network by selecting a subgraph to connect to at random. One population (the followers) follows preferential attachment, while the other population (the potential leaders) connects via anti-preferential attachment: they link to lower degree nodes when added to the network. By selecting the lower degree nodes, the potential leader nodes maintain high visibility during the growth process, eventually growing into hubs. The evolution of links in Facebook empirically validates the connection between the initial anti-preferential attachment and long term high degree. In this way, our work sheds new light on the structure and evolution of social networks.

The early evolution of land plants, from fossils to genomics: a commentary on Lang (1937) 'On the plant-remains from the Downtonian of England and Wales'.

PubMed

Edwards, Dianne; Kenrick, Paul

2015-04-19

During the 1920s, the botanist W. H. Lang set out to collect and investigate some very unpromising fossils of uncertain affinity, which predated the known geological record of life on land. His discoveries led to a landmark publication in 1937, 'On the plant-remains from the Downtonian of England and Wales', in which he revealed a diversity of small fossil organisms of great simplicity that shed light on the nature of the earliest known land plants. These and subsequent discoveries have taken on new relevance as botanists seek to understand the plant genome and the early evolution of fundamental organ systems. Also, our developing knowledge of the composition of early land-based ecosystems and the interactions among their various components is contributing to our understanding of how life on land affects key Earth Systems (e.g. carbon cycle). The emerging paradigm is one of early life on land dominated by microbes, small bryophyte-like organisms and lichens. Collectively called cryptogamic covers, these are comparable with those that dominate certain ecosystems today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

In Vitro Evolution of Bovine Foamy Virus Variants with Enhanced Cell-Free Virus Titers and Transmission.

PubMed

Bao, Qiuying; Hipp, Michaela; Hugo, Annette; Lei, Janet; Liu, Yang; Kehl, Timo; Hechler, Torsten; Löchelt, Martin

2015-11-11

Virus transmission is essential for spreading viral infections and is a highly coordinated process which occurs by cell-free transmission or cell-cell contact. The transmission of Bovine Foamy Virus (BFV) is highly cell-associated, with undetectable cell-free transmission. However, BFV particle budding can be induced by overexpression of wild-type (wt) BFV Gag and Env or artificial retargeting of Gag to the plasma membrane via myristoylation membrane targeting signals, closely resembling observations in other foamy viruses. Thus, the particle release machinery of wt BFV appears to be an excellent model system to study viral adaption to cell-free transmission by in vitro selection and evolution. Using selection for BFV variants with high cell-free infectivity in bovine and non-bovine cells, infectivity dramatically increased from almost no infectious units to about 105-106 FFU (fluorescent focus forming units)/mL in both cell types. Importantly, the selected BFV variants with high titer (HT) cell-free infectivity could still transmit via cell-cell contacts and were neutralized by serum from naturally infected cows. These selected HT-BFV variants will shed light into virus transmission and potential routes of intervention in the spread of viral infections. It will also allow the improvement or development of new promising approaches for antiretroviral therapies.

In Vitro Evolution of Bovine Foamy Virus Variants with Enhanced Cell-Free Virus Titers and Transmission

PubMed Central

Bao, Qiuying; Hipp, Michaela; Hugo, Annette; Lei, Janet; Liu, Yang; Kehl, Timo; Hechler, Torsten; Löchelt, Martin

2015-01-01

Virus transmission is essential for spreading viral infections and is a highly coordinated process which occurs by cell-free transmission or cell–cell contact. The transmission of Bovine Foamy Virus (BFV) is highly cell-associated, with undetectable cell-free transmission. However, BFV particle budding can be induced by overexpression of wild-type (wt) BFV Gag and Env or artificial retargeting of Gag to the plasma membrane via myristoylation membrane targeting signals, closely resembling observations in other foamy viruses. Thus, the particle release machinery of wt BFV appears to be an excellent model system to study viral adaption to cell-free transmission by in vitro selection and evolution. Using selection for BFV variants with high cell-free infectivity in bovine and non-bovine cells, infectivity dramatically increased from almost no infectious units to about 105–106 FFU (fluorescent focus forming units)/mL in both cell types. Importantly, the selected BFV variants with high titer (HT) cell-free infectivity could still transmit via cell-cell contacts and were neutralized by serum from naturally infected cows. These selected HT–BFV variants will shed light into virus transmission and potential routes of intervention in the spread of viral infections. It will also allow the improvement or development of new promising approaches for antiretroviral therapies. PMID:26569290

Mineralized periodontia in extinct relatives of mammals shed light on the evolutionary history of mineral homeostasis in periodontal tissue maintenance.

PubMed

LeBlanc, Aaron R H; Reisz, Robert R; Brink, Kirstin S; Abdala, Fernando

2016-04-01

Dental ankylosis is a rare pathological condition in mammals, however, it is prevalent in their extinct relatives, the stem mammals. This study seeks to compare the mineralized state of the periodontal attachment apparatus between stem and crown mammals and discuss its implications for the evolution of non-mineralized periodontal attachment in crown mammals, including humans. Thin sections of a fossil mammal and three stem mammals were compared to reconstruct periodontal tissue development across distantly related lineages. Comparisons revealed that the extinct relatives of mammals possessed the same periodontal tissues as those in mammals, albeit in different arrangements. The ankylotic condition in stem mammals was achieved through extensive alveolar bone deposition, which eventually contacted the root cementum, thus forming a calcified periodontal ligament. Dental ankylosis was part of the normal development of the stem mammal periodontium for millions of years prior to the evolution of a permanent gomphosis in mammals. Mammals may have evolved a permanent gomphosis by delaying the processes that produced dental ankylosis in stem mammals. Pathological ankylosis may represent a reversion to the ancestral condition, which now only forms via advanced ageing and pathology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Asteroid Secular Dynamics: Ceres’ Fingerprint Identified

NASA Astrophysics Data System (ADS)

Novaković, Bojan; Maurel, Clara; Tsirvoulis, Georgios; Knežević, Zoran

2015-07-01

Here we report on the significant role of a so far overlooked dynamical aspect, namely, a secular resonance between the dwarf planet Ceres and other asteroids. We demonstrate that this type of secular resonance can be the dominant dynamical factor in certain regions of the main asteroid belt. Specifically, we performed a dynamical analysis of the asteroids belonging to the (1726) Hoffmeister family. To identify which dynamical mechanisms are actually at work in this part of the main asteroid belt, i.e., to isolate the main perturber(s), we study the evolution of this family in time. The study is accomplished using numerical integrations of test particles performed within different dynamical models. The obtained results reveal that the post-impact evolution of the Hoffmeister asteroid family is a direct consequence of the nodal secular resonance with Ceres. This leads us to the conclusion that similar effects must exist in other parts of the asteroid belt. In this respect, the obtained results shed light on an important and entirely new aspect of the long-term dynamics of small bodies. Ceres’ fingerprint in asteroid dynamics, expressed through the discovered secular resonance effect, completely changes our understanding of the way in which perturbations by Ceres-like objects affect the orbits of nearby bodies.

Structural and Molecular Basis for the Novel Catalytic Mechanism and Evolution of DddP, an Abundant Peptidase-Like Bacterial Dimethylsulfoniopropionate Lyase: A New Enzyme from an Old Fold

NASA Astrophysics Data System (ADS)

Zhang, Y. Z.; Wang, P.; Chen, X. L.; Li, C. Y.; Gao, X.; Zhu, D.; Xie, B. B.; Qin, Q. L.; Zhang, X. Y.; Su, H. N.; Zhou, B. C.; Xun, L.

2015-12-01

The microbial cleavage of dimethylsulfoniopropionate (DMSP) generates volatile dimethyl sulfide (DMS) and is an important step in global sulfur and carbon cycles. DddP is a DMSP lyase in marine bacteria and the deduced dddP gene product is abundant in marine metagenomic data sets. However, DddP belongs to the M24 peptidase family according to sequence alignment. Peptidases hydrolyze C-N bonds but DddP is deduced to cleave C-S bonds. Mechanisms responsible for this striking functional shift are currently unknown. We determined the structures of DMSP lyase RlDddP (the DddP from Ruegeria lacuscaerulensis ITI_1157) bound to inhibitory 2-(N-morpholino) ethanesulfonic acid or PO43- and of two mutants of RlDddP bound to acrylate. Based on structural, mutational and biochemical analyses, we characterized a new ion-shift catalytic mechanism of RlDddP for DMSP cleavage. Further, we suggested the structural mechanism leading to the loss of peptidase activity and the subsequent development of DMSP lyase activity in DddP. This study sheds light on the catalytic mechanism and the divergent evolution of DddP, leading to a better understanding of marine bacterial DMSP catabolism and global DMS production.

Palaeoecological inferences for the fossil Australian snakes Yurlunggur and Wonambi (Serpentes, Madtsoiidae)

NASA Astrophysics Data System (ADS)

Palci, Alessandro; Hutchinson, Mark N.; Caldwell, Michael W.; Scanlon, John D.; Lee, Michael S. Y.

2018-03-01

Madtsoiids are among the most basal snakes, with a fossil record dating back to the Upper Cretaceous (Cenomanian). Most representatives went extinct by the end of the Eocene, but some survived in Australia until the Late Cenozoic. Yurlunggur and Wonambi are two of these late forms, and also the best-known madtsoiids to date. A better understanding of the anatomy and palaeoecology of these taxa may shed light on the evolution and extinction of this poorly known group of snakes and on early snake evolution in general. A digital endocast of the inner ear of Yurlunggur was compared to those of 81 species of snakes and lizards with known ecological preferences using three-dimensional geometric morphometrics. The inner ear of Yurlunggur most closely resembles both that of certain semiaquatic snakes and that of some semifossorial snakes. Other cranial and postcranial features of this snake support the semifossorial interpretation. While the digital endocast of the inner ear of Wonambi is too incomplete to be included in a geometric morphometrics study, its preserved morphology is very different from that of Yurlunggur and suggests a more generalist ecology. Osteology, palaeoclimatic data and the palaeobiogeographic distribution of these two snakes are all consistent with these inferred ecological differences.

The early evolution of land plants, from fossils to genomics: a commentary on Lang (1937) ‘On the plant-remains from the Downtonian of England and Wales'

PubMed Central

Edwards, Dianne; Kenrick, Paul

2015-01-01

During the 1920s, the botanist W. H. Lang set out to collect and investigate some very unpromising fossils of uncertain affinity, which predated the known geological record of life on land. His discoveries led to a landmark publication in 1937, ‘On the plant-remains from the Downtonian of England and Wales’, in which he revealed a diversity of small fossil organisms of great simplicity that shed light on the nature of the earliest known land plants. These and subsequent discoveries have taken on new relevance as botanists seek to understand the plant genome and the early evolution of fundamental organ systems. Also, our developing knowledge of the composition of early land-based ecosystems and the interactions among their various components is contributing to our understanding of how life on land affects key Earth Systems (e.g. carbon cycle). The emerging paradigm is one of early life on land dominated by microbes, small bryophyte-like organisms and lichens. Collectively called cryptogamic covers, these are comparable with those that dominate certain ecosystems today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society. PMID:25750238

Evolution of lactase persistence: an example of human niche construction

PubMed Central

Gerbault, Pascale; Liebert, Anke; Itan, Yuval; Powell, Adam; Currat, Mathias; Burger, Joachim; Swallow, Dallas M.; Thomas, Mark G.

2011-01-01

Niche construction is the process by which organisms construct important components of their local environment in ways that introduce novel selection pressures. Lactase persistence is one of the clearest examples of niche construction in humans. Lactase is the enzyme responsible for the digestion of the milk sugar lactose and its production decreases after the weaning phase in most mammals, including most humans. Some humans, however, continue to produce lactase throughout adulthood, a trait known as lactase persistence. In European populations, a single mutation (−13910*T) explains the distribution of the phenotype, whereas several mutations are associated with it in Africa and the Middle East. Current estimates for the age of lactase persistence-associated alleles bracket those for the origins of animal domestication and the culturally transmitted practice of dairying. We report new data on the distribution of −13910*T and summarize genetic studies on the diversity of lactase persistence worldwide. We review relevant archaeological data and describe three simulation studies that have shed light on the evolution of this trait in Europe. These studies illustrate how genetic and archaeological information can be integrated to bring new insights to the origins and spread of lactase persistence. Finally, we discuss possible improvements to these models. PMID:21320900

The Origins of Transmembrane Ion Channels

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Wilson, Michael A.

2012-01-01

Even though membrane proteins that mediate transport of ions and small molecules across cell walls are among the largest and least understood biopolymers in contemporary cells, it is still possible to shed light on their origins and early evolution. The central observation is that transmembrane portions of most ion channels are simply bundles of -helices. By combining results of experimental and computer simulation studies on synthetic models and natural channels, mostly of non-genomic origin, we show that the emergence of -helical channels was protobiologically plausible, and did not require highly specific amino acid sequences. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. Specifically, we explain how the antiamoebin channels, which are made of identical helices, 16 amino acids in length, achieve efficiency comparable to that of highly evolved channels. We further show that antiamoebin channels are extremely flexible, compared to modern, genetically coded channels. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire stable rigid structures and mechanisms for precise regulation rather than improve efficiency. In general, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

Differential Expression of Non-Coding RNAs and Continuous Evolution of the X Chromosome in Testicular Transcriptome of Two Mouse Species

PubMed Central

Homolka, David; Ivanek, Robert; Forejt, Jiri; Jansa, Petr

2011-01-01

Background Tight regulation of testicular gene expression is a prerequisite for male reproductive success, while differentiation of gene activity in spermatogenesis is important during speciation. Thus, comparison of testicular transcriptomes between closely related species can reveal unique regulatory patterns and shed light on evolutionary constraints separating the species. Methodology/Principal Findings Here, we compared testicular transcriptomes of two closely related mouse species, Mus musculus and Mus spretus, which diverged more than one million years ago. We analyzed testicular expression using tiling arrays overlapping Chromosomes 2, X, Y and mitochondrial genome. An excess of differentially regulated non-coding RNAs was found on Chromosome 2 including the intronic antisense RNAs, intergenic RNAs and premature forms of Piwi-interacting RNAs (piRNAs). Moreover, striking difference was found in the expression of X-linked G6pdx gene, the parental gene of the autosomal retrogene G6pd2. Conclusions/Significance The prevalence of non-coding RNAs among differentially expressed transcripts indicates their role in species-specific regulation of spermatogenesis. The postmeiotic expression of G6pdx in Mus spretus points towards the continuous evolution of X-chromosome silencing and provides an example of expression change accompanying the out-of-the X-chromosomal retroposition. PMID:21347268

Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon.

PubMed

Campos, Rafael K; Boratto, Paulo V; Assis, Felipe L; Aguiar, Eric R G R; Silva, Lorena C F; Albarnaz, Jonas D; Dornas, Fabio P; Trindade, Giliane S; Ferreira, Paulo P; Marques, João T; Robert, Catherine; Raoult, Didier; Kroon, Erna G; La Scola, Bernard; Abrahão, Jônatas S

2014-05-14

The identification of novel giant viruses from the nucleocytoplasmic large DNA viruses group and their virophages has increased in the last decade and has helped to shed light on viral evolution. This study describe the discovery, isolation and characterization of Samba virus (SMBV), a novel giant virus belonging to the Mimivirus genus, which was isolated from the Negro River in the Brazilian Amazon. We also report the isolation of an SMBV-associated virophage named Rio Negro (RNV), which is the first Mimivirus virophage to be isolated in the Americas. Based on a phylogenetic analysis, SMBV belongs to group A of the putative Megavirales order, possibly a new virus related to Acanthamoeba polyphaga mimivirus (APMV). SMBV is the largest virus isolated in Brazil, with an average particle diameter about 574 nm. The SMBV genome contains 938 ORFs, of which nine are ORFans. The 1,213.6 kb SMBV genome is one of the largest genome of any group A Mimivirus described to date. Electron microscopy showed RNV particle accumulation near SMBV and APMV factories resulting in the production of defective SMBV and APMV particles and decreasing the infectivity of these two viruses by several logs. This discovery expands our knowledge of Mimiviridae evolution and ecology.

The edge of galaxy formation - I. Formation and evolution of MW-satellite analogues before accretion

NASA Astrophysics Data System (ADS)

Macciò, Andrea V.; Frings, Jonas; Buck, Tobias; Penzo, Camilla; Dutton, Aaron A.; Blank, Marvin; Obreja, Aura

2017-12-01

The satellites of the Milky Way and Andromeda represent the smallest galaxies we can observe in our Universe. In this series of papers, we aim to shed light on their formation and evolution using cosmological hydrodynamical simulations. In this first paper, we focus on the galaxy properties before accretion, by simulating 27 haloes with masses between 5 × 108 and 1010 M⊙. Out of this set 19 haloes successfully form stars, while 8 remain dark. The simulated galaxies match quite well present day observed scaling relations between stellar mass, size and metallicity, showing that such relations are in place before accretion. Our galaxies show a large variety of star formation histories, from extended star formation periods to single bursts. As in more massive galaxies, large star formation bursts are connected with major mergers events, which greatly contribute to the overall stellar mass build up. The intrinsic stochasticity of mergers induces a large scatter in the stellar mass-halo mass relation, up to two orders of magnitude. Despite the bursty star formation history, on these mass scales baryons are very ineffective in modifying the dark matter profiles, and galaxies with a stellar mass below ≈106 M⊙ retain their cuspy central dark matter distribution, very similar to results from pure N-body simulations.

Local Structure Evolution and Modes of Charge Storage in Secondary Li–FeS 2 Cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Butala, Megan M.; Mayo, Martin; Doan-Nguyen, Vicky V. T.

2017-03-27

In the pursuit of high-capacity electrochemical energy storage, a promising domain of research involves conversion reaction schemes, wherein electrode materials are fully transformed during charge and discharge. There are, however, numerous difficulties in realizing theoretical capacity and high rate capability in many conversion schemes. Here we employ operando studies to understand the conversion material FeS2, focusing on the local structure evolution of this relatively reversible material. X-ray absorption spectroscopy, pair distribution function analysis, and first-principles calculations of intermediate structures shed light on the mechanism of charge storage in the Li-FeS2 system, with some general principles emerging for charge storage inmore » chalcogenide materials. Focusing on second and later charge/discharge cycles, we find small, disordered domains that locally resemble Fe and Li2S at the end of the first discharge. Upon charge, this is converted to a Li-Fe-S composition whose local structure reveals tetrahedrally coordinated Fe. With continued charge, this ternary composition displays insertion extraction behavior at higher potentials and lower Li content. The finding of hybrid modes of charge storage, rather than simple conversion, points to the important role of intermediates that appear to store charge by mechanisms that more closely resemble intercalation.« less

Elastic and failure response of imperfect three-dimensional metallic lattices: the role of geometric defects induced by Selective Laser Melting

NASA Astrophysics Data System (ADS)

Liu, Lu; Kamm, Paul; García-Moreno, Francisco; Banhart, John; Pasini, Damiano

2017-10-01

This paper examines three-dimensional metallic lattices with regular octet and rhombicuboctahedron units fabricated with geometric imperfections via Selective Laser Sintering. We use X-ray computed tomography to capture morphology, location, and distribution of process-induced defects with the aim of studying their role in the elastic response, damage initiation, and failure evolution under quasi-static compression. Testing results from in-situ compression tomography show that each lattice exhibits a distinct failure mechanism that is governed not only by cell topology but also by geometric defects induced by additive manufacturing. Extracted from X-ray tomography images, the statistical distributions of three sets of defects, namely strut waviness, strut thickness variation, and strut oversizing, are used to develop numerical models of statistically representative lattices with imperfect geometry. Elastic and failure responses are predicted within 10% agreement from the experimental data. In addition, a computational study is presented to shed light into the relationship between the amplitude of selected defects and the reduction of elastic properties compared to their nominal values. The evolution of failure mechanisms is also explained with respect to strut oversizing, a parameter that can critically cause failure mode transitions that are not visible in defect-free lattices.

Complex patterns of multivariate selection on the ejaculate of a broadcast spawning marine invertebrate.

PubMed

Fitzpatrick, John L; Simmons, Leigh W; Evans, Jonathan P

2012-08-01

Assessing how selection operates on several, potentially interacting, components of the ejaculate is a challenging endeavor. Ejaculates can be subject to natural and/or sexual selection, which can impose both linear (directional) and nonlinear (stabilizing, disruptive, and correlational) selection on different ejaculate components. Most previous studies have examined linear selection of ejaculate components and, consequently, we know very little about patterns of nonlinear selection on the ejaculate. Even less is known about how selection acts on the ejaculate as a functionally integrated unit, despite evidence of covariance among ejaculate components. Here, we assess how selection acts on multiple ejaculate components simultaneously in the broadcast spawning sessile invertebrate Mytilus galloprovincialis using the statistical tools of multivariate selection analyses. Our analyses of relative fertilization rates revealed complex patterns of selection on sperm velocity, motility, and morphology. Interestingly, the most successful ejaculates were made up of slower swimming sperm with relatively low percentages of motile cells, and sperm with smaller head volumes that swam in highly pronounced curved swimming trajectories. These results are consistent with an emerging body of literature on fertilization kinetics in broadcast spawners, and shed light on the fundamental nature of selection acting on the ejaculate as a functionally integrated unit. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

The Evolution of an Interprofessional Shared Decision-Making Research Program: Reflective Case Study of an Emerging Paradigm

PubMed Central

Menear, Matthew; Stacey, Dawn; Brière, Nathalie; Légaré, France

2016-01-01

Introduction: Healthcare research increasingly focuses on interprofessional collaboration and on shared decision making, but knowledge gaps remain about effective strategies for implementing interprofessional collaboration and shared decision-making together in clinical practice. We used Kuhn’s theory of scientific revolutions to reflect on how an integrated interprofessional shared decision-making approach was developed and implemented over time. Methods: In 2007, an interdisciplinary team initiated a new research program to promote the implementation of an interprofessional shared decision-making approach in clinical settings. For this reflective case study, two new team members analyzed the team’s four projects, six research publications, one unpublished and two published protocols and organized them into recognizable phases according to Kuhn’s theory. Results: The merging of two young disciplines led to challenges characteristic of emerging paradigms. Implementation of interprofessional shared-decision making was hindered by a lack of conceptual clarity, a dearth of theories and models, little methodological guidance, and insufficient evaluation instruments. The team developed a new model, identified new tools, and engaged knowledge users in a theory-based approach to implementation. However, several unresolved challenges remain. Discussion: This reflective case study sheds light on the evolution of interdisciplinary team science. It offers new approaches to implementing emerging knowledge in the clinical context. PMID:28435417

Distinct neural and neuromuscular strategies underlie independent evolution of simplified advertisement calls.

PubMed

Leininger, Elizabeth C; Kelley, Darcy B

2013-04-07

Independent or convergent evolution can underlie phenotypic similarity of derived behavioural characters. Determining the underlying neural and neuromuscular mechanisms sheds light on how these characters arose. One example of evolutionarily derived characters is a temporally simple advertisement call of male African clawed frogs (Xenopus) that arose at least twice independently from a more complex ancestral pattern. How did simplification occur in the vocal circuit? To distinguish shared from divergent mechanisms, we examined activity from the calling brain and vocal organ (larynx) in two species that independently evolved simplified calls. We find that each species uses distinct neural and neuromuscular strategies to produce the simplified calls. Isolated Xenopus borealis brains produce fictive vocal patterns that match temporal patterns of actual male calls; the larynx converts nerve activity faithfully into muscle contractions and single clicks. In contrast, fictive patterns from isolated Xenopus boumbaensis brains are short bursts of nerve activity; the isolated larynx requires stimulus bursts to produce a single click of sound. Thus, unlike X. borealis, the output of the X. boumbaensis hindbrain vocal pattern generator is an ancestral burst-type pattern, transformed by the larynx into single clicks. Temporally simple advertisement calls in genetically distant species of Xenopus have thus arisen independently via reconfigurations of central and peripheral vocal neuroeffectors.

The cellular immune response of Daphnia magna under host-parasite genetic variation and variation in initial dose.

PubMed

Auld, Stuart K J R; Edel, Kai H; Little, Tom J

2012-10-01

In invertebrate-parasite systems, the likelihood of infection following parasite exposure is often dependent on the specific combination of host and parasite genotypes (termed genetic specificity). Genetic specificity can maintain diversity in host and parasite populations and is a major component of the Red Queen hypothesis. However, invertebrate immune systems are thought to only distinguish between broad classes of parasite. Using a natural host-parasite system with a well-established pattern of genetic specificity, the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa, we found that only hosts from susceptible host-parasite genetic combinations mounted a cellular response following exposure to the parasite. These data are compatible with the hypothesis that genetic specificity is attributable to barrier defenses at the site of infection (the gut), and that the systemic immune response is general, reporting the number of parasite spores entering the hemocoel. Further supporting this, we found that larger cellular responses occurred at higher initial parasite doses. By studying the natural infection route, where parasites must pass barrier defenses before interacting with systemic immune responses, these data shed light on which components of invertebrate defense underlie genetic specificity. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

An Exploration into Fern Genome Space.

PubMed

Wolf, Paul G; Sessa, Emily B; Marchant, Daniel Blaine; Li, Fay-Wei; Rothfels, Carl J; Sigel, Erin M; Gitzendanner, Matthew A; Visger, Clayton J; Banks, Jo Ann; Soltis, Douglas E; Soltis, Pamela S; Pryer, Kathleen M; Der, Joshua P

2015-08-26

Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Origin of High-Frequency Hearing in Whales.

PubMed

Churchill, Morgan; Martinez-Caceres, Manuel; de Muizon, Christian; Mnieckowski, Jessica; Geisler, Jonathan H

2016-08-22

Odontocetes (toothed whales) rely upon echoes of their own vocalizations to navigate and find prey underwater [1]. This sensory adaptation, known as echolocation, operates most effectively when using high frequencies, and odontocetes are rivaled only by bats in their ability to perceive ultrasonic sound greater than 100 kHz [2]. Although features indicative of ultrasonic hearing are present in the oldest known odontocetes [3], the significance of this finding is limited by the methods employed and taxa sampled. In this report, we describe a new xenorophid whale (Echovenator sandersi, gen. et sp. nov.) from the Oligocene of South Carolina that, as a member of the most basal clade of odontocetes, sheds considerable light on the evolution of ultrasonic hearing. By placing high-resolution CT data from Echovenator sandersi, 2 hippos, and 23 fossil and extant whales in a phylogenetic context, we conclude that ultrasonic hearing, albeit in a less specialized form, evolved at the base of the odontocete radiation. Contrary to the hypothesis that odontocetes evolved from low-frequency specialists [4], we find evidence that stem cetaceans, the archaeocetes, were more sensitive to high-frequency sound than their terrestrial ancestors. This indicates that selection for high-frequency hearing predates the emergence of Odontoceti and the evolution of echolocation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multi-gene phylogenetic analysis reveals the multiple origin and evolution of mangrove physiological traits through exaptation

NASA Astrophysics Data System (ADS)

Sahu, Sunil Kumar; Singh, Reena; Kathiresan, Kandasamy

2016-12-01

Mangroves are taxonomically diverse group of salt-tolerant, mainly arboreal, flowering plants that grow in tropical and sub-tropical regions and have adapted themselves to thrive in such obdurate surroundings. While evolution is often understood exclusively in terms of adaptation, innovation often begins when a feature adapted for one function is co-opted for a different purpose and the co-opted features are called exaptations. Thus, one of the fundamental issues is what features of mangroves have evolved through exaptation. We attempt to address these questions through molecular phylogenetic approach using chloroplast and nuclear markers. First, we determined if these mangroves specific traits have evolved multiple times in the phylogeny. Once the multiple origins were established, we then looked at related non-mangrove species for characters that could have been co-opted by mangrove species. We also assessed the efficacy of these molecular sequences in distinguishing mangroves at the species level. This study revealed the multiple origin of mangroves and shed light on the ancestral characters that might have led certain lineages of plants to adapt to estuarine conditions and also traces the evolutionary history of mangroves and hitherto unexplained theory that mangroves traits (aerial roots and viviparous propagules) evolved as a result of exaptation rather than adaptation to saline habitats.

The Evolution of an Interprofessional Shared Decision-Making Research Program: Reflective Case Study of an Emerging Paradigm.

PubMed

Dogba, Maman Joyce; Menear, Matthew; Stacey, Dawn; Brière, Nathalie; Légaré, France

2016-07-19

Healthcare research increasingly focuses on interprofessional collaboration and on shared decision making, but knowledge gaps remain about effective strategies for implementing interprofessional collaboration and shared decision-making together in clinical practice. We used Kuhn's theory of scientific revolutions to reflect on how an integrated interprofessional shared decision-making approach was developed and implemented over time. In 2007, an interdisciplinary team initiated a new research program to promote the implementation of an interprofessional shared decision-making approach in clinical settings. For this reflective case study, two new team members analyzed the team's four projects, six research publications, one unpublished and two published protocols and organized them into recognizable phases according to Kuhn's theory. The merging of two young disciplines led to challenges characteristic of emerging paradigms. Implementation of interprofessional shared-decision making was hindered by a lack of conceptual clarity, a dearth of theories and models, little methodological guidance, and insufficient evaluation instruments. The team developed a new model, identified new tools, and engaged knowledge users in a theory-based approach to implementation. However, several unresolved challenges remain. This reflective case study sheds light on the evolution of interdisciplinary team science. It offers new approaches to implementing emerging knowledge in the clinical context.

Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.

PubMed

Kersting, Anna R; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A

2015-06-01

Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families. © 2014 University of Pretoria New Phytologist © 2014 New Phytologist Trust.

Experimentally Infected Domestic Ducks Show Efficient Transmission of Indonesian H5N1 Highly Pathogenic Avian Influenza Virus, but Lack Persistent Viral Shedding

PubMed Central

Wibawa, Hendra; Bingham, John; Nuradji, Harimurti; Lowther, Sue; Payne, Jean; Harper, Jenni; Junaidi, Akhmad; Middleton, Deborah; Meers, Joanne

2014-01-01

Ducks are important maintenance hosts for avian influenza, including H5N1 highly pathogenic avian influenza viruses. A previous study indicated that persistence of H5N1 viruses in ducks after the development of humoral immunity may drive viral evolution following immune selection. As H5N1 HPAI is endemic in Indonesia, this mechanism may be important in understanding H5N1 evolution in that region. To determine the capability of domestic ducks to maintain prolonged shedding of Indonesian clade 2.1 H5N1 virus, two groups of Pekin ducks were inoculated through the eyes, nostrils and oropharynx and viral shedding and transmission investigated. Inoculated ducks (n = 15), which were mostly asymptomatic, shed infectious virus from the oral route from 1 to 8 days post inoculation, and from the cloacal route from 2–8 dpi. Viral ribonucleic acid was detected from 1–15 days post inoculation from the oral route and 1–24 days post inoculation from the cloacal route (cycle threshold <40). Most ducks seroconverted in a range of serological tests by 15 days post inoculation. Virus was efficiently transmitted during acute infection (5 inoculation-infected to all 5 contact ducks). However, no evidence for transmission, as determined by seroconversion and viral shedding, was found between an inoculation-infected group (n = 10) and contact ducks (n = 9) when the two groups only had contact after 10 days post inoculation. Clinical disease was more frequent and more severe in contact-infected (2 of 5) than inoculation-infected ducks (1 of 15). We conclude that Indonesian clade 2.1 H5N1 highly pathogenic avian influenza virus does not persist in individual ducks after acute infection. PMID:24392085

77 FR 62491 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-15

... understand the relationship between meteorological phenomena and road conditions, as well as public.... Additionally, the project will shed light upon the interrelationship between meteorological phenomena, road...

Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions.

PubMed

Peer, Asaf; Margalit, Hanah

2014-07-01

Most bacterial small RNAs (sRNAs) are post-transcriptional regulators of gene expression, exerting their regulatory function by base-pairing with their target mRNAs. While it has become evident that sRNAs play central regulatory roles in the cell, little is known about their evolution and the evolution of their regulatory interactions. Here we used the prokaryotic phylogenetic tree to reconstruct the evolutionary history of Escherichia coli sRNAs and their binding sites on target mRNAs. We discovered that sRNAs currently present in E. coli mainly accumulated inside the Enterobacteriales order, succeeding the appearance of other types of noncoding RNAs and concurrently with the evolution of a variant of the Hfq protein exhibiting a longer C-terminal region. Our analysis of the evolutionary ages of sRNA-mRNA interactions revealed that while all sRNAs were evolutionarily older than most of their known binding sites on mRNA targets, for quite a few sRNAs there was at least one binding site that coappeared with or preceded them. It is conceivable that the establishment of these first interactions forced selective pressure on the sRNAs, after which additional targets were acquired by fitting a binding site to the active region of the sRNA. This conjecture is supported by the appearance of many binding sites on target mRNAs only after the sRNA gain, despite the prior presence of the target gene in ancestral genomes. Our results suggest a selective mechanism that maintained the sRNAs across the phylogenetic tree, and shed light on the evolution of E. coli post-transcriptional regulatory network. © 2014 Peer and Margalit; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects : Insect insulator proteins.

PubMed

Pauli, Thomas; Vedder, Lucia; Dowling, Daniel; Petersen, Malte; Meusemann, Karen; Donath, Alexander; Peters, Ralph S; Podsiadlowski, Lars; Mayer, Christoph; Liu, Shanlin; Zhou, Xin; Heger, Peter; Wiehe, Thomas; Hering, Lars; Mayer, Georg; Misof, Bernhard; Niehuis, Oliver

2016-11-03

Body plan development in multi-cellular organisms is largely determined by homeotic genes. Expression of homeotic genes, in turn, is partially regulated by insulator binding proteins (IBPs). While only a few enhancer blocking IBPs have been identified in vertebrates, the common fruit fly Drosophila melanogaster harbors at least twelve different enhancer blocking IBPs. We screened recently compiled insect transcriptomes from the 1KITE project and genomic and transcriptomic data from public databases, aiming to trace the origin of IBPs in insects and other arthropods. Our study shows that the last common ancestor of insects (Hexapoda) already possessed a substantial number of IBPs. Specifically, of the known twelve insect IBPs, at least three (i.e., CP190, Su(Hw), and CTCF) already existed prior to the evolution of insects. Furthermore we found GAF orthologs in early branching insect orders, including Zygentoma (silverfish and firebrats) and Diplura (two-pronged bristletails). Mod(mdg4) is most likely a derived feature of Neoptera, while Pita is likely an evolutionary novelty of holometabolous insects. Zw5 appears to be restricted to schizophoran flies, whereas BEAF-32, ZIPIC and the Elba complex, are probably unique to the genus Drosophila. Selection models indicate that insect IBPs evolved under neutral or purifying selection. Our results suggest that a substantial number of IBPs either pre-date the evolution of insects or evolved early during insect evolution. This suggests an evolutionary history of insulator binding proteins in insects different to that previously thought. Moreover, our study demonstrates the versatility of the 1KITE transcriptomic data for comparative analyses in insects and other arthropods.

Thermal Casimir-Polder forces on a V-type three-level atom

NASA Astrophysics Data System (ADS)

Xu, Chen-Ran; Xu, Jing-Ping; Al-amri, M.; Zhu, Cheng-Jie; Xie, Shuang-Yuan; Yang, Ya-Ping

2017-09-01

We study the thermal Casimir-Polder (CP) forces on a V-type three-level atom. The competition between the thermal effect and the quantum interference of the two transition dipoles on the force is investigated. To shed light onto the role of the quantum interference, we analyze two kinds of initial states of the atom, i.e., the superradiant state and the subradiant state. Considering the atom being in the thermal reservoir, the resonant CP force arising from the real photon emission dominates in the evolution of the CP force. Under the zero-temperature condition, the quantum interference can effectively modify the amplitude and the evolution of the force, leading to a long-time force or even the cancellation of the force. Our results reveal that in the finite-temperature case, the thermal photons can enhance the amplitude of all force elements, but have no influence on the net resonant CP force in the steady state, which means that the second law of thermodynamics still works. For the ideal degenerate V-type atom with parallel dipoles under the initial subradiant state, the robust destructive quantum interference overrides the thermal fluctuations, leading to the trapping of the atom in the subradiant state and the disappearance of the CP force. However, in terms of a realistic Zeeman atom, the thermal photons play a significant role during the evolution of the CP force. The thermal fluctuations can enhance the amplitude of the initial CP force by increasing the temperature, and weaken the influence of the quantum interference on the evolution of the CP force from the initial superradiant (subradiant) state to the steady state.

What do Simulations Predict for the Galaxy Stellar Mass Function and its Evolution in Different Environments?

NASA Astrophysics Data System (ADS)

Vulcani, Benedetta; De Lucia, Gabriella; Poggianti, Bianca M.; Bundy, Kevin; More, Surhud; Calvi, Rosa

2014-06-01

We present a comparison between the observed galaxy stellar mass function and the one predicted from the De Lucia & Blaizot semi-analytic model applied to the Millennium Simulation, for cluster satellites and galaxies in the field (meant as a wide portion of the sky, including all environments), in the local universe (z ~ 0.06), and at intermediate redshift (z ~ 0.6), with the aim to shed light on the processes which regulate the mass distribution in different environments. While the mass functions in the field and in its finer environments (groups, binary, and single systems) are well matched in the local universe down to the completeness limit of the observational sample, the model overpredicts the number of low-mass galaxies in the field at z ~ 0.6 and in clusters at both redshifts. Above M * = 1010.25 M ⊙, it reproduces the observed similarity of the cluster and field mass functions but not the observed evolution. Our results point out two shortcomings of the model: an incorrect treatment of cluster-specific environmental effects and an overefficient galaxy formation at early times (as already found by, e.g., Weinmann et al.). Next, we consider only simulations. Also using the Guo et al. model, we find that the high-mass end of the mass functions depends on halo mass: only very massive halos host massive galaxies, with the result that their mass function is flatter. Above M * = 109.4 M ⊙, simulations show an evolution in the number of the most massive galaxies in all environments. Mass functions obtained from the two prescriptions are different, however, results are qualitatively similar, indicating that the adopted methods to model the evolution of central and satellite galaxies still have to be better implemented in semi-analytic models.

The Arrow of Time in the Collapse of Collisionless Self-gravitating Systems: Non-validity of the Vlasov-Poisson Equation during Violent Relaxation

NASA Astrophysics Data System (ADS)

Beraldo e Silva, Leandro; de Siqueira Pedra, Walter; Sodré, Laerte; Perico, Eder L. D.; Lima, Marcos

2017-09-01

The collapse of a collisionless self-gravitating system, with the fast achievement of a quasi-stationary state, is driven by violent relaxation, with a typical particle interacting with the time-changing collective potential. It is traditionally assumed that this evolution is governed by the Vlasov-Poisson equation, in which case entropy must be conserved. We run N-body simulations of isolated self-gravitating systems, using three simulation codes, NBODY-6 (direct summation without softening), NBODY-2 (direct summation with softening), and GADGET-2 (tree code with softening), for different numbers of particles and initial conditions. At each snapshot, we estimate the Shannon entropy of the distribution function with three different techniques: Kernel, Nearest Neighbor, and EnBiD. For all simulation codes and estimators, the entropy evolution converges to the same limit as N increases. During violent relaxation, the entropy has a fast increase followed by damping oscillations, indicating that violent relaxation must be described by a kinetic equation other than the Vlasov-Poisson equation, even for N as large as that of astronomical structures. This indicates that violent relaxation cannot be described by a time-reversible equation, shedding some light on the so-called “fundamental paradox of stellar dynamics.” The long-term evolution is well-described by the orbit-averaged Fokker-Planck model, with Coulomb logarithm values in the expected range 10{--}12. By means of NBODY-2, we also study the dependence of the two-body relaxation timescale on the softening length. The approach presented in the current work can potentially provide a general method for testing any kinetic equation intended to describe the macroscopic evolution of N-body systems.

A 1-D evolutionary model for icy satellites, applied to Enceladus

NASA Astrophysics Data System (ADS)

Prialnik, Dina; Malamud, Uri

2015-11-01

A 1-D long-term evolution code for icy satellites is presented, which couples multiple processes: water migration, geochemical reactions, water and silicate phase transitions, crystallization, compaction by self-gravity, and ablation. The code takes into account various energy sources: tidal heating, radiogenic heating, geochemical energy released by serpentinization or absorbed by mineral dehydration, gravitational energy, and insolation. It includes heat transport by conduction, convection, and advection.The code is applied to Enceladus, by guessing the initial conditions that would render a structure compatible with present-day observations, and adopting a homogeneous initial structure. Assuming that the satellite has been losing water continually along its evolution, it follows that it was formed as a more massive, more ice-rich and more porous object, and gradually transformed into its present day state, due to sustained tidal heating. Several initial compositions and evolution scenarios are considered, and the evolution is simulated for the age of the Solar System. The results corresponding to the present configuration are confronted with the available observational constraints. The present configuration is shown to be differentiated into a pure icy mantle, several tens of km thick, overlying a rocky core, composed of dehydrated rock in the central part and hydrated rock in the outer part. Such a differentiated structure is obtained not only for Enceladus, but for other medium size ice-rich bodies as well.Predictions for Enceladus are a higher rock/ice mass ratio than previously assumed, and a thinner ice mantle, compatible with recent estimates based on gravity field measurements. Although, obviously, the 1-D model cannot be used to explain local phenomena, it sheds light on the internal structure invoked in explanations of localized features and activities.

Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence

PubMed Central

2013-01-01

Background A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. Results 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. Conclusions These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches. PMID:23402223

Evolution and function of the Mycoplasma hyopneumoniae peroxiredoxin, a 2-Cys-like enzyme with a single Cys residue.

PubMed

Gonchoroski, Taylor; Virginio, Veridiana G; Thompson, Claudia E; Paes, Jéssica A; Machado, Cláudio X; Ferreira, Henrique B

2017-04-01

The minimal genome of the mollicute Mycoplasma hyopneumoniae, the etiological agent of porcine enzootic pneumonia, encodes a limited repertoire of antioxidant enzymes that include a single and atypical peroxiredoxin (MhPrx), whose evolution and function were studied here. MhPrx has only one catalytic cysteine, in contrast with some of its possible ancestors (2-Cys peroxiredoxins), which have two. Although it is more similar to 2-Cys orthologs, MhPrx can still function with a single peroxidatic cysteine (Cys P ), using non-thiolic electron donors to reduce it. Therefore, MhPrx could be a representative of a possible group of 2-Cys peroxiredoxins, which have lost the resolving cysteine (Cys R ) residue without losing their catalytic properties. To further investigate MhPrx evolution, we performed a comprehensive phylogenetic analysis in the context of several bacterial families, including Prxs belonging to Tpx and AhpE families, shedding light on the evolutionary history of Mycoplasmataceae Prxs and giving support to the hypothesis of a relatively recent loss of the Cys R within this family. Moreover, mutational analyses provided insights into MhPrx function with one, two, or without catalytic cysteines. While removal of the MhPrx putative Cys P caused complete activity loss, confirming its catalytic role, the introduction of a second cysteine in a site correspondent to that of the Cys R of a 2-Cys orthologue, as in the MhPrx supposed ancestral form, was compatible with enzyme activity. Overall, our phylogenetic and mutational studies support that MhPrx recently diverged from a 2-Cys Prx ancestor and pave the way for future studies addressing structural, functional, and evolutive aspects of peroxiredoxin subfamilies in Mollicutes and other bacteria.

The first multi-gene phylogeny of the Macrostomorpha sheds light on the evolution of sexual and asexual reproduction in basal Platyhelminthes.

PubMed

Janssen, Toon; Vizoso, Dita B; Schulte, Gregor; Littlewood, D Timothy J; Waeschenbach, Andrea; Schärer, Lukas

2015-11-01

The Macrostomorpha-an early branching and species-rich clade of free-living flatworms-is attracting interest because it contains Macrostomum lignano, a versatile model organism increasingly used in evolutionary, developmental, and molecular biology. We elucidate the macrostomorphan molecular phylogeny inferred from both nuclear (18S and 28S rDNA) and mitochondrial (16S rDNA and COI) marker genes from 40 representatives. Although our phylogeny does not recover the Macrostomorpha as a statistically supported monophyletic grouping, it (i) confirms many taxa previously proposed based on morphological evidence, (ii) permits the first placement of many families and genera, and (iii) reveals a number of unexpected placements. Specifically, Myozona and Bradynectes are outside the three classic families (Macrostomidae, Microstomidae and Dolichomacrostomidae) and the asexually fissioning Myomacrostomum belongs to a new subfamily, the Myozonariinae nov. subfam. (Dolichomacrostomidae), rather than diverging early. While this represents the first evidence for asexuality among the Dolichomacrostomidae, we show that fissioning also occurs in another Myozonariinae, Myozonaria fissipara nov. sp. Together with the placement of the (also fissioning) Microstomidae, namely as the sister taxon of Dolichomacrostomidae, this suggests that fissioning is not basal within the Macrostomorpha, but rather restricted to the new taxon Dolichomicrostomida (Dolichomacrostomidae+Microstomidae). Furthermore, our phylogeny allows new insights into the evolution of the reproductive system, as ancestral state reconstructions reveal convergent evolution of gonads, and male and female genitalia. Finally, the convergent evolution of sperm storage organs in the female genitalia appears to be linked to the widespread occurrence of hypodermic insemination among the Macrostomorpha. Copyright © 2015 Elsevier Inc. All rights reserved.

Cell population heterogeneity and evolution towards drug resistance in cancer: Biological and mathematical assessment, theoretical treatment optimisation.

PubMed

Chisholm, Rebecca H; Lorenzi, Tommaso; Clairambault, Jean

2016-11-01

Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level. We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies. Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies. Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang. Copyright © 2016 Elsevier B.V. All rights reserved.

Computer Learning Through Piaget's Eyes.

ERIC Educational Resources Information Center

Huber, Leonard N.

1985-01-01

Discusses Piaget's pre-operational, concrete operational, and formal operational stages and shows how this information sheds light on how children approach computers and computing, particularly with the LOGO programming language. (JN)

Enemies with benefits: mutualistic interactions of viruses with lower eukaryotes.

PubMed

Jagdale, Shounak S; Joshi, Rakesh S

2018-04-01

Viruses represent some of the deadliest pathogens known to science. Recently they have been reported to have mutualistic interactions with their hosts, providing them direct or indirect benefits. The mutualism and symbiogenesis of such viruses with lower eukaryotic partners such as fungi, yeast, and insects have been reported but the full mechanism of interaction often remains an enigma. In many instances, these viral interactions provide resistance against several biotic and abiotic stresses, which could be the prime reason for the ecological success and positive selection of the hosts. These viruses modulate host metabolism and behavior, so both can obtain maximum benefits from the environment. They bring about micro- and macro-level changes in the hosts, benefiting their adaptation, reproduction, development, and survival. These virus-host interactions can be bilateral or tripartite with a variety of interacting partners. Exploration of these interactions can shed light on one of the well-coordinated biological phenomena of co-evolution and can be highly utilized for various applications in agriculture, fermentation and the pharmaceutical industries.

Chromosomal polymorphism in mammals: an evolutionary perspective.

PubMed

Dobigny, Gauthier; Britton-Davidian, Janice; Robinson, Terence J

2017-02-01

Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species. © 2015 Cambridge Philosophical Society.

Development of heavy-flavour flow-harmonics in high-energy nuclear collisions

NASA Astrophysics Data System (ADS)

Beraudo, Andrea; De Pace, Arturo; Monteno, Marco; Nardi, Marzia; Prino, Francesco

2018-02-01

We employ the POWLANG transport setup, developed over the last few years, to provide new predictions for several heavy-flavour observables in relativistic heavy-ion collisions from RHIC to LHC center-of-mass energies. In particular, we focus on the development of the flow-harmonics v 2 and v 3 arising from the initial geometric asymmetry in the initial conditions and its associated event-by-event fluctuations. Within the same transport framework, for the sake of consistency, we also compare the nuclear modification factor of the p T spectra of charm and beauty quarks, heavy hadrons and their decay electrons. We compare our findings to the most recent data from the experimental collaborations. We also study in detail the contribution to the flow harmonics from the quarks decoupling from the fireball during the various stages of its evolution: although not directly accessible to the experiments, this information can shed light on the major sources of the final measured effect.

An impact analysis of a flexible bat using an iterative solver.

PubMed

Penrose, J M; Hose, D R

1999-08-01

Although technology has now infiltrated and prompted evolution in most mass participation sports, the advances in bat technology in such sports as baseball and cricket have been relatively minor. In this study, we used a simple finite element modelling approach to try to shed new light upon the underlying mechanics of the bat-ball impact, with a view to the future optimization of bat design. The analysis of a flexible bat showed that the point of impact that produced the maximum post-impact ball velocity was a function of the bat's vibrational properties and was not necessarily at the centre of percussion. The details of the analysis agreed well with traditional Hertzian impact theory, and broadly with empirical data. An inspection of the relative modal contributions to the deformations during impact also showed that the position of the node of the first flexure mode was important. In conclusion, considerable importance should be attached to the bat's vibrational properties in future design and analysis.

The evolution of ecosystem ascendency in a complex systems based model.

PubMed

Brinck, Katharina; Jensen, Henrik Jeldtoft

2017-09-07

General patterns in ecosystem development can shed light on driving forces behind ecosystem formation and recovery and have been of long interest. In recent years, the need for integrative and process oriented approaches to capture ecosystem growth, development and organisation, as well as the scope of information theory as a descriptive tool has been addressed from various sides. However data collection of ecological network flows is difficult and tedious and comprehensive models are lacking. We use a hierarchical version of the Tangled Nature Model of evolutionary ecology to study the relationship between structure, flow and organisation in model ecosystems, their development over evolutionary time scales and their relation to ecosystem stability. Our findings support the validity of ecosystem ascendency as a meaningful measure of ecosystem organisation, which increases over evolutionary time scales and significantly drops during periods of disturbance. The results suggest a general trend towards both higher integrity and increased stability driven by functional and structural ecosystem coadaptation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pathophysiological analyses of cortical malformation using gyrencephalic mammals

PubMed Central

Masuda, Kosuke; Toda, Tomohisa; Shinmyo, Yohei; Ebisu, Haruka; Hoshiba, Yoshio; Wakimoto, Mayu; Ichikawa, Yoshie; Kawasaki, Hiroshi

2015-01-01

One of the most prominent features of the cerebral cortex of higher mammals is the presence of gyri. Because malformations of the cortical gyri are associated with severe disability in brain function, the mechanisms underlying malformations of the cortical gyri have been of great interest. Combining gyrencephalic carnivore ferrets and genetic manipulations using in utero electroporation, here we successfully recapitulated the cortical phenotypes of thanatophoric dysplasia (TD) by expressing fibroblast growth factor 8 in the ferret cerebral cortex. Strikingly, in contrast to TD mice, our TD ferret model showed not only megalencephaly but also polymicrogyria. We further uncovered that outer radial glial cells (oRGs) and intermediate progenitor cells (IPs) were markedly increased. Because it has been proposed that increased oRGs and/or IPs resulted in the appearance of cortical gyri during evolution, it seemed possible that increased oRGs and IPs underlie the pathogenesis of polymicrogyria. Our findings should help shed light on the molecular mechanisms underlying the formation and malformation of cortical gyri in higher mammals. PMID:26482531

A HapMap harvest of insights into the genetics of common disease

PubMed Central

Manolio, Teri A.; Brooks, Lisa D.; Collins, Francis S.

2008-01-01

The International HapMap Project was designed to create a genome-wide database of patterns of human genetic variation, with the expectation that these patterns would be useful for genetic association studies of common diseases. This expectation has been amply fulfilled with just the initial output of genome-wide association studies, identifying nearly 100 loci for nearly 40 common diseases and traits. These associations provided new insights into pathophysiology, suggesting previously unsuspected etiologic pathways for common diseases that will be of use in identifying new therapeutic targets and developing targeted interventions based on genetically defined risk. In addition, HapMap-based discoveries have shed new light on the impact of evolutionary pressures on the human genome, suggesting multiple loci important for adapting to disease-causing pathogens and new environments. In this review we examine the origin, development, and current status of the HapMap; its prospects for continued evolution; and its current and potential future impact on biomedical science. PMID:18451988

Previously unknown class of metalorganic compounds revealed in meteorites

PubMed Central

Ruf, Alexander; Kanawati, Basem; Hertkorn, Norbert; Yin, Qing-Zhu; Moritz, Franco; Harir, Mourad; Lucio, Marianna; Michalke, Bernhard; Wimpenny, Joshua; Shilobreeva, Svetlana; Bronsky, Basil; Saraykin, Vladimir; Gabelica, Zelimir; Gougeon, Régis D.; Quirico, Eric; Ralew, Stefan; Jakubowski, Tomasz; Haack, Henning; Gonsior, Michael; Jenniskens, Peter; Hinman, Nancy W.; Schmitt-Kopplin, Philippe

2017-01-01

The rich diversity and complexity of organic matter found in meteorites is rapidly expanding our knowledge and understanding of extreme environments from which the early solar system emerged and evolved. Here, we report the discovery of a hitherto unknown chemical class, dihydroxymagnesium carboxylates [(OH)2MgO2CR]−, in meteoritic soluble organic matter. High collision energies, which are required for fragmentation, suggest substantial thermal stability of these Mg-metalorganics (CHOMg compounds). This was corroborated by their higher abundance in thermally processed meteorites. CHOMg compounds were found to be present in a set of 61 meteorites of diverse petrological classes. The appearance of this CHOMg chemical class extends the previously investigated, diverse set of CHNOS molecules. A connection between the evolution of organic compounds and minerals is made, as Mg released from minerals gets trapped into organic compounds. These CHOMg metalorganic compounds and their relation to thermal processing in meteorites might shed new light on our understanding of carbon speciation at a molecular level in meteorite parent bodies. PMID:28242686

Prospects for regulated competition in the health care system: what can China learn from Russia's experience?

PubMed

Xu, Weiwei; Sheiman, Igor; van de Ven, Wynand P M M; Zhang, Wei

2011-05-01

As China explores new directions to reform its health care system, regulated competition among both insurers and providers of care might be one potential model. The Russian Federation in 1993 implemented legislation intended to stimulate such regulated competition in the health care sector. The subsequent progress and lessons learned over these 17 years can shed light on and inform the future evolution of the Chinese system. In this paper, we list the necessary pre-conditions for reaping the benefits of regulated competition in the health care sector. We indicate to what extent these conditions are being fulfilled in the post-reform Russian and current Chinese health care systems. We draw lessons from the Russian experience for the Chinese health care system, which shares a similar economic and political background with the pre-reform Russian health care system in terms of the starting point of the reform, and analyse the prospects for regulated competition in China.

Status competition, inequality, and fertility: implications for the demographic transition

PubMed Central

Kaplan, Hillard S.; Hooper, Paul L.

2016-01-01

The role that social status plays in small-scale societies suggests that status may be important for understanding the evolution of human fertility decisions, and for understanding how such decisions play out in modern contexts. This paper explores whether modelling competition for status—in the sense of relative rank within a society—can help shed light on fertility decline and the demographic transition. We develop a model of how levels of inequality and status competition affect optimal investment by parents in the embodied capital (health, strength, and skills) and social status of offspring, focusing on feedbacks between individual decisions and socio-ecological conditions. We find that conditions similar to those in demographic transition societies yield increased investment in both embodied capital and social status, generating substantial decreases in fertility, particularly under conditions of high inequality and intense status competition. We suggest that a complete explanation for both fertility variation in small-scale societies and modern fertility decline will take into account the effects of status competition and inequality. PMID:27022077

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon

PubMed Central

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-01-01

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H+ translocation across the cytoplasmic membrane that then drives Na+ translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na+/H+ antiporter module. The electrochemical Na+ gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na+/H+ antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains. PMID:25049407

Energy conservation by oxidation of formate to carbon dioxide and hydrogen via a sodium ion current in a hyperthermophilic archaeon.

PubMed

Lim, Jae Kyu; Mayer, Florian; Kang, Sung Gyun; Müller, Volker

2014-08-05

Thermococcus onnurineus NA1 is known to grow by the anaerobic oxidation of formate to CO2 and H2, a reaction that operates near thermodynamic equilibrium. Here we demonstrate that this reaction is coupled to ATP synthesis by a transmembrane ion current. Formate oxidation leads to H(+) translocation across the cytoplasmic membrane that then drives Na(+) translocation. The ion-translocating electron transfer system is rather simple, consisting of only a formate dehydrogenase module, a membrane-bound hydrogenase module, and a multisubunit Na(+)/H(+) antiporter module. The electrochemical Na(+) gradient established then drives ATP synthesis. These data give a mechanistic explanation for chemiosmotic energy conservation coupled to formate oxidation to CO2 and H2. Because it is discussed that the membrane-bound hydrogenase with the Na(+)/H(+) antiporter module are ancestors of complex I of mitochondrial and bacterial electron transport these data also shed light on the evolution of ion transport in complex I-like electron transport chains.

Evolutionary dynamics of 3D genome architecture following polyploidization in cotton.

PubMed

Wang, Maojun; Wang, Pengcheng; Lin, Min; Ye, Zhengxiu; Li, Guoliang; Tu, Lili; Shen, Chao; Li, Jianying; Yang, Qingyong; Zhang, Xianlong

2018-02-01

The formation of polyploids significantly increases the complexity of transcriptional regulation, which is expected to be reflected in sophisticated higher-order chromatin structures. However, knowledge of three-dimensional (3D) genome structure and its dynamics during polyploidization remains poor. Here, we characterize 3D genome architectures for diploid and tetraploid cotton, and find the existence of A/B compartments and topologically associated domains (TADs). By comparing each subgenome in tetraploids with its extant diploid progenitor, we find that genome allopolyploidization has contributed to the switching of A/B compartments and the reorganization of TADs in both subgenomes. We also show that the formation of TAD boundaries during polyploidization preferentially occurs in open chromatin, coinciding with the deposition of active chromatin modification. Furthermore, analysis of inter-subgenomic chromatin interactions has revealed the spatial proximity of homoeologous genes, possibly associated with their coordinated expression. This study advances our understanding of chromatin organization in plants and sheds new light on the relationship between 3D genome evolution and transcriptional regulation.

Discovery of a new family of amphibians from northeast India with ancient links to Africa

PubMed Central

Kamei, Rachunliu G.; Mauro, Diego San; Gower, David J.; Van Bocxlaer, Ines; Sherratt, Emma; Thomas, Ashish; Babu, Suresh; Bossuyt, Franky; Wilkinson, Mark; Biju, S. D.

2012-01-01

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians. PMID:22357266

Multi-phase inversion tectonics related to the Hendijan-Nowrooz-Khafji Fault activity, Zagros Mountains, SW Iran

NASA Astrophysics Data System (ADS)

Kazem Shiroodi, Sadjad; Ghafoori, Mohammad; Faghih, Ali; Ghanadian, Mostafa; Lashkaripour, Gholamreza; Hafezi Moghadas, Naser

2015-11-01

Distinctive characteristics of inverted structures make them important criteria for the identification of certain structural styles of folded belts. The interpretation of 3D seismic reflection and well data sheds new light on the structural evolution and age of inverted structures associated to the Hendijan-Nowrooz-Khafji Fault within the Persian Gulf Basin and northeastern margin of Afro-Arabian plate. Analysis of thickness variations of growth strata using "T-Z plot" (thickness versus throw plot) method revealed the kinematics of the fault. Obtained results show that the fault has experienced a multi-phase evolutionary history over six different extension and compression deformation events (i.e. positive and negative inversion) between 252.2 and 11.62 Ma. This cyclic activity of the growth fault was resulted from alteration of sedimentary processes during continuous fault slip. The structural development of the study area both during positive and negative inversion geometry styles was ultimately controlled by the relative motion between the Afro-Arabian and Central-Iranian plates.

Engineering A-kinase Anchoring Protein (AKAP)-selective Regulatory Subunits of Protein Kinase A (PKA) through Structure-based Phage Selection*

PubMed Central

Gold, Matthew G.; Fowler, Douglas M.; Means, Christopher K.; Pawson, Catherine T.; Stephany, Jason J.; Langeberg, Lorene K.; Fields, Stanley; Scott, John D.

2013-01-01

PKA is retained within distinct subcellular environments by the association of its regulatory type II (RII) subunits with A-kinase anchoring proteins (AKAPs). Conventional reagents that universally disrupt PKA anchoring are patterned after a conserved AKAP motif. We introduce a phage selection procedure that exploits high-resolution structural information to engineer RII mutants that are selective for a particular AKAP. Selective RII (RSelect) sequences were obtained for eight AKAPs following competitive selection screening. Biochemical and cell-based experiments validated the efficacy of RSelect proteins for AKAP2 and AKAP18. These engineered proteins represent a new class of reagents that can be used to dissect the contributions of different AKAP-targeted pools of PKA. Molecular modeling and high-throughput sequencing analyses revealed the molecular basis of AKAP-selective interactions and shed new light on native RII-AKAP interactions. We propose that this structure-directed evolution strategy might be generally applicable for the investigation of other protein interaction surfaces. PMID:23625929

Abell 1142 and the Missing Central Galaxy – A Cluster in Transition?

NASA Astrophysics Data System (ADS)

Jones, Alexander; Su, Yuanyuan; Buote, David; Forman, William; van Weeren, Reinout; Jones, Christine; Gastaldello, Fabio; Kraft, Ralph; Randall, Scott

2018-01-01

Two types of galaxy clusters exist: cool core (CC) clusters which exhibit centrally-peaked metallicity and X-ray emission and non-cool core (NCC) clusters, possessing comparably homogeneous metallicity and X-ray emission distributions. However, the origin of this dichotomy is still unknown. The current prevailing theories state that either there is a primordial entropy limit, above which a CC is unable to form, or that clusters can change type through major mergers and radiative cooling. Abell 1142 is a galaxy cluster that can provide a unique probe of the root of this cluster-type division. It is formed of two merging sub-clusters, each with its own brightest cluster galaxies (BCG). Its enriched X-ray centroid (possible CC remnant) lies between these two BCGs. We present the thermal and chemical distributions of this system using deep (180ks) XMM-Newton observations to shed light on the role of mergers in the evolution of galaxy clusters.

Novel Trypanosomatid-Bacterium Association: Evolution of Endosymbiosis in Action

PubMed Central

Kostygov, Alexei Y.; Dobáková, Eva; Grybchuk-Ieremenko, Anastasiia; Váhala, Dalibor; Maslov, Dmitri A.; Votýpka, Jan

2016-01-01

ABSTRACT We describe a novel symbiotic association between a kinetoplastid protist, Novymonas esmeraldas gen. nov., sp. nov., and an intracytoplasmic bacterium, “Candidatus Pandoraea novymonadis” sp. nov., discovered as a result of a broad-scale survey of insect trypanosomatid biodiversity in Ecuador. We characterize this association by describing the morphology of both organisms, as well as their interactions, and by establishing their phylogenetic affinities. Importantly, neither partner is closely related to other known organisms previously implicated in eukaryote-bacterial symbiosis. This symbiotic association seems to be relatively recent, as the host does not exert a stringent control over the number of bacteria harbored in its cytoplasm. We argue that this unique relationship may represent a suitable model for studying the initial stages of establishment of endosymbiosis between a single-cellular eukaryote and a prokaryote. Based on phylogenetic analyses, Novymonas could be considered a proxy for the insect-only ancestor of the dixenous genus Leishmania and shed light on the origin of the two-host life cycle within the subfamily Leishmaniinae. PMID:26980834

Late Oligocene and Early Miocene Muroidea of the Zinda Pir Dome.

PubMed

Lindsay, Everett H; Flynn, Lawrence J

2016-02-17

A series of Oligocene through Early Miocene terrestrial deposits preserved in the foothills of the Zinda Pir Dome of western Pakistan produce multiple, superposed fossil mammal localities. These include small mammal assemblages that shed light on the evolution of rodent lineages, especially Muroidea, in South Asia. Nine small mammal localities span approximately 28-19 Ma, an interval encompassing the Oligocene-Miocene boundary. The Early Miocene rodent fossil assemblages are dominated by muroid rodents, but muroids are uncommon and archaic in earlier Oligocene horizons. The Zinda Pir sequence includes the evolutionary transition to modern Muroidea at about the Oligocene-Miocene boundary. We review the muroid record for the Zinda Pir Dome, which includes the early radiation of primitive bamboo rats (Rhizomyinae) and early members of the modern muroid radiation, which lie near crown Cricetidae and Muridae. The Zinda Pir record dates diversification of modern muroids in the Indian Subcontintent and establishment by 19 Ma of muroid assemblages characteristic of the later Siwaliks.

A VLT/FORS2 spectroscopic survey of individual stars in a transforming dwarf galaxy

NASA Astrophysics Data System (ADS)

Battaglia, G.; Kacharov, N.; Rejkuba, M.

2017-03-01

Understanding the properties of dwarf galaxies is important not only to put them in their proper cosmological context, but also to understand the formation and evolution of the most common type of galaxies. Dwarf galaxies are divided into two main classes, dwarf irregulars (dIrrs) and dwarf spheroidals (dSphs), which differ from each other mainly because the former are gas-rich objects currently forming stars, while the latter are gas-deficient with no on-going star formation. Transition types (dT) are thought to represent dIs in the process of losing their gas, and can therefore shed light into the possible process of dwarf irregulars (dIrrs) becoming gas-deficient, passively evolving galaxies. Here we present preliminary results from our wide-area VLT/FORS2 MXU spectroscopic survey of the Phoenix dT, from which we obtained line-of-sight velocities and metallicities from the nIR Ca II triplet lines for a large sample of individual Red Giant Branch stars.

Higgs cosmology

NASA Astrophysics Data System (ADS)

Rajantie, Arttu

2018-01-01

The discovery of the Higgs boson in 2012 and other results from the Large Hadron Collider have confirmed the standard model of particle physics as the correct theory of elementary particles and their interactions up to energies of several TeV. Remarkably, the theory may even remain valid all the way to the Planck scale of quantum gravity, and therefore it provides a solid theoretical basis for describing the early Universe. Furthermore, the Higgs field itself has unique properties that may have allowed it to play a central role in the evolution of the Universe, from inflation to cosmological phase transitions and the origin of both baryonic and dark matter, and possibly to determine its ultimate fate through the electroweak vacuum instability. These connections between particle physics and cosmology have given rise to a new and growing field of Higgs cosmology, which promises to shed new light on some of the most puzzling questions about the Universe as new data from particle physics experiments and cosmological observations become available. This article is part of the Theo Murphy meeting issue `Higgs cosmology'.

Anomalous anisotropic compression behavior of superconducting CrAs under high pressure

PubMed Central

Yu, Zhenhai; Wu, Wei; Hu, Qingyang; Zhao, Jinggeng; Li, Chunyu; Yang, Ke; Cheng, Jinguang; Luo, Jianlin; Wang, Lin; Mao, Ho-kwang

2015-01-01

CrAs was observed to possess the bulk superconductivity under high-pressure conditions. To understand the superconducting mechanism and explore the correlation between the structure and superconductivity, the high-pressure structural evolution of CrAs was investigated using the angle-dispersive X-ray diffraction (XRD) method. The structure of CrAs remains stable up to 1.8 GPa, whereas the lattice parameters exhibit anomalous compression behaviors. With increasing pressure, the lattice parameters a and c both demonstrate a nonmonotonic change, and the lattice parameter b undergoes a rapid contraction at ∼0.18−0.35 GPa, which suggests that a pressure-induced isostructural phase transition occurs in CrAs. Above the phase transition pressure, the axial compressibilities of CrAs present remarkable anisotropy. A schematic band model was used to address the anomalous compression behavior of CrAs. The present results shed light on the structural and related electronic responses to high pressure, which play a key role toward understanding the superconductivity of CrAs. PMID:26627230

The dynamic genome of Hydra.

PubMed

Chapman, Jarrod A; Kirkness, Ewen F; Simakov, Oleg; Hampson, Steven E; Mitros, Therese; Weinmaier, Thomas; Rattei, Thomas; Balasubramanian, Prakash G; Borman, Jon; Busam, Dana; Disbennett, Kathryn; Pfannkoch, Cynthia; Sumin, Nadezhda; Sutton, Granger G; Viswanathan, Lakshmi Devi; Walenz, Brian; Goodstein, David M; Hellsten, Uffe; Kawashima, Takeshi; Prochnik, Simon E; Putnam, Nicholas H; Shu, Shengquiang; Blumberg, Bruce; Dana, Catherine E; Gee, Lydia; Kibler, Dennis F; Law, Lee; Lindgens, Dirk; Martinez, Daniel E; Peng, Jisong; Wigge, Philip A; Bertulat, Bianca; Guder, Corina; Nakamura, Yukio; Ozbek, Suat; Watanabe, Hiroshi; Khalturin, Konstantin; Hemmrich, Georg; Franke, André; Augustin, René; Fraune, Sebastian; Hayakawa, Eisuke; Hayakawa, Shiho; Hirose, Mamiko; Hwang, Jung Shan; Ikeo, Kazuho; Nishimiya-Fujisawa, Chiemi; Ogura, Atshushi; Takahashi, Toshio; Steinmetz, Patrick R H; Zhang, Xiaoming; Aufschnaiter, Roland; Eder, Marie-Kristin; Gorny, Anne-Kathrin; Salvenmoser, Willi; Heimberg, Alysha M; Wheeler, Benjamin M; Peterson, Kevin J; Böttger, Angelika; Tischler, Patrick; Wolf, Alexander; Gojobori, Takashi; Remington, Karin A; Strausberg, Robert L; Venter, J Craig; Technau, Ulrich; Hobmayer, Bert; Bosch, Thomas C G; Holstein, Thomas W; Fujisawa, Toshitaka; Bode, Hans R; David, Charles N; Rokhsar, Daniel S; Steele, Robert E

2010-03-25

The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.

Microstructural investigation of Sr-modified Al-15 wt%Si alloys in the range from micrometer to atomic scale.

PubMed

Timpel, M; Wanderka, N; Vinod Kumar, G S; Banhart, J

2011-05-01

Strontium-modified Al-15 wt%Si casting alloys were investigated after 5 and 60 min of melt holding. The eutectic microstructures were studied using complementary methods at different length scales: focused ion beam-energy selective backscattered tomography, transmission electron microscopy and 3D atom probe. Whereas the samples after 5 min of melt holding show that the structure of eutectic Si changes into a fine fibrous morphology, the increase of prolonged melt holding (60 min) leads to the loss of Sr within the alloy with an evolution of an unmodified eutectic microstructure displaying coarse interconnected Si plates. Strontium was found at the Al/Si eutectic interfaces on the side of the eutectic Al region, measured by 3D atom probe. The new results obtained using 3D atom probe shed light on the location of Sr within the Al-Si eutectic microstructure. Copyright © 2010 Elsevier B.V. All rights reserved.

Gaydar, Marriage, and Rip-Roaring Homosexuals: Discourses About Homosexuality in Dear Abby and Ann Landers Advice Columns, 1967-1982.

PubMed

Johnson, Patrick M; Holmes, Kwame A

2017-12-04

Over the past 70 years, the history of acceptance of the lesbian, gay and bisexual (LGB) community within the United States has seen much change and fluctuation. One of the places that this dialogue has been preserved is through the syndicated advice columns of Dear Abby and Ann Landers, in which individuals in the United States were writing in for advice to deal with their anxiety over a newly emerging and highly visible new community of individuals once considered to be mentally ill and dangerous. Using discourse analysis, this article traces the evolution of public and scientific opinions about the LGBT community during the years leading up to the Stonewall riots all the way to right before the AIDs epidemic. This analysis sheds light on several moral panics that emerged regarding this newly visible population, especially in regard to disturbances within the domestic sphere and a stigmatization of bisexuality.

Hydrogenation-controlled phase transition on two-dimensional transition metal dichalcogenides and their unique physical and catalytic properties.

PubMed

Qu, Yuanju; Pan, Hui; Kwok, Chi Tat

2016-09-30

Two-dimensional (2D) transition metal dichalcogenides (TMDs) have been widely used from nanodevices to energy harvesting/storage because of their tunable physical and chemical properties. In this work, we systematically investigate the effects of hydrogenation on the structural, electronic, magnetic, and catalytic properties of 33 TMDs based on first-principles calculations. We find that the stable phases of TMD monolayers can transit from 1T to 2H phase or vice versa upon the hydrogenation. We show that the hydrogenation can switch their magnetic and electronic states accompanying with the phase transition. The hydrogenation can tune the magnetic states of TMDs among non-, ferro, para-, and antiferro-magnetism and their electronic states among semiconductor, metal, and half-metal. We further show that, out of 33 TMD monolayers, 2H-TiS 2 has impressive catalytic ability comparable to Pt in hydrogen evolution reaction in a wide range of hydrogen coverages. Our findings would shed the light on the multi-functional applications of TMDs.

Size does Matter

NASA Astrophysics Data System (ADS)

Vespignani, Alessandro

From schools of fish and flocks of birds, to digital networks and self-organizing biopolymers, our understanding of spontaneously emergent phenomena, self-organization, and critical behavior is in large part due to complex systems science. The complex systems approach is indeed a very powerful conceptual framework to shed light on the link between the microscopic dynamical evolution of the basic elements of the system and the emergence of oscopic phenomena; often providing evidence for mathematical principles that go beyond the particulars of the individual system, thus hinting to general modeling principles. By killing the myth of the ant queen and shifting the focus on the dynamical interaction across the elements of the systems, complex systems science has ushered our way into the conceptual understanding of many phenomena at the core of major scientific and social challenges such as the emergence of consensus, social opinion dynamics, conflicts and cooperation, contagion phenomena. For many years though, these complex systems approaches to real-world problems were often suffering from being oversimplified and not grounded on actual data...

Population genomics reveals the origin and asexual evolution of human infective trypanosomes

PubMed Central

Weir, William; Capewell, Paul; Foth, Bernardo; Clucas, Caroline; Pountain, Andrew; Steketee, Pieter; Veitch, Nicola; Koffi, Mathurin; De Meeûs, Thierry; Kaboré, Jacques; Camara, Mamadou; Cooper, Anneli; Tait, Andy; Jamonneau, Vincent; Bucheton, Bruno; Berriman, Matt; MacLeod, Annette

2016-01-01

Evolutionary theory predicts that the lack of recombination and chromosomal re-assortment in strictly asexual organisms results in homologous chromosomes irreversibly accumulating mutations and thus evolving independently of each other, a phenomenon termed the Meselson effect. We apply a population genomics approach to examine this effect in an important human pathogen, Trypanosoma brucei gambiense. We determine that T.b. gambiense is evolving strictly asexually and is derived from a single progenitor, which emerged within the last 10,000 years. We demonstrate the Meselson effect for the first time at the genome-wide level in any organism and show large regions of loss of heterozygosity, which we hypothesise to be a short-term compensatory mechanism for counteracting deleterious mutations. Our study sheds new light on the genomic and evolutionary consequences of strict asexuality, which this pathogen uses as it exploits a new biological niche, the human population. DOI: http://dx.doi.org/10.7554/eLife.11473.001 PMID:26809473

STM study of the Ga thin films grown on Si(111) surface

NASA Astrophysics Data System (ADS)

Tao, Min-Long; Tu, Yu-Bing; Sun, Kai; Ye, Juan; Hao, Shao-Jie; Xiao, Hua-Fang; Wang, Ya-Li; Xie, Zheng-Bo; Wang, Jun-Zhong

2017-09-01

Structural evolution of Ga thin films grown on the Si(111)-√{ 3 } × √{ 3 } -Ga template have been investigated with a low-temperature scanning tunneling microscopy (STM). The first Ga layer exhibits a stripe structure along the base vectors of Si(111) lattices. Individual Ga dimers have been directly visualized from the high-resolution STM images of the first Ga layer. The second Ga layer reveals a pseudo 1×1 structure with respect to the Si(111). A new 5×5 phase has been found in the second Ga layer when annealing the sample to 120 ℃. Further annealing to 150 ℃ leads to the formation of 6.3×6.3 phase, which is more stable than the 5×5 phase. The existences of a variety of superstructures of Ga films demonstrates the delicate balance between the interactions of Si(111)-Ga and Ga-Ga. These results shed important light on the epitaxial growth mechanism of Ga films on semiconductor surfaces.

SIGNALS AND REGULATORS THAT GOVERN STREPTOMYCES DEVELOPMENT

PubMed Central

McCormick, Joseph R.; Flärdh, Klas

2012-01-01

Streptomyces coelicolor is the genetically best characterized species of a populous genus belonging to the Gram-positive Actinobacteria. Streptomycetes are filamentous soil organisms, well known for the production of a plethora of biologically active secondary metabolic compounds. The Streptomyces developmental life cycle is uniquely complex, and involves coordinated multicellular development with both physiological and morphological differentiation of several cell types, culminating in production of secondary metabolites and dispersal of mature spores. This review presents a current appreciation of the signaling mechanisms used to orchestrate the decision to undergo morphological differentiation, and the regulators and regulatory networks that direct the intriguing development of multigenomic hyphae, first to form specialized aerial hyphae, and then to convert them into chains of dormant spores. This current view of S. coelicolor development is destined for rapid evolution as data from “-omics” studies shed light on gene regulatory networks, new genetic screens identify hitherto unknown players, and the resolution of our insights into the underlying cell biological processes steadily improve. PMID:22092088

The Effect of Format on Performance: Editing Text in Print versus Digital Formats

ERIC Educational Resources Information Center

Eden, Sigal; Eshet-Alkalai, Yoram

2013-01-01

In light of the present-day proliferation of digital texts and the increase in situations that require active digital text reading in learning, it is becoming increasingly important to shed light on the comparison between print and digital reading under active reading conditions. In this study, the active reading abilities of 93 university…

Carbon allocation to growth and storage in two evergreen species of contrasting successional status.

PubMed

Piper, Frida I; Sepúlveda, Paulina; Bustos-Salazar, Angela; Zúñiga-Feest, Alejandra

2017-05-01

A prevailing hypothesis in forest succession is that shade-tolerant species grow more slowly than shade-intolerant species, across light conditions, because they prioritize carbon (C) allocation to storage. We examined this hypothesis in a confamilial pair of species, including one of the fastest-growing tree species in the world ( Eucalyptus globulus ) and a shade-tolerant, slow-growing species ( Luma apiculata ). Seedlings were subjected to one out of four combinations of light (high vs. low) and initial defoliation (90% defoliated vs. nondefoliated) for four months. Growth, C storage concentration in different organs, leaf shedding, and lateral shoot formation were measured at the end of the experiment. Eucalyptus globulus grew faster than L. apiculata in high light, but not in low light. Both species had lower C storage concentration in low than in high light, but similar C storage concentrations in each light condition. Defoliation had no effect on C storage, except in the case of the old leaves of both species, which showed lower C storage levels in response to defoliation. Across treatments, leaf shedding was 96% higher in E. globulus than in L. apiculata while, in contrast, lateral shoot formation was 87% higher in L. apiculata . In low light, E. globulus prioritized C storage instead of growth, whereas L. apiculata prioritized growth and lateral branching. Our results suggest that shade tolerance depends on efficient light capture rather than C conservation traits. © 2017 Botanical Society of America.

The Emergence of Hadrons from QCD Color

NASA Astrophysics Data System (ADS)

Brooks, William; Color Dynamics in Cold Matter (CDCM) Collaboration

2015-10-01

The formation of hadrons from energetic quarks, the dynamical enforcement of QCD confinement, is not well understood at a fundamental level. In Deep Inelastic Scattering, modifications of the distributions of identified hadrons emerging from nuclei of different sizes reveal a rich variety of spatial and temporal characteristics of the hadronization process, including its dependence on spin, flavor, energy, and hadron mass and structure. The EIC will feature a wide range of kinematics, allowing a complete investigation of medium-induced gluon bremsstrahlung by the propagating quarks, leading to partonic energy loss. This fundamental process, which is also at the heart of jet quenching in heavy ion collisions, can be studied for light and heavy quarks at the EIC through observables quantifying hadron ``attenuation'' for a variety of hadron species. Transverse momentum broadening of hadrons, which is sensitive to the nuclear gluonic field, will also be accessible, and can be used to test our understanding from pQCD of how this quantity evolves with pathlength, as well as its connection to partonic energy loss. The evolution of the forming hadrons in the medium will shed new light on the dynamical origins of the forces between hadrons, and thus ultimately on the nuclear force. Supported by the Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT) of Chile.

Follow-up observations of SN 2010dn

NASA Astrophysics Data System (ADS)

Botticella, Maria Teresa; Kotak, Rubina; Meikle, Peter; Smartt, Stephen; Pastorello, Andrea; Benetti, Stefano

2010-06-01

A new intriguing transient, SN 2010dn in NGC 3184, was discovered ten days ago. The spectroscopic and photometric evolution make this transient similar to SN 2008S, the 2006 optical transient in M85 and the 2008 optical transient in NGC 300, members of a new class of transient events given the similar pre-explosion?and post-explosion properties. The nature of these transient is still debated?and our experience with SN 2008S proved that?Spitzer data are?invaluable to shed light on it providing a critical information in the understanding?the geometry of the circumstellar environment of these transients both for the dust enshrouded progenitor stars and after?their explosion. We would like to obtain a rapid follow-up of SN 2010dn with Spitzer to check if also this transient is producing an IR echo from substantial circumstellar material around the progenitor star. The modeling of the light echo will allow us to constrain the mass and?physical scale?of the circumstellar dust around this transient and as consequence to probe the mass loss history of the progenitor star. The proposed observations will be coordinated with an extensive optical follow up and?will be of interest to the broad scientific community. To obtain prompt observations after the discovery?is crucial.

Grantee Spotlight: Nathan Ellis, Ph.D.

Cancer.gov

Dr. Nathan Ames Ellis, a CRCHD U01 grantee, uses comparative population-genetic analysis to shed new light on cancer susceptibility and the biological basis of colorectal cancer disparities in African Americans.

Baroclinic Instability and Energy Transfer underlying the Kuroshio eddy shedding process in Luzon Strait

NASA Astrophysics Data System (ADS)

Lu, J.

2016-02-01

The Kuroshio eddy shedding in Luzon Strait has been intensively studied, due to its important role in the energy budgets of the special gap-passing western boundary current and its potential influence to South China Sea. In this study, the eddy-mean flow interaction is first diagnosed with two classical "stationary" methods. Both show that, in a "time-averaged" sense, baroclinic instability and energy transfer provides the energy source for Kuroshio anticyclonic eddy shedding and the accompanied cyclonic eddy growth in Luzon Strait (this eddy pair will be called AC/C-Es for short). To take into account the "nonstationary and intermittent" nature, the temporal evolutions of energy transfer during a typical Kuroshio eddy shedding process are investigated using the localized multi-scale-window energy and vorticity analysis, or MS-EVA for short. Two stages are roughly distinguished according to the evolutionary nature of this process: the growing stage and the shedding stage. In the growing stage, the energy source straddles both the AC/C-Es, indicating mean flow supplies potential energy to both AC/C-Es for growth; the energy transfer hot spot persistently strengthens and expands horizontally as well as vertically from 200-300m to 100-400m depth range, culminating in a maximum of approximately 1.5×10-7 m2s-3. In the shedding stage, the energy source moves onto the accompanied cyclonic eddy, i.e., the mean flow now supplies energy mainly to the cyclonic eddy, making it strong enough to cut off the anticyclonic eddy from Kuroshio, leading to the Kuroshio eddy shedding.

Numerical analyses of ventilated cavitation over a 2-D NACA0015 hydrofoil using two turbulence modeling methods

NASA Astrophysics Data System (ADS)

Yang, Dan-dan; Yu, An; Ji, Bin; Zhou, Jia-jian; Luo, Xian-wu

2018-04-01

The present paper studies the ventilated cavitation over a NACA0015 hydrofoil by numerical methods. The corresponding cavity evolutions are obtained at three ventilation rates by using the level set method. To depict the complicated turbulent flow structure, the filter-based density corrected model (FBDCM) and the modified partially-averaged Navier-Stokes (MPANS) model are applied in the present numerical analyses. It is indicated that the predicted results of the cavitation shedding dynamics by both turbulence models agree fairly well with the experimental data. It is also noted that the shedding frequency and the super cavity length predicted by the MPANS method are closer to the experiment data as compared to that predicted by the FBDCM model. The simulation results show that in the ventilated cavitation, the vapor cavity and the air cavity have the same shedding frequency. As the ventilated rate increases, the vapor cavity is depressed rapidly. The cavitation-vortex interaction in the ventilated cavitation is studied based on the vorticity transport equation (VTE) and the Lagrangian coherent structure (LCS). Those results demonstrate that the vortex dilatation and baroclinic torque terms are highly dependent on the evolution of the cavitation. In addition, from the LCSs and the tracer particles in the flow field, one may see the process from the attached cavity to the cloud cavity.

Rapid evolution and copy number variation of primate RHOXF2, an X-linked homeobox gene involved in male reproduction and possibly brain function.

PubMed

Niu, Ao-lei; Wang, Yin-qiu; Zhang, Hui; Liao, Cheng-hong; Wang, Jin-kai; Zhang, Rui; Che, Jun; Su, Bing

2011-10-12

Homeobox genes are the key regulators during development, and they are in general highly conserved with only a few reported cases of rapid evolution. RHOXF2 is an X-linked homeobox gene in primates. It is highly expressed in the testicle and may play an important role in spermatogenesis. As male reproductive system is often the target of natural and/or sexual selection during evolution, in this study, we aim to dissect the pattern of molecular evolution of RHOXF2 in primates and its potential functional consequence. We studied sequences and copy number variation of RHOXF2 in humans and 16 nonhuman primate species as well as the expression patterns in human, chimpanzee, white-browed gibbon and rhesus macaque. The gene copy number analysis showed that there had been parallel gene duplications/losses in multiple primate lineages. Our evidence suggests that 11 nonhuman primate species have one RHOXF2 copy, and two copies are present in humans and four Old World monkey species, and at least 6 copies in chimpanzees. Further analysis indicated that the gene duplications in primates had likely been mediated by endogenous retrovirus (ERV) sequences flanking the gene regions. In striking contrast to non-human primates, humans appear to have homogenized their two RHOXF2 copies by the ERV-mediated non-allelic recombination mechanism. Coding sequence and phylogenetic analysis suggested multi-lineage strong positive selection on RHOXF2 during primate evolution, especially during the origins of humans and chimpanzees. All the 8 coding region polymorphic sites in human populations are non-synonymous, implying on-going selection. Gene expression analysis demonstrated that besides the preferential expression in the reproductive system, RHOXF2 is also expressed in the brain. The quantitative data suggests expression pattern divergence among primate species. RHOXF2 is a fast-evolving homeobox gene in primates. The rapid evolution and copy number changes of RHOXF2 had been driven by Darwinian positive selection acting on the male reproductive system and possibly also on the central nervous system, which sheds light on understanding the role of homeobox genes in adaptive evolution.

Light-Induced Capacitance Tunability in Ferroelectric Crystals.

PubMed

Páez-Margarit, David; Rubio-Marcos, Fernando; Ochoa, Diego A; Del Campo, Adolfo; Fernández, José F; García, José E

2018-06-25

The remote controlling of ferroic properties with light is nowadays a hot and highly appealing topic in materials science. Here, we shed light on some of the unresolved issues surrounding light-matter coupling in ferroelectrics. Our findings show that the capacitance and, consequently, its related intrinsic material property, i.e., the dielectric constant, can be reversibly adjusted through the light power control. High photodielectric performance is exhibited across a wide range of the visible light wavelength because of the wavelength-independence of the phenomenon. We have verified that this counterintuitive behavior can be strongly ascribed to the existence of "locally free charges" at domain wall.

Rethinking Normative Literacy Practices, Behaviors, and Interactions: Learning from Young Immigrant Boys

ERIC Educational Resources Information Center

Souto-Manning, Mariana; Dernikos, Bessie; Yu, Hae Min

2016-01-01

In light of the historical failure of boys of color in US schools, this article sheds light onto the ways in which normative discourses of literacy and learning shape the experiences of immigrant boys and how they are perceived and defined as un/successful students. Findings indicate that although these boys--deemed to be "at-risk" or…

Examining the Relationship between Career Decision Self-Efficacy, Ethnic Identity, and Academic Self-Concept and Achievement of African American High School Students

ERIC Educational Resources Information Center

Bounds, Patrice Sheri Robinson

2013-01-01

The exploration of African American adolescents' career development has gained increasing attention in light of literature describing various barriers impacting their educational and career development and goals. Social Cognitive Career Theory (SCCT) was used as a theoretical framework to help shed light on the contextual factors that influence…

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

PubMed

El Karkouri, Khalid; Kowalczewska, Malgorzata; Armstrong, Nicholas; Azza, Said; Fournier, Pierre-Edouard; Raoult, Didier

2017-01-01

Arthropod-borne Rickettsia species are obligate intracellular bacteria which are pathogenic for humans. Within this genus, Rickettsia slovaca and Rickettsia conorii cause frequent and potentially severe infections, whereas Rickettsia raoultii and Rickettsia massiliae cause rare and milder infections. All four species belong to spotted fever group (SFG) rickettsiae. However, R. slovaca and R. raoultii cause scalp eschar and neck lymphadenopathy (SENLAT) and are mainly associated with Dermacentor ticks, whereas the other two species cause Mediterranean spotted fever (MSF) and are mainly transmitted by Rhipicephalus ticks. To identify the potential genes and protein profiles and to understand the evolutionary processes that could, comprehensively, relate to the differences in virulence and pathogenicity observed between these four species, we compared their genomes and proteomes. The virulent and milder agents displayed divergent phylogenomic evolution in two major clades, whereas either SENLAT or MSF disease suggests a discrete convergent evolution of one virulent and one milder agent, despite their distant genetic relatedness. Moreover, the two virulent species underwent strong reductive genomic evolution and protein structural variations, as well as a probable loss of plasmid(s), compared to the two milder species. However, an abundance of mobilome genes was observed only in the less pathogenic species. After infecting Xenopus laevis cells, the virulent agents displayed less up-regulated than down-regulated proteins, as well as less number of identified core proteins. Furthermore, their similar and distinct protein profiles did not contain some genes (e.g., omp A/B and rick A) known to be related to rickettsial adhesion, motility and/or virulence, but may include other putative virulence-, antivirulence-, and/or disease-related proteins. The identified evolutionary forces herein may have a strong impact on intracellular expressions and strategies in these rickettsiae, and that may contribute to the emergence of distinct virulence and diseases in humans. Thus, the current multi-omics data provide new insights into the evolution and fitness of SFG virulence and pathogenicity, and intracellular pathogenic bacteria.

Multi Vitamin E: E-lusive E-ffects

PubMed Central

2015-01-01

Investigations into vitamin E’s anti-inflammatory effects must be more comprehensive: Dr Joan Cook-Mills explains how their research could redefine medical perceptions and shed new light on previous studies PMID:27175228

Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer

PubMed Central

Remigi, Philippe; Capela, Delphine; Clerissi, Camille; Tasse, Léna; Torchet, Rachel; Bouchez, Olivier; Batut, Jacques; Cruveiller, Stéphane; Rocha, Eduardo P. C.; Masson-Boivin, Catherine

2014-01-01

Horizontal gene transfer (HGT) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists. Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully spread over large phylogenetic distances. Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont. Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant. The generated burst in genetic diversity accelerated symbiotic adaptation of the recipient genome under plant selection pressure, presumably by improving the exploration of the fitness landscape. Finally, we show that plasmid imuABC cassettes are over-represented in rhizobial lineages harboring symbiotic plasmids. Our findings shed light on a mechanism that may have facilitated the dissemination of symbiotic competency among α- and β-proteobacteria in natura and provide evidence for the positive role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait. We speculate that co-transfer of complex phenotypic traits with mutagenesis determinants might frequently enhance the ecological success of HGT. PMID:25181317

Sexual conflict over the maintenance of sex: effects of sexually antagonistic coevolution for reproductive isolation of parthenogenesis.

PubMed

Kawatsu, Kazutaka

2013-01-01

Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction.

Sexual Conflict over the Maintenance of Sex: Effects of Sexually Antagonistic Coevolution for Reproductive Isolation of Parthenogenesis

PubMed Central

Kawatsu, Kazutaka

2013-01-01

Sexual reproduction involves many costs. Therefore, females acquiring a capacity for parthenogenetic (or asexual) reproduction will gain a reproductive advantage over obligately sexual females. In contrast, for males, any trait coercing parthenogens into sexual reproduction (male coercion) increases their fitness and should be under positive selection because parthenogenesis deprives them of their genetic contribution to future generations. Surprisingly, although such sexual conflict is a possible outcome whenever reproductive isolation is incomplete between parthenogens and the sexual ancestors, it has not been given much attention in the studies of the maintenance of sex. Using two mathematical models, I show here that the evolution of male coercion substantially favours the maintenance of sex even though a female barrier against the coercion can evolve. First, the model based on adaptive-dynamics theory demonstrates that the resultant antagonistic coevolution between male coercion and a female barrier fundamentally ends in either the prevalence of sex or the co-occurrence of two reproductive modes. This is because the coevolution between the two traits additionally involves sex-ratio selection, that is, an increase in parthenogenetic reproduction leads to a female-biased population sex ratio, which will enhance reproductive success of more coercive males and directly promotes the evolution of the coercion among males. Therefore, as shown by the individual-based model, the establishment of obligate parthenogenesis in the population requires the simultaneous evolution of strong reproductive isolation between males and parthenogens. These findings should shed light on the interspecific diversity of reproductive modes as well as help to explain the prevalence of sexual reproduction. PMID:23469150

Transformation of a metaphor: semantic shift in a Cantonese term 'Chi Sin' denoting insanity.

PubMed

Ng, J Y W; Chen, E Y H

2015-03-01

The historical evolution of the existing terms used to describe insanity may be able to shed light on the formation of stigma towards psychosis patients. In Hong Kong, a widely used Cantonese term for insanity 'Chi Sin' provides a unique example because of its neutral original sense, as it literally means misconnection in a network circuit. We attempt to trace the origin and subsequent evolution of the term 'Chi Sin' from its early use to the present day to understand how local Hong Kong people have attached increasingly negative connotations to this scientific term since the mid-20th century. We sampled as many newspapers and magazines published in Hong Kong from 1939 to June 2014 as possible, and sampled 7 popular local movies from the 1950s and 1960s. We also searched all the newspapers published in Hong Kong, Macau, Taiwan, and Mainland China from January 1998 to June 2014, and searched several other local historical resources. In one early use of 'Chi Sin' in 1939, the term was only used in a technical sense to describe 'short circuiting'. We found that the development of the telephone system, the Strowger system, in Hong Kong is closely related to the evolution of the semantics of the term 'Chi Sin'. The original meaning of short circuitry of the term 'Chi Sin' is no longer used, and it has become a dead metaphor through repeated use with negative emotional connotations. This illustrates some of the factors facilitating the emergence of a metaphor with subsequent semantic drift.

Pre-adaptations and the evolution of pollination by sexual deception: Cope's rule of specialization revisited.

PubMed

Vereecken, Nicolas J; Wilson, Carol A; Hötling, Susann; Schulz, Stefan; Banketov, Sergey A; Mardulyn, Patrick

2012-12-07

Pollination by sexual deception is arguably one of the most unusual liaisons linking plants and insects, and perhaps the most illustrative example of extreme floral specialization in angiosperms. While considerable progress has been made in understanding the floral traits involved in sexual deception, less is known about how this remarkable mimicry system might have arisen, the role of pre-adaptations in promoting its evolution and its extent as a pollination mechanism outside the few groups of plants (primarily orchids) where it has been described to date. In the Euro-Mediterranean region, pollination by sexual deception is traditionally considered to be the hallmark of the orchid genus Ophrys. Here, we introduce two new cases outside of Ophrys, in plant groups dominated by generalized, shelter-mimicking species. On the basis of phylogenetic reconstructions of ancestral pollination strategies, we provide evidence for independent and bidirectional evolutionary transitions between generalized (shelter mimicry) and specialized (sexual deception) pollination strategies in three groups of flowering plants, and suggest that pseudocopulation has evolved from pre-adaptations (floral colours, shapes and odour bouquets) that selectively attract male pollinators through shelter mimicry. These findings, along with comparative analyses of floral traits (colours and scents), shed light on particular phenotypic changes that might have fuelled the parallel evolution of these extraordinary pollination strategies. Collectively, our results provide the first substantive insights into how pollination sexual deception might have evolved in the Euro-Mediterranean region, and demonstrate that even the most extreme cases of pollinator specialization can reverse to more generalized interactions, breaking 'Cope's rule of specialization'.

How comparative psychology can shed light on human evolution: Response to Beran et al.'s discussion of "Cognitive capacities for cooking in chimpanzees".

PubMed

Rosati, Alexandra G; Warneken, Felix

2016-06-01

We recently reported a study (Warneken & Rosati Proceedings of the Royal Society B, 282, 20150229, 2015) examining whether chimpanzees possess several cognitive capacities that are critical to engage in cooking. In a subsequent commentary, Beran, Hopper, de Waal, Sayers, and Brosnan Learning & Behavior (2015) asserted that our paper has several flaws. Their commentary (1) critiques some aspects of our methodology and argues that our work does not constitute evidence that chimpanzees can actually cook; (2) claims that these results are old news, as previous work had already demonstrated that chimpanzees possess most or all of these capacities; and, finally, (3) argues that comparative psychological studies of chimpanzees cannot adequately address questions about human evolution, anyway. However, their critique of the premise of our study simply reiterates several points we made in the original paper. To quote ourselves: "As chimpanzees neither control fire nor cook food in their natural behavior, these experiments therefore focus not on whether chimpanzees can actually cook food, but rather whether they can apply their cognitive skills to novel problems that emulate cooking" (Warneken & Rosati Proceedings of the Royal Society B, 282, 20150229, 2015, p. 2). Furthermore, the methodological issues they raise are standard points about psychological research with animals-many of which were addressed synthetically across our 9 experiments, or else are orthogonal to our claims. Finally, we argue that comparative studies of extant apes (and other nonhuman species) are a powerful and indispensable method for understanding human cognitive evolution.

The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology

PubMed Central

2011-01-01

Background The major human intestinal pathogen Giardia lamblia is a very early branching eukaryote with a minimal genome of broad evolutionary and biological interest. Results To explore early kinase evolution and regulation of Giardia biology, we cataloged the kinomes of three sequenced strains. Comparison with published kinomes and those of the excavates Trichomonas vaginalis and Leishmania major shows that Giardia's 80 core kinases constitute the smallest known core kinome of any eukaryote that can be grown in pure culture, reflecting both its early origin and secondary gene loss. Kinase losses in DNA repair, mitochondrial function, transcription, splicing, and stress response reflect this reduced genome, while the presence of other kinases helps define the kinome of the last common eukaryotic ancestor. Immunofluorescence analysis shows abundant phospho-staining in trophozoites, with phosphotyrosine abundant in the nuclei and phosphothreonine and phosphoserine in distinct cytoskeletal organelles. The Nek kinase family has been massively expanded, accounting for 198 of the 278 protein kinases in Giardia. Most Neks are catalytically inactive, have very divergent sequences and undergo extensive duplication and loss between strains. Many Neks are highly induced during development. We localized four catalytically active Neks to distinct parts of the cytoskeleton and one inactive Nek to the cytoplasm. Conclusions The reduced kinome of Giardia sheds new light on early kinase evolution, and its highly divergent sequences add to the definition of individual kinase families as well as offering specific drug targets. Giardia's massive Nek expansion may reflect its distinctive lifestyle, biphasic life cycle and complex cytoskeleton. PMID:21787419

The critical role of fossils in inferring deep-node phylogenetic relationships and macroevolutionary patterns in Cornales.

PubMed

Atkinson, Brian A

2018-05-24

The basal asterid order, Cornales, experienced a rapid radiation during the Cretaceous, which has made it difficult to elucidate the early evolution of the order using extant taxa only. Recent paleobotanical studies, however, have begun to shed light on the early diversification of Cornales. Herein, fossils are directly incorporated in phylogenetic and quantitative morphological analyses to reconstruct early cornalean evolution. A morphological matrix of 77 fruit characters and 58 taxa (24 extinct) was assembled. Parsimony analyses including and excluding fossils were conducted. A fossil inclusive tree was time-scaled to visualize the timing of the initial cornalean radiation. Disparity analyses were utilized to infer the morphological evolution of cornaleans with drupaceous fruits. Fossil inclusive and exclusive parsimony analyses resulted in well-resolved deep-node relationships within Cornales. Resolution in the fossil inclusive analysis is substantially higher, revealing a basal grade including Loasaceae, Hydrangeaceae, Hydrostachyaceae, Grubbiaceae, a Hironoia+Amersinia clade, and Curtisiaceae, respectively, that leads to a "core" group containing a clade comprising a Cretaceous grade leading to clade of Nyssaceae, Mastixiaceae, and Davidiaceae that is sister to a Cornaceae+Alangiaceae clade. The time-scaled tree indicates that the initial cornalean diversification occurred before 89.8 Ma. Disparity analyses suggest the morphological diversity of Cornales peaked during the Paleogene. Phylogenetic analyses clearly demonstrate that novel character mosaics of Cretaceous cornaleans play a critical role in resolving deep-node relationships within Cornales. The post-Cretaceous increase of cornalean disparity is associated with a shift in morphospace occupation, which can be explained from ecological and developmental perspectives. © 2018 Botanical Society of America.

Centromere Binding and Evolution of Chromosomal Partition Systems in the Burkholderiales

PubMed Central

Passot, Fanny M.; Calderon, Virginie; Fichant, Gwennaele; Lane, David

2012-01-01

How split genomes arise and evolve in bacteria is poorly understood. Since each replicon of such genomes encodes a specific partition (Par) system, the evolution of Par systems could shed light on their evolution. The cystic fibrosis pathogen Burkholderia cenocepacia has three chromosomes (c1, c2, and c3) and one plasmid (pBC), whose compatibility depends on strictly specific interactions of the centromere sequences (parS) with their cognate binding proteins (ParB). However, the Par systems of B. cenocepacia c2, c3, and pBC share many features, suggesting that they arose within an extended family. Database searching revealed seven subfamilies of Par systems like those of B. cenocepacia. All are from plasmids and secondary chromosomes of the Burkholderiales, which reinforces the proposal of an extended family. The subfamily of the Par system of B. cenocepacia c3 includes plasmid variants with parS sequences divergent from that of c3. Using electrophoretic mobility shift assay (EMSA), we found that ParB-c3 binds specifically to centromeres of these variants, despite high DNA sequence divergence. We suggest that the Par system of B. cenocepacia c3 has preserved the features of an ancestral system. In contrast, these features have diverged variably in the plasmid descendants. One such descendant is found both in Ralstonia pickettii 12D, on a free plasmid, and in Ralstonia pickettii 12J, on a plasmid integrated into the main chromosome. These observations suggest that we are witnessing a plasmid-chromosome interaction from which a third chromosome will emerge in a two-chromosome species. PMID:22522899

Centromere binding and evolution of chromosomal partition systems in the Burkholderiales.

PubMed

Passot, Fanny M; Calderon, Virginie; Fichant, Gwennaele; Lane, David; Pasta, Franck

2012-07-01

How split genomes arise and evolve in bacteria is poorly understood. Since each replicon of such genomes encodes a specific partition (Par) system, the evolution of Par systems could shed light on their evolution. The cystic fibrosis pathogen Burkholderia cenocepacia has three chromosomes (c1, c2, and c3) and one plasmid (pBC), whose compatibility depends on strictly specific interactions of the centromere sequences (parS) with their cognate binding proteins (ParB). However, the Par systems of B. cenocepacia c2, c3, and pBC share many features, suggesting that they arose within an extended family. Database searching revealed seven subfamilies of Par systems like those of B. cenocepacia. All are from plasmids and secondary chromosomes of the Burkholderiales, which reinforces the proposal of an extended family. The subfamily of the Par system of B. cenocepacia c3 includes plasmid variants with parS sequences divergent from that of c3. Using electrophoretic mobility shift assay (EMSA), we found that ParB-c3 binds specifically to centromeres of these variants, despite high DNA sequence divergence. We suggest that the Par system of B. cenocepacia c3 has preserved the features of an ancestral system. In contrast, these features have diverged variably in the plasmid descendants. One such descendant is found both in Ralstonia pickettii 12D, on a free plasmid, and in Ralstonia pickettii 12J, on a plasmid integrated into the main chromosome. These observations suggest that we are witnessing a plasmid-chromosome interaction from which a third chromosome will emerge in a two-chromosome species.

Evolution of Cooperation in Continuous Prisoner's Dilemma Games on Barabasi—Albert Networks with Degree-Dependent Guilt Mechanism

NASA Astrophysics Data System (ADS)

Wang, Xian-Jia; Quan, Ji; Liu, Wei-Bing

2012-05-01

This paper studies the continuous prisoner's dilemma games (CPDG) on Barabasi—Albert (BA) networks. In the model, each agent on a vertex of the networks makes an investment and interacts with all of his neighboring agents. Making an investment is costly, but which benefits its neighboring agents, where benefit and cost depend on the level of investment made. The payoff of each agent is given by the sum of payoffs it receives in its interactions with all its neighbors. Not only payoff, individual's guilty emotion in the games has also been considered. The negative guilty emotion produced in comparing with its neighbors can reduce the utility of individuals directly. We assume that the reduction amount depends on the individual's degree and a baseline level parameter. The group's cooperative level is characterized by the average investment of the population. Each player makes his investment in the next step based on a convex combination of the investment of his best neighbors in the last step, his best history strategies in the latest steps which number is controlled by a memory length parameter, and a uniformly distributed random number. Simulation results show that this degree-dependent guilt mechanism can promote the evolution of cooperation dramatically comparing with degree-independent guilt or no guilt cases. Imitation, memory, uncertainty coefficients and network structure also play determinant roles in the cooperation level of the population. All our results may shed some new light on studying the evolution of cooperation based on network reciprocity mechanisms.

Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans.

PubMed

Chintalapati, Manjusha; Dannemann, Michael; Prüfer, Kay

2017-08-04

Small insertions and deletions occur in humans at a lower rate compared to nucleotide changes, but evolve under more constraint than nucleotide changes. While the evolution of insertions and deletions have been investigated using ape outgroups, the now available genome of a Neandertal can shed light on the evolution of indels in more recent times. We used the Neandertal genome together with several primate outgroup genomes to differentiate between human insertion/deletion changes that likely occurred before the split from Neandertals and those that likely arose later. Changes that pre-date the split from Neandertals show a smaller proportion of deletions than those that occurred later. The presence of a Neandertal-shared allele in Europeans or Asians but the absence in Africans was used to detect putatively introgressed indels in Europeans and Asians. A larger proportion of these variants reside in intergenic regions compared to other modern human variants, and some variants are linked to SNPs that have been associated with traits in modern humans. Our results are in agreement with earlier results that suggested that deletions evolve under more constraint than insertions. When considering Neandertal introgressed variants, we find some evidence that negative selection affected these variants more than other variants segregating in modern humans. Among introgressed variants we also identify indels that may influence the phenotype of their carriers. In particular an introgressed deletion associated with a decrease in the time to menarche may constitute an example of a former Neandertal-specific trait contributing to modern human phenotypic diversity.

Pre-adaptations and the evolution of pollination by sexual deception: Cope's rule of specialization revisited

PubMed Central

Vereecken, Nicolas J.; Wilson, Carol A.; Hötling, Susann; Schulz, Stefan; Banketov, Sergey A.; Mardulyn, Patrick

2012-01-01

Pollination by sexual deception is arguably one of the most unusual liaisons linking plants and insects, and perhaps the most illustrative example of extreme floral specialization in angiosperms. While considerable progress has been made in understanding the floral traits involved in sexual deception, less is known about how this remarkable mimicry system might have arisen, the role of pre-adaptations in promoting its evolution and its extent as a pollination mechanism outside the few groups of plants (primarily orchids) where it has been described to date. In the Euro-Mediterranean region, pollination by sexual deception is traditionally considered to be the hallmark of the orchid genus Ophrys. Here, we introduce two new cases outside of Ophrys, in plant groups dominated by generalized, shelter-mimicking species. On the basis of phylogenetic reconstructions of ancestral pollination strategies, we provide evidence for independent and bidirectional evolutionary transitions between generalized (shelter mimicry) and specialized (sexual deception) pollination strategies in three groups of flowering plants, and suggest that pseudocopulation has evolved from pre-adaptations (floral colours, shapes and odour bouquets) that selectively attract male pollinators through shelter mimicry. These findings, along with comparative analyses of floral traits (colours and scents), shed light on particular phenotypic changes that might have fuelled the parallel evolution of these extraordinary pollination strategies. Collectively, our results provide the first substantive insights into how pollination sexual deception might have evolved in the Euro-Mediterranean region, and demonstrate that even the most extreme cases of pollinator specialization can reverse to more generalized interactions, breaking ‘Cope's rule of specialization’. PMID:23055065

Axial-Current Matrix Elements in Light Nuclei from Lattice QCD

NASA Astrophysics Data System (ADS)

Savage, M.; Beane, S.; Chang, E.; Davoudi, Z.; Detmold, W.; Orginos, K.; Shanahan, P.; Tiburzi, B.; Wagman, M.; Winter, F.; Nplqcd Collaboration

I present results from the first lattice QCD calculations of axial-current matrix elements in light nuclei, performed by the NPLQCD collaboration. Precision calculations of these matrix elements, and the subsequent extraction of multi-nucleon axial-current operators, are essential in refining theoretical predictions of the proton-proton fusion cross section, neutrino-nucleus cross sections and $\\beta\\beta$-decay rates of nuclei. In addition, they are expected to shed light on the phenomenological quenching of $g_A$ that is required in nuclear many-body calculations.

Modeling of low-finesse, extrinsic fiber optic Fabry-Perot white light interferometers

NASA Astrophysics Data System (ADS)

Ma, Cheng; Tian, Zhipeng; Wang, Anbo

2012-06-01

This article introduces an approach for modeling the fiber optic low-finesse extrinsic Fabry-Pérot Interferometers (EFPI), aiming to address signal processing problems in EFPI demodulation algorithms based on white light interferometry. The main goal is to seek physical interpretations to correlate the sensor spectrum with the interferometer geometry (most importantly, the optical path difference). Because the signal demodulation quality and reliability hinge heavily on the understanding of such relationships, the model sheds light on optimizing the sensor performance.

History of Hubble Space Telescope (HST)

NASA Image and Video Library

1969-01-01

This image of the Egg Nebula, also known as CRL-2688 and located roughly 3,000 light-years from us, was taken in red light with the Wide Field Planetary Camera 2 (WF/PC2) aboard the Hubble Space Telescope (HST). The image shows a pair of mysterious searchlight beams emerging from a hidden star, crisscrossed by numerous bright arcs. This image sheds new light on the poorly understood ejection of stellar matter that accompanies the slow death of Sun-like stars. The image is shown in false color.

23. RW Meyer Sugar Mill: 18761889. Boiling House Interior, 1878. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

23. RW Meyer Sugar Mill: 1876-1889. Boiling House Interior, 1878. View: North Wall of boiling house. In the original structure the three windows on the right admitted light and air from the outside. A shed occupied the left side of the wall outside (hence no windows). in 1881 the construction of the cooling shed closed in the right three windows. The sorghum is in the foreground. The centrifugals are in the left rear. - R. W. Meyer Sugar Mill, State Route 47, Kualapuu, Maui County, HI

WHAT'S the Matter at Rhic?

NASA Astrophysics Data System (ADS)

de Cassagnac, Raphael Granier

I present here a concise review of the experimental results obtained at the Relativistic Heavy Ion Collider (RHIC), which shed light on the hot and dense quark gluon matter produced at these high temperature and density conditions.

Clinical Trials Shed Light on Minority Health

MedlinePlus

... determine whether FDA approves a manufacturer’s application for marketing approval. "Potential racial, ethnic and other differences in ... patient advocates and the scientific community to discuss strategies for increasing the participation of women and minorities ...

Study Sheds New Light on Postmenopausal Breast Cancer Risk | Poster

Cancer.gov

A collaborative study conducted at the Frederick National Lab and published in Cancer Research has provided new insight as to why elevated estrogen levels are associated with an increased risk of breast cancer.

Microfabrics in Siliceous Hotsprings: Yellowstone National Park, Wyoming

NASA Technical Reports Server (NTRS)

Guidry, S. A.; Chafetz, H. S.; Westall, F.

2001-01-01

Microfabrics shed light on the mechanisms governing siliceous sinter precipitation, the profound effects of microorganisms, as well as a conventional facies model for siliceous hotsprings. Additional information is contained in the original extended abstract.

Poverty-Exploitation-Alienation.

ERIC Educational Resources Information Center

Bronfenbrenner, Martin

1980-01-01

Illustrates how knowledge derived from the discipline of economics can be used to help shed light on social problems such as poverty, exploitation, and alienation, and can help decision makers form policy to minimize these and similar problems. (DB)

Using High-Powered Laser, Scientists Record Images of Chemical Interactions in RNA | Poster

Cancer.gov

A recent study at the Department of Energy’s Stanford Linear Accelerator Center National Accelerator Laboratory has literally shed new light on the structural interactions between RNA and another biomolecule.

Maths meets myths

NASA Astrophysics Data System (ADS)

Kenna, Ralph; Mac Carron, Pádraig

2016-06-01

Scholars have long debated whether the Sagas of Icelanders - ancient narratives set in the Viking Age - are fact or fiction. Ralph Kenna and Pádraig Mac Carron analysed the structures of the saga societies to shed light on this question.

1. General view looking northeast showing (from left to right) ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

1. General view looking northeast showing (from left to right) storage shed, keepers' dwelling, and tower with attached oil house. - Bodie Island Light Station, Off Highway 12, Nags Head, Dare County, NC

The distribution of actin immunoreactivity in rhabdomeres of tipulid flies in relation to extracellular membrane shedding.

PubMed

Blest, A D; Stowe, S; Clausen, J A; Carter, M

1991-09-01

Rhabdomeres of tipulid flies lose membrane during turnover from a 'shedding zone' composed of microvillar tips. These distal domains lack intramicrovillar cytoskeletons and appear to be empty sacs of membrane. Recent concerns about the role of ninaC mechano-enzymes in the architecture of dipteran rhabdomeral microvilli and the dynamic role that they may play in the creation of shedding zones demand an examination of the distribution of actin in tipulid rhabdomeres. We compared rhabdomeres from tipulid retinae incubated before fixation for immunocytochemistry in a buffer without additives and a stabilising buffer that contained a cocktail of cysteine protease inhibitors; both were challenged by an anti-actin antibody for immunogold labelling after embedding in LR White Resin. Shedding zones thus processed collapse to structureless detritus. Stabilised and unstabilized shedding zones were immunonegative to anti-actin. To ensure that the negative results were not consequent upon conformational changes generated by the processing protocol, we examined microvilli of degenerating rhabdomeres of the Drosophila light-dependent retinal degeneration mutant rdgBKS222 (which separate and collapse without creating a shedding zone) and found the detritus they generate to be immunopositive to anti-actin. Stabilised and unstabilized regions of basal regions of tipulid rhabdomeres were equally immunopositive. We infer that (a) actin is absent from shedding zones; (b) actin is not degraded by microvillar cysteine proteases. The implications of these conclusions are discussed in relation to some functional models of arthropod photoreceptor microvilli.

Formation and behavior of counter-rotating vortex rings

NASA Astrophysics Data System (ADS)

Sadri, V.; Krueger, P. S.

2017-08-01

Concentric, counter-rotating vortex ring formation by transient jet ejection between concentric cylinders was studied numerically to determine the effects of cylinder gap ratio, Δ R/R, and jet stroke length-to-gap ratio, L/Δ R, on the evolution of the vorticity and the trajectories of the resulting axisymmetric vortex pair. The flow was simulated at a jet Reynolds number of 1000 (based on Δ R and the jet velocity), L/Δ R in the range 1-20, and Δ R/R in the range 0.05-0.25. Five characteristic flow evolution patterns were observed and classified based on L/Δ R and Δ R/R. The results showed that the relative position, relative strength, and radii of the vortex rings during and soon after formation played a prominent role in the evolution of the trajectories of their vorticity centroids at the later time. The conditions on relative strength of the vortices necessary for them to travel together as a pair following formation were studied, and factors affecting differences in vortex circulation following formation were investigated. In addition to the characteristics of the primary vortices, the stopping vortices had a strong influence on the initial vortex configuration and effected the long-time flow evolution at low L/Δ R and small Δ R/R. For long L/Δ R and small Δ R/R, shedding of vorticity was sometimes observed and this shedding was related to the Kelvin-Benjamin variational principle of maximal energy for steadily translating vortex rings.

Cooperation and charity in spatial public goods game under different strategy update rules

NASA Astrophysics Data System (ADS)

Li, Yixiao; Jin, Xiaogang; Su, Xianchuang; Kong, Fansheng; Peng, Chengbin

2010-03-01

Human cooperation can be influenced by other human behaviors and recent years have witnessed the flourishing of studying the coevolution of cooperation and punishment, yet the common behavior of charity is seldom considered in game-theoretical models. In this article, we investigate the coevolution of altruistic cooperation and egalitarian charity in spatial public goods game, by considering charity as the behavior of reducing inter-individual payoff differences. Our model is that, in each generation of the evolution, individuals play games first and accumulate payoff benefits, and then each egalitarian makes a charity donation by payoff transfer in its neighborhood. To study the individual-level evolutionary dynamics, we adopt different strategy update rules and investigate their effects on charity and cooperation. These rules can be classified into two global rules: random selection rule in which individuals randomly update strategies, and threshold selection rule where only those with payoffs below a threshold update strategies. Simulation results show that random selection enhances the cooperation level, while threshold selection lowers the threshold of the multiplication factor to maintain cooperation. When charity is considered, it is incapable in promoting cooperation under random selection, whereas it promotes cooperation under threshold selection. Interestingly, the evolution of charity strongly depends on the dispersion of payoff acquisitions of the population, which agrees with previous results. Our work may shed light on understanding human egalitarianism.

Host behaviour–parasite feedback: an essential link between animal behaviour and disease ecology

PubMed Central

Archie, Elizabeth A.; Craft, Meggan E.; Hawley, Dana M.; Martin, Lynn B.; Moore, Janice; White, Lauren

2016-01-01

Animal behaviour and the ecology and evolution of parasites are inextricably linked. For this reason, animal behaviourists and disease ecologists have been interested in the intersection of their respective fields for decades. Despite this interest, most research at the behaviour–disease interface focuses either on how host behaviour affects parasites or how parasites affect behaviour, with little overlap between the two. Yet, the majority of interactions between hosts and parasites are probably reciprocal, such that host behaviour feeds back on parasites and vice versa. Explicitly considering these feedbacks is essential for understanding the complex connections between animal behaviour and parasite ecology and evolution. To illustrate this point, we discuss how host behaviour–parasite feedbacks might operate and explore the consequences of feedback for studies of animal behaviour and parasites. For example, ignoring the feedback of host social structure on parasite dynamics can limit the accuracy of predictions about parasite spread. Likewise, considering feedback in studies of parasites and animal personalities may provide unique insight about the maintenance of variation in personality types. Finally, applying the feedback concept to links between host behaviour and beneficial, rather than pathogenic, microbes may shed new light on transitions between mutualism and parasitism. More generally, accounting for host behaviour–parasite feedbacks can help identify critical gaps in our understanding of how key host behaviours and parasite traits evolve and are maintained. PMID:27053751

Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question

PubMed Central

Koonin, Eugene V.; Starokadomskyy, Petro

2016-01-01

The question whether or not “viruses are alive” has caused considerable debate over many years. Yet, the question is effectively without substance because the answer depends entirely on the definition of life or the state of “being alive” that is bound to be arbitrary. In contrast, the status of viruses among biological entities is readily defined within the replicator paradigm. All biological replicators form a continuum along the selfishness-cooperativity axis, from the completely selfish to fully cooperative forms. Within this range, typical, lytic viruses represent the selfish extreme whereas temperate viruses and various mobile elements occupy positions closer to the middle of the range. Selfish replicators not only belong to the biological realm but are intrinsic to any evolving system of replicators. No such system can evolve without the emergence of parasites, and moreover, parasites drive the evolution of biological complexity at multiple levels. The history of life is a story of parasite-host coevolution that includes both the incessant arms race and various forms of cooperation. All organisms are communities of interacting, coevolving replicators of different classes. A complete theory of replicator coevolution remains to be developed, but it appears likely that not only the differentiation between selfish and cooperative replicators but the emergence of the entire range of replication strategies, from selfish to cooperative, is intrinsic to biological evolution. PMID:26965225

Molecular mechanisms underlying the exceptional adaptations of batoid fins.

PubMed

Nakamura, Tetsuya; Klomp, Jeff; Pieretti, Joyce; Schneider, Igor; Gehrke, Andrew R; Shubin, Neil H

2015-12-29

Extreme novelties in the shape and size of paired fins are exemplified by extinct and extant cartilaginous and bony fishes. Pectoral fins of skates and rays, such as the little skate (Batoid, Leucoraja erinacea), show a strikingly unique morphology where the pectoral fin extends anteriorly to ultimately fuse with the head. This results in a morphology that essentially surrounds the body and is associated with the evolution of novel swimming mechanisms in the group. In an approach that extends from RNA sequencing to in situ hybridization to functional assays, we show that anterior and posterior portions of the pectoral fin have different genetic underpinnings: canonical genes of appendage development control posterior fin development via an apical ectodermal ridge (AER), whereas an alternative Homeobox (Hox)-Fibroblast growth factor (Fgf)-Wingless type MMTV integration site family (Wnt) genetic module in the anterior region creates an AER-like structure that drives anterior fin expansion. Finally, we show that GLI family zinc finger 3 (Gli3), which is an anterior repressor of tetrapod digits, is expressed in the posterior half of the pectoral fin of skate, shark, and zebrafish but in the anterior side of the pelvic fin. Taken together, these data point to both highly derived and deeply ancestral patterns of gene expression in skate pectoral fins, shedding light on the molecular mechanisms behind the evolution of novel fin morphologies.

Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals

PubMed Central

Hecker, Nikolai; Sharma, Virag

2017-01-01

Abstract Kallikrein related peptidase 8 (KLK8; also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we examined the evolution of KLK8 in mammals and discovered that, out of 70 placental mammals, KLK8 is exclusively lost in three independent fully-aquatic lineages, comprising dolphin, killer whale, minke whale, and manatee. In addition, while the sperm whale has an intact KLK8 reading frame, the gene evolves neutrally in this species. We suggest that the distinct functions of KLK8 likely became obsolete in the aquatic environment, leading to the subsequent loss of KLK8 in several fully-aquatic mammalian lineages. First, the cetacean and manatee skin lacks sweat glands as an adaptation to the aquatic environment, which likely made the epidermal function of KLK8 obsolete. Second, cetaceans and manatees exhibit a proportionally small hippocampus, which may have rendered the hippocampal functions of KLK8 obsolete. Together, our results shed light on the genomic changes that correlate with skin and neuroanatomical differences of aquatic mammals, and show that even pleiotropic genes can be lost during evolution if an environmental change nullifies the need for the different functions of such genes. PMID:29145610

Evolution and mechanisms of plant tolerance to flooding stress

PubMed Central

Jackson, Michael B.; Ishizawa, Kimiharu; Ito, Osamu

2009-01-01

Background In recognition of the 200th anniversary of Charles Darwin's birth, this short article on flooding stress acknowledges not only Darwin's great contribution to the concept of evolution but also to the study of plant physiology. In modern biology, Darwin-inspired reductionist physiology continues to shed light on mechanisms that confer competitive advantage in many varied and challenging environments, including those where flooding is prevalent. Scope Mild flooding is experienced by most land plants but as its severity increases, fewer species are able to grow and survive. At the extreme, a highly exclusive aquatic lifestyle appears to have evolved numerous times over the past 120 million years. Although only 1–2% of angiosperms are aquatics, some of their adaptive characteristics are also seen in those adopting an amphibious lifestyle where flooding is less frequent. Lowland rice, the staple cereal for much of tropical Asia falls into this category. But, even amongst dry-land dwellers, or certain of their sub-populations, modest tolerance to occasional flooding is to be found, for example in wheat. The collection of papers summarized in this article describes advances to the understanding of mechanisms that explain flooding tolerance in aquatic, amphibious and dry-land plants. Work to develop more tolerant crops or manage flood-prone environments more effectively is also included. The experimental approaches range from molecular analyses, through biochemistry and metabolomics to whole-plant physiology, plant breeding and ecology. PMID:19145714

Boundary Conditions for the Paleoenvironment: Chemical and Physical Processes in Dense Interstellar Clouds: Summary of Research

NASA Technical Reports Server (NTRS)

Irvine, William M.

1999-01-01

The basic theme of this program was the study of molecular complexity and evolution for the biogenic elements and compounds in interstellar clouds and in primitive solar system objects. Research included the detection and study of new interstellar and cometary molecules and investigation of reaction pathways for astrochemistry from a comparison of theory and observed molecular abundances. The latter includes studies of cold, dark clouds in which ion-molecule chemistry should predominate, searches for the effects of interchange of material between the gas and solid phases in interstellar clouds, unbiased spectral surveys of particular sources, and systematic investigation of the interlinked chemistry and physics of dense interstellar clouds. In addition, the study of comets has allowed a comparison between the chemistry of such minimally thermally processed objects and that of interstellar clouds, shedding light on the evolution of the biogenic elements during the process of solar system formation. One PhD dissertation on this research was completed by a graduate student at the University of Massachusetts. An additional 4 graduate students at the University of Massachusetts and 5 graduate students from other institutions participated in research supported by this grant, with 6 of these thus far receiving PhD degrees from the University of Massachusetts or their home institutions. Four postdoctoral research associates at the University of Massachusetts also participated in research supported by this grant, receiving valuable training.

Novel features of ARS selection in budding yeast Lachancea kluyveri

PubMed Central

2011-01-01

Background The characterization of DNA replication origins in yeast has shed much light on the mechanisms of initiation of DNA replication. However, very little is known about the evolution of origins or the evolution of mechanisms through which origins are recognized by the initiation machinery. This lack of understanding is largely due to the vast evolutionary distances between model organisms in which origins have been examined. Results In this study we have isolated and characterized autonomously replicating sequences (ARSs) in Lachancea kluyveri - a pre-whole genome duplication (WGD) budding yeast. Through a combination of experimental work and rigorous computational analysis, we show that L. kluyveri ARSs require a sequence that is similar but much longer than the ARS Consensus Sequence well defined in Saccharomyces cerevisiae. Moreover, compared with S. cerevisiae and K. lactis, the replication licensing machinery in L. kluyveri seems more tolerant to variations in the ARS sequence composition. It is able to initiate replication from almost all S. cerevisiae ARSs tested and most Kluyveromyces lactis ARSs. In contrast, only about half of the L. kluyveri ARSs function in S. cerevisiae and less than 10% function in K. lactis. Conclusions Our findings demonstrate a replication initiation system with novel features and underscore the functional diversity within the budding yeasts. Furthermore, we have developed new approaches for analyzing biologically functional DNA sequences with ill-defined motifs. PMID:22204614

Novel features of ARS selection in budding yeast Lachancea kluyveri.

PubMed

Liachko, Ivan; Tanaka, Emi; Cox, Katherine; Chung, Shau Chee Claire; Yang, Lu; Seher, Arael; Hallas, Lindsay; Cha, Eugene; Kang, Gina; Pace, Heather; Barrow, Jasmine; Inada, Maki; Tye, Bik-Kwoon; Keich, Uri

2011-12-28

The characterization of DNA replication origins in yeast has shed much light on the mechanisms of initiation of DNA replication. However, very little is known about the evolution of origins or the evolution of mechanisms through which origins are recognized by the initiation machinery. This lack of understanding is largely due to the vast evolutionary distances between model organisms in which origins have been examined. In this study we have isolated and characterized autonomously replicating sequences (ARSs) in Lachancea kluyveri - a pre-whole genome duplication (WGD) budding yeast. Through a combination of experimental work and rigorous computational analysis, we show that L. kluyveri ARSs require a sequence that is similar but much longer than the ARS Consensus Sequence well defined in Saccharomyces cerevisiae. Moreover, compared with S. cerevisiae and K. lactis, the replication licensing machinery in L. kluyveri seems more tolerant to variations in the ARS sequence composition. It is able to initiate replication from almost all S. cerevisiae ARSs tested and most Kluyveromyces lactis ARSs. In contrast, only about half of the L. kluyveri ARSs function in S. cerevisiae and less than 10% function in K. lactis. Our findings demonstrate a replication initiation system with novel features and underscore the functional diversity within the budding yeasts. Furthermore, we have developed new approaches for analyzing biologically functional DNA sequences with ill-defined motifs.

Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security.

PubMed

McDonald, Bruce A; Stukenbrock, Eva H

2016-12-05

Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems. These studies document the speed with which pathogens evolve to overcome crop resistance genes and pesticides. They also show that crop pathogens can be disseminated very quickly across and among continents through human activities. In this review, we discuss how the peculiar architecture of agro-ecosystems facilitates pathogen emergence, evolution and dispersal. We present four example pathosystems that illustrate both pathogen specialization and pathogen speciation, including different time frames for emergence and different mechanisms underlying the emergence process. Lastly, we argue for a re-design of agro-ecosystems that embraces the concept of dynamic diversity to improve their resilience to pathogens. This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'. © 2016 The Author(s).

Host behaviour-parasite feedback: an essential link between animal behaviour and disease ecology.

PubMed

Ezenwa, Vanessa O; Archie, Elizabeth A; Craft, Meggan E; Hawley, Dana M; Martin, Lynn B; Moore, Janice; White, Lauren

2016-04-13

Animal behaviour and the ecology and evolution of parasites are inextricably linked. For this reason, animal behaviourists and disease ecologists have been interested in the intersection of their respective fields for decades. Despite this interest, most research at the behaviour-disease interface focuses either on how host behaviour affects parasites or how parasites affect behaviour, with little overlap between the two. Yet, the majority of interactions between hosts and parasites are probably reciprocal, such that host behaviour feeds back on parasites and vice versa. Explicitly considering these feedbacks is essential for understanding the complex connections between animal behaviour and parasite ecology and evolution. To illustrate this point, we discuss how host behaviour-parasite feedbacks might operate and explore the consequences of feedback for studies of animal behaviour and parasites. For example, ignoring the feedback of host social structure on parasite dynamics can limit the accuracy of predictions about parasite spread. Likewise, considering feedback in studies of parasites and animal personalities may provide unique insight about the maintenance of variation in personality types. Finally, applying the feedback concept to links between host behaviour and beneficial, rather than pathogenic, microbes may shed new light on transitions between mutualism and parasitism. More generally, accounting for host behaviour-parasite feedbacks can help identify critical gaps in our understanding of how key host behaviours and parasite traits evolve and are maintained. © 2016 The Author(s).

MassiveNuS: cosmological massive neutrino simulations

NASA Astrophysics Data System (ADS)

Liu, Jia; Bird, Simeon; Zorrilla Matilla, José Manuel; Hill, J. Colin; Haiman, Zoltán; Madhavacheril, Mathew S.; Petri, Andrea; Spergel, David N.

2018-03-01

The non-zero mass of neutrinos suppresses the growth of cosmic structure on small scales. Since the level of suppression depends on the sum of the masses of the three active neutrino species, the evolution of large-scale structure is a promising tool to constrain the total mass of neutrinos and possibly shed light on the mass hierarchy. In this work, we investigate these effects via a large suite of N-body simulations that include massive neutrinos using an analytic linear-response approximation: the Cosmological Massive Neutrino Simulations (MassiveNuS). The simulations include the effects of radiation on the background expansion, as well as the clustering of neutrinos in response to the nonlinear dark matter evolution. We allow three cosmological parameters to vary: the neutrino mass sum Mν in the range of 0–0.6 eV, the total matter density Ωm, and the primordial power spectrum amplitude As. The rms density fluctuation in spheres of 8 comoving Mpc/h (σ8) is a derived parameter as a result. Our data products include N-body snapshots, halo catalogues, merger trees, ray-traced galaxy lensing convergence maps for four source redshift planes between zs=1–2.5, and ray-traced cosmic microwave background lensing convergence maps. We describe the simulation procedures and code validation in this paper. The data are publicly available at http://columbialensing.org.

Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes.

PubMed

Puterova, Janka; Razumova, Olga; Martinek, Tomas; Alexandrov, Oleg; Divashuk, Mikhail; Kubat, Zdenek; Hobza, Roman; Karlov, Gennady; Kejnovsky, Eduard

2017-01-01

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Testing palaeotectonic models for the Internal Hellenides with sediment provenance

NASA Astrophysics Data System (ADS)

Meinhold, G.

2009-04-01

The Internal Hellenides of Greece are a result of the Alpine-Himalayan orogen. The relationships between different pre-Alpine crustal fragments of the Internal Hellenides are now masked by younger (Mesozoic to Cenozoic) complex structural and metamorphic events. This, together with the scarcity of biostratigraphic, geochronological and palaeomagnetic data, has given rise to equivocal palaeotectonic models and interpretations. However, the age and origin of pre-Alpine basement units in the Internal Hellenides has important implications for our in-depth understanding of the evolution of North Gondwana-derived terranes and consequently for alternative palaeotectonic reconstructions for the Palaeozoic and Mesozoic. A multidisciplinary sediment provenance study was undertaken since sedimentary rocks can provide information about rock lithologies in the source area, which have often been destroyed and recycled during ancient plate tectonic processes. Palaeozoic and Mesozoic sedimentary rocks from key areas of the Internal Hellenides were analysed using whole-rock major- and trace-element geochemistry (XRF, ICPMS), detrital chrome spinel, garnet, white mica and rutile chemistry (EMP), detrital zircon geochronology (SHRIMP, LA-ICPMS) and biostratigraphic analysis. These new data are used to constrain terrane accretion processes and the provenance of crustal sources for sediments during Palaeozoic and Mesozoic times and thus will test palaeotectonic models for the Internal Hellenides. This is expected to shed light on the Palaeo- and Neotethyan evolution in the Eastern Mediterranean.

Dispersal Polymorphisms in Invasive Fire Ants.

PubMed

Helms, Jackson A; Godfrey, Aaron

2016-01-01

In the Found or Fly (FoF) hypothesis ant queens experience reproduction-dispersal tradeoffs such that queens with heavier abdomens are better at founding colonies but are worse flyers. We tested predictions of FoF in two globally invasive fire ants, Solenopsis geminata (Fabricius, 1804) and S. invicta (Buren, 1972). Colonies of these species may produce two different monogyne queen types-claustral queens with heavy abdomens that found colonies independently, and parasitic queens with small abdomens that enter conspecific nests. Claustral and parasitic queens were similarly sized, but the abdomens of claustral queens weighed twice as much as those of their parasitic counterparts. Their heavier abdomens adversely impacted morphological predictors of flight ability, resulting in 32-38% lower flight muscle ratios, 55-63% higher wing loading, and 32-33% higher abdomen drag. In lab experiments maximum flight durations in claustral S. invicta queens decreased by about 18 minutes for every milligram of abdomen mass. Combining our results into a simple fitness tradeoff model, we calculated that an average parasitic S. invicta queen could produce only 1/3 as many worker offspring as a claustral queen, but could fly 4 times as long and have a 17- to 36-fold larger potential colonization area. Investigations of dispersal polymorphisms and their associated tradeoffs promises to shed light on range expansions in invasive species, the evolution of alternative reproductive strategies, and the selective forces driving the recurrent evolution of parasitism in ants.

Origin of the Eumetazoa: testing ecological predictions of molecular clocks against the Proterozoic fossil record

NASA Technical Reports Server (NTRS)

Peterson, Kevin J.; Butterfield, Nicholas J.

2005-01-01

Molecular clocks have the potential to shed light on the timing of early metazoan divergences, but differing algorithms and calibration points yield conspicuously discordant results. We argue here that competing molecular clock hypotheses should be testable in the fossil record, on the principle that fundamentally new grades of animal organization will have ecosystem-wide impacts. Using a set of seven nuclear-encoded protein sequences, we demonstrate the paraphyly of Porifera and calculate sponge/eumetazoan and cnidarian/bilaterian divergence times by using both distance [minimum evolution (ME)] and maximum likelihood (ML) molecular clocks; ME brackets the appearance of Eumetazoa between 634 and 604 Ma, whereas ML suggests it was between 867 and 748 Ma. Significantly, the ME, but not the ML, estimate is coincident with a major regime change in the Proterozoic acritarch record, including: (i) disappearance of low-diversity, evolutionarily static, pre-Ediacaran acanthomorphs; (ii) radiation of the high-diversity, short-lived Doushantuo-Pertatataka microbiota; and (iii) an order-of-magnitude increase in evolutionary turnover rate. We interpret this turnover as a consequence of the novel ecological challenges accompanying the evolution of the eumetazoan nervous system and gut. Thus, the more readily preserved microfossil record provides positive evidence for the absence of pre-Ediacaran eumetazoans and strongly supports the veracity, and therefore more general application, of the ME molecular clock.

The Impact of Human Papilloma Viruses, Matrix Metallo-Proteinases and HIV Protease Inhibitors on the Onset and Progression of Uterine Cervix Epithelial Tumors: A Review of Preclinical and Clinical Studies

PubMed Central

Barillari, Giovanni; Monini, Paolo

2018-01-01

Infection of uterine cervix epithelial cells by the Human Papilloma Viruses (HPV) is associated with the development of dysplastic/hyperplastic lesions, termed cervical intraepithelial neoplasia (CIN). CIN lesions may regress, persist or progress to invasive cervical carcinoma (CC), a leading cause of death worldwide. CIN is particularly frequent and aggressive in women infected by both HPV and the Human Immunodeficiency Virus (HIV), as compared to the general female population. In these individuals, however, therapeutic regimens employing HIV protease inhibitors (HIV-PI) have reduced CIN incidence and/or clinical progression, shedding light on the mechanism(s) of its development. This article reviews published work concerning: (i) the role of HPV proteins (including HPV-E5, E6 and E7) and of matrix-metalloproteinases (MMPs) in CIN evolution into invasive CC; and (ii) the effect of HIV-PI on events leading to CIN progression such as basement membrane and extracellular matrix invasion by HPV-positive CIN cells and the formation of new blood vessels. Results from the reviewed literature indicate that CIN clinical progression can be monitored by evaluating the expression of MMPs and HPV proteins and they suggest the use of HIV-PI or their derivatives for the block of CIN evolution into CC in both HIV-infected and uninfected women. PMID:29747434

Deep Photometry of Galaxies in the VEGAS Survey: The Case of NGC 4472

NASA Astrophysics Data System (ADS)

Spavone, M.

The VST-VEGAS project is aimed at observing and studying a rich sample of nearby early-type galaxies in order to systematically characterize their properties over a wide baseline of sizes and out to the faint outskirts where data are rather scarce so far. The external regions of galaxies more easily retain signatures about the formation and evolution mechanisms which shaped them, as their relaxation time are longer, and they are more weakly influenced by processes such as mergers, secular evolution, central black hole activity, and supernova feedback on the ISM, which tend to level age and metallicity gradients. The collection of a wide photometric dataset of a large number of galaxies in various environmental conditions, may help to shed light on these questions. To this end VEGAS exploits the potential of the VLT Survey Telescope (VST) which provides high quality images of 1 deg2 field of view in order to satisfy both the requirement of high resolution data and the need of studying nearby, and thus large, objects. We present a detailed study of the surface photometry of the elliptical galaxy NGC4472 and of smaller ETGs in its field, performed by using new g and i bands images to constrain the formation history of this nearby giant galaxy, and to investigate the presence of very faint substructures in its surroundings.

Genetic Architecture of Natural Variation Underlying Adult Foraging Behavior That Is Essential for Survival of Drosophila melanogaster.

PubMed

Lee, Yuh Chwen G; Yang, Qian; Chi, Wanhao; Turkson, Susie A; Du, Wei A; Kemkemer, Claus; Zeng, Zhao-Bang; Long, Manyuan; Zhuang, Xiaoxi

2017-05-01

Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior. We found that adult foraging behavior has a strong genetic component and, unlike larval foraging behavior, depends on multiple loci. Identified candidate genes are enriched in those with high expression in adult heads and, demonstrated by expression knock down assay, are involved in maintaining normal functions of the nervous system. Our study not only identified candidate genes for foraging behavior that is relevant to individual fitness, but also shed light on the initial stage underlying the evolution of the behavior. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Molecular mechanisms underlying the exceptional adaptations of batoid fins

PubMed Central

Nakamura, Tetsuya; Klomp, Jeff; Pieretti, Joyce; Schneider, Igor; Gehrke, Andrew R.; Shubin, Neil H.

2015-01-01

Extreme novelties in the shape and size of paired fins are exemplified by extinct and extant cartilaginous and bony fishes. Pectoral fins of skates and rays, such as the little skate (Batoid, Leucoraja erinacea), show a strikingly unique morphology where the pectoral fin extends anteriorly to ultimately fuse with the head. This results in a morphology that essentially surrounds the body and is associated with the evolution of novel swimming mechanisms in the group. In an approach that extends from RNA sequencing to in situ hybridization to functional assays, we show that anterior and posterior portions of the pectoral fin have different genetic underpinnings: canonical genes of appendage development control posterior fin development via an apical ectodermal ridge (AER), whereas an alternative Homeobox (Hox)–Fibroblast growth factor (Fgf)–Wingless type MMTV integration site family (Wnt) genetic module in the anterior region creates an AER-like structure that drives anterior fin expansion. Finally, we show that GLI family zinc finger 3 (Gli3), which is an anterior repressor of tetrapod digits, is expressed in the posterior half of the pectoral fin of skate, shark, and zebrafish but in the anterior side of the pelvic fin. Taken together, these data point to both highly derived and deeply ancestral patterns of gene expression in skate pectoral fins, shedding light on the molecular mechanisms behind the evolution of novel fin morphologies. PMID:26644578

Recent coselection in human populations revealed by protein-protein interaction network.

PubMed

Qian, Wei; Zhou, Hang; Tang, Kun

2014-12-21

Genome-wide scans for signals of natural selection in human populations have identified a large number of candidate loci that underlie local adaptations. This is surprising given the relatively short evolutionary time since the divergence of the human population. One hypothesis that has not been formally examined is whether and how the recent human evolution may have been shaped by coselection in the context of complex molecular interactome. In this study, genome-wide signals of selection were scanned in East Asians, Europeans, and Africans using 1000 Genome data, and subsequently mapped onto the protein-protein interaction (PPI) network. We found that the candidate genes of recent positive selection localized significantly closer to each other on the PPI network than expected, revealing substantial clustering of selected genes. Furthermore, gene pairs of shorter PPI network distances showed higher similarities of their recent evolutionary paths than those further apart. Last, subnetworks enriched with recent coselection signals were identified, which are substantially overrepresented in biological pathways related to signal transduction, neurogenesis, and immune function. These results provide the first genome-wide evidence for association of recent selection signals with the PPI network, shedding light on the potential mechanisms of recent coselection in the human genome. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Towards a gene regulatory network perspective on phenotypic plasticity, genetic accommodation and genetic assimilation

PubMed Central

Pfennig, David W.; Ehrenreich, Ian M.

2014-01-01

Many organisms can produce alternative phenotypes in direct response to different environmental conditions, a phenomenon known as phenotypic plasticity. The environmentally sensitive gene regulatory networks (GRNs) that mediate such developmental flexibility are largely unknown. Yet, characterizing these GRNs is important not only for elucidating plasticity’s molecular basis, but also for shedding light onto whether and how plasticity might impact evolution. In this issue of Molecular Ecology, Schneider et al.) describe one of the first efforts to determine the GRN underlying a plastic trait. They focus on diet-induced plasticity in the cichlid fish, Astatoreochromis alluaudi. Depending on whether soft food (e.g. insects) or hard food (e.g. molluscs) is consumed, this species forms a lower pharyngeal jaw (LPJ) with many fine teeth or with fewer molar-like teeth, respectively (Fig. 1). The authors previously identified genes that are differentially expressed between LPJ morphs during early development. In the present study, they examine the expression of 19 of these genes across development and diet. By analysing these transcriptional data in combination with information on putative transcription factor binding sites, they construct a GRN that explains observed gene expression patterns and is likely to control LPJ morphology. This work advances our understanding of how plasticity can arise as a consequence of environmentally sensitive GRNs and promises to help illuminate how changes in such GRNs could facilitate evolution. PMID:25208504

Understanding the large-scale structure from the cosmic microwave background: shear calibration with CMB lensing; gas physics from the kinematic Sunyaev-Zel'dovich effect

NASA Astrophysics Data System (ADS)

Schaan, Emmanuel

2017-01-01

I will present two promising ways in which the cosmic microwave background (CMB) sheds light on critical uncertain physics and systematics of the large-scale structure. Shear calibration with CMB lensing: Realizing the full potential of upcoming weak lensing surveys requires an exquisite understanding of the errors in galaxy shape estimation. In particular, such errors lead to a multiplicative bias in the shear, degenerate with the matter density parameter and the amplitude of fluctuations. Its redshift-evolution can hide the true evolution of the growth of structure, which probes dark energy and possible modifications to general relativity. I will show that CMB lensing from a stage 4 experiment (CMB S4) can self-calibrate the shear for an LSST-like optical lensing survey. This holds in the presence of photo-z errors and intrinsic alignment. Evidence for the kinematic Sunyaev-Zel'dovich (kSZ) effect; cluster energetics: Through the kSZ effect, the baryon momentum field is imprinted on the CMB. I will report significant evidence for the kSZ effect from ACTPol and peculiar velocities reconstructed from BOSS. I will present the prospects for constraining cluster gas profiles and energetics from the kSZ effect with SPT-3G, AdvACT and CMB S4. This will provide constraints on galaxy formation and feedback models.