Conformational Preference of ‘CαNN’ Short Peptide Motif towards Recognition of Anions

PubMed Central

Banerjee, Raja

2013-01-01

Among several ‘anion binding motifs’, the recently described ‘CαNN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘CαNN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘CαNN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘CαNN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘CαNN’ sequence for anion recognition through “local” interaction. PMID:23516403

Leaving the Faith: How Religious Switching Changes Pathways to Adulthood among Conservative Protestant Youth

PubMed Central

Glass, Jennifer L.; Sutton, April; Fitzgerald, Scott T.

2015-01-01

Research revealing associations between conservative Protestantism and lower socioeconomic status is bedeviled by questions of causal inference. Religious switching offers another way to understand the causal ordering of religious participation and demographic markers of class position. In this paper, we look at adolescents who change their religious affiliation across four waves of data from the National Longitudinal Study of Adolescent Health (Add Health) and then observe their transition to adulthood using four crucial markers – completed educational attainment, age at first marriage, age at first birth, and income at the final wave. Results show that switching out of a conservative Protestant denomination in adolescence can alter some, but not all, of the negative consequences associated with growing up in a conservative Protestant household. Specifically, family formation is delayed among switchers, but early cessation of education is not. PMID:26322318

Time and spatial evolution of spin-orbit torque-induced magnetization switching in W/CoFeB/MgO structures with various sizes

NASA Astrophysics Data System (ADS)

Zhang, Chaoliang; Fukami, Shunsuke; DuttaGupta, Samik; Sato, Hideo; Ohno, Hideo

2018-04-01

We study spin-orbit torque (SOT) switching in W/CoFeB/MgO structures with various dot sizes (120-3500 nm) using pulsed current of various widths τ (800 ps-100 ms) to examine the time and spatial evolution of magnetization switching. We show that the switching behavior and the resultant threshold switching current density J th strongly depend on device size and pulse width. The switching mode in a 3500 nm dot device changes from probabilistic switching to reproducible partial switching as τ decreases. At τ = 800 ps, J th becomes more than 3 times larger than that in the long-pulse regime. A decrease in dot size to 700 nm does not significantly change the switching characteristics, suggesting that domain-wall propagation among the nucleated multiple domains governs switching. In contrast, devices with further reduced size (120 nm) show normal full switching with increasing probability with current and insignificant dependence of J th on τ, indicating that nucleation governs switching.

Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability

PubMed Central

Torres-Sosa, Christian; Huang, Sui; Aldana, Maximino

2012-01-01

Accumulating experimental evidence suggests that the gene regulatory networks of living organisms operate in the critical phase, namely, at the transition between ordered and chaotic dynamics. Such critical dynamics of the network permits the coexistence of robustness and flexibility which are necessary to ensure homeostatic stability (of a given phenotype) while allowing for switching between multiple phenotypes (network states) as occurs in development and in response to environmental change. However, the mechanisms through which genetic networks evolve such critical behavior have remained elusive. Here we present an evolutionary model in which criticality naturally emerges from the need to balance between the two essential components of evolvability: phenotype conservation and phenotype innovation under mutations. We simulated the Darwinian evolution of random Boolean networks that mutate gene regulatory interactions and grow by gene duplication. The mutating networks were subjected to selection for networks that both (i) preserve all the already acquired phenotypes (dynamical attractor states) and (ii) generate new ones. Our results show that this interplay between extending the phenotypic landscape (innovation) while conserving the existing phenotypes (conservation) suffices to cause the evolution of all the networks in a population towards criticality. Furthermore, the networks produced by this evolutionary process exhibit structures with hubs (global regulators) similar to the observed topology of real gene regulatory networks. Thus, dynamical criticality and certain elementary topological properties of gene regulatory networks can emerge as a byproduct of the evolvability of the phenotypic landscape. PMID:22969419

Task-switching costs promote the evolution of division of labor and shifts in individuality

PubMed Central

Goldsby, Heather J.; Dornhaus, Anna; Kerr, Benjamin; Ofria, Charles

2012-01-01

From microbes to humans, the success of many organisms is achieved by dividing tasks among specialized group members. The evolution of such division of labor strategies is an important aspect of the major transitions in evolution. As such, identifying specific evolutionary pressures that give rise to group-level division of labor has become a topic of major interest among biologists. To overcome the challenges associated with studying this topic in natural systems, we use actively evolving populations of digital organisms, which provide a unique perspective on the de novo evolution of division of labor in an open-ended system. We provide experimental results that address a fundamental question regarding these selective pressures: Does the ability to improve group efficiency through the reduction of task-switching costs promote the evolution of division of labor? Our results demonstrate that as task-switching costs rise, groups increasingly evolve division of labor strategies. We analyze the mechanisms by which organisms coordinate their roles and discover strategies with striking biological parallels, including communication, spatial patterning, and task-partitioning behaviors. In many cases, under high task-switching costs, individuals cease to be able to perform tasks in isolation, instead requiring the context of other group members. The simultaneous loss of functionality at a lower level and emergence of new functionality at a higher level indicates that task-switching costs may drive both the evolution of division of labor and also the loss of lower-level autonomy, which are both key components of major transitions in evolution. PMID:22872867

Release from prey preservation behavior via prey switch allowed diversification of cuticular hydrocarbon profiles in digger wasps.

PubMed

Wurdack, Mareike; Polidori, Carlo; Keller, Alexander; Feldhaar, Heike; Schmitt, Thomas

2017-11-01

The cuticle of insects is covered by a layer of hydrocarbons (CHC), whose original function is the protection from desiccation and pathogens. However, in most insects CHC profiles are species specific. While this variability among species was largely linked to communication and recognition functions, additional selective forces may shape insect CHC profiles. Here, we show that in Philanthinae digger wasps (Crabronidae) the CHC profile coevolved with a peculiar brood-care strategy. In particular, we found that the behavior to embalm prey stored in the nest with hydrocarbons is adaptive to protect larval food from fungi in those species hunting for Hymenoptera. The prey embalming secretion is identical in composition to the alkene-dominated CHC profile in these species, suggesting that their profile is adaptively conserved for this purpose. In contrast, prey embalming is not required in those species that switched to Coleoptera as prey. Released from this chemical brood-care strategy, Coleoptera-hunting species considerably diversified their CHC profiles. Differential needs to successfully protect prey types used as larval food have thus driven the diversification of CHCs profiles of female Philanthinae wasps. To the best of our knowledge, this is the first evidence of a direct link between selection pressure for food preservation and CHC diversity. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin

PubMed Central

Rognoni, Lorenz; Möst, Tobias; Žoldák, Gabriel; Rief, Matthias

2014-01-01

Proline switches, controlled by cis–trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and how prolyl isomerization modulates the force-sensing mechanism. Proline isomerization toggles domain 20 between two conformations. A stable cis conformation with slow unfolding, favoring the autoinhibited closed conformation of filamin’s force-sensing domain pair 20–21, and a less stable, uninhibited conformation promoted by the trans form. The data provide detailed insight into the folding mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency in modulating force-sensing, thus combining two previously unconnected regulatory mechanisms, proline switches and mechanosensing. PMID:24706888

Genomic Investigation Reveals Highly Conserved, Mosaic, Recombination Events Associated with Capsular Switching among Invasive Neisseria meningitidis Serogroup W Sequence Type (ST)-11 Strains.

PubMed

Mustapha, Mustapha M; Marsh, Jane W; Krauland, Mary G; Fernandez, Jorge O; de Lemos, Ana Paula S; Dunning Hotopp, Julie C; Wang, Xin; Mayer, Leonard W; Lawrence, Jeffrey G; Hiller, N Luisa; Harrison, Lee H

2016-07-03

Neisseria meningitidis is an important cause of meningococcal disease globally. Sequence type (ST)-11 clonal complex (cc11) is a hypervirulent meningococcal lineage historically associated with serogroup C capsule and is believed to have acquired the W capsule through a C to W capsular switching event. We studied the sequence of capsule gene cluster (cps) and adjoining genomic regions of 524 invasive W cc11 strains isolated globally. We identified recombination breakpoints corresponding to two distinct recombination events within W cc11: A 8.4-kb recombinant region likely acquired from W cc22 including the sialic acid/glycosyl-transferase gene, csw resulted in a C→W change in capsular phenotype and a 13.7-kb recombinant segment likely acquired from Y cc23 lineage includes 4.5 kb of cps genes and 8.2 kb downstream of the cps cluster resulting in allelic changes in capsule translocation genes. A vast majority of W cc11 strains (497/524, 94.8%) retain both recombination events as evidenced by sharing identical or very closely related capsular allelic profiles. These data suggest that the W cc11 capsular switch involved two separate recombination events and that current global W cc11 meningococcal disease is caused by strains bearing this mosaic capsular switch. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Conservative Management and End-of-Life Care in an Australian Cohort with ESRD

PubMed Central

Webster, Angela C.; McGeechan, Kevin; Howard, Kirsten; Murtagh, Fliss E.M.; Gray, Nicholas A.; Kerr, Peter G.; Germain, Michael J.; Snelling, Paul

2016-01-01

Background and objectives We aimed to determine the proportion of patients who switched to dialysis after confirmed plans for conservative care and compare survival and end-of-life care among patients choosing conservative care with those initiating RRT. Design, setting, participants, & measurements A cohort study of 721 patients on incident dialysis, patients receiving transplants, and conservatively managed patients from 66 Australian renal units entered into the Patient Information about Options for Treatment Study from July 1 to September 30, 2009 were followed for 3 years. A two–sided binomial test assessed the proportion of patients who switched from conservative care to RRT. Cox regression, stratified by center and adjusted for patient and treatment characteristics, estimated factors associated with 3-year survival. Results In total, 102 of 721 patients planned for conservative care, and median age was 80 years old. Of these, 8% (95% confidence interval, 3% to 13%), switched to dialysis, predominantly for symptom management. Of 94 patients remaining on a conservative pathway, 18% were alive at 3 years. Of the total 721 patients, 247 (34%) died by study end. In multivariable analysis, factors associated with all-cause mortality included older age (hazard ratio, 1.55; 95% confidence interval, 1.36 to 1.77), baseline serum albumin <3.0 versus 3.7–5.4 g/dl (hazard ratio, 4.31; 95% confidence interval, 2.72 to 6.81), and management with conservative care compared with RRT (hazard ratio, 2.18; 95% confidence interval, 1.39 to 3.40). Of 247 deaths, patients managed with RRT were less likely to receive specialist palliative care (26% versus 57%; P<0.001), more likely to die in the hospital (66% versus 42%; P<0.001) than home or hospice, and more likely to receive palliative care only within the last week of life (42% versus 15%; P<0.001) than those managed conservatively. Conclusions Survival after 3 years of conservative management is common, with relatively few patients switching to dialysis. Specialist palliative care services are used more frequently and at an earlier time point for conservatively managed patients, a practice associated with better symptom management and quality of life. PMID:27697783

Vertebrate sex-determining genes play musical chairs

PubMed Central

Pan, Qiaowei; Anderson, Jennifer; Bertho, Sylvain; Herpin, Amaury; Wilson, Catherine; Postlethwait, John H.; Schartl, Manfred; Guiguen, Yann

2017-01-01

Sexual reproduction is one of the most highly conserved processes in evolution. However, the genetic and cellular mechanisms making the decision of whether the undifferentiated gonad of animal embryos develops either towards male or female are manifold and quite diverse. In vertebrates, sex-determining mechanisms range from environmental to simple or complex genetic mechanisms and different mechanisms have evolved repeatedly and independently. In species with simple genetic sex-determination, master sex-determining genes lying on sex chromosomes drive the gonadal differentiation process by switching on a developmental program, which ultimately leads to testicular or ovarian differentiation. So far, very few sex-determining genes have been identified in vertebrates and apart from mammals and birds, these genes are apparently not conserved over a larger number of related orders, families, genera, or even species. To fill this knowledge gap and to better explore genetic sex-determination, we propose a strategy (RAD-Sex) that makes use of next-generation sequencing technology to identify genetic markers that define sex-specific segments of the male or female genome. PMID:27291506

Thermal plasticity of growth and development varies adaptively among alternative developmental pathways.

PubMed

Kivelä, Sami M; Svensson, Beatrice; Tiwe, Alma; Gotthard, Karl

2015-09-01

Polyphenism, the expression of discrete alternative phenotypes, is often a consequence of a developmental switch. Physiological changes induced by a developmental switch potentially affect reaction norms, but the evolution and existence of alternative reaction norms remains poorly understood. Here, we demonstrate that, in the butterfly Pieris napi (Lepidoptera: Pieridae), thermal reaction norms of several life history traits vary adaptively among switch-induced alternative developmental pathways of diapause and direct development. The switch was affected both by photoperiod and temperature, ambient temperature during late development having the potential to override earlier photoperiodic cues. Directly developing larvae had higher development and growth rates than diapausing ones across the studied thermal gradient. Reaction norm shapes also differed between the alternative developmental pathways, indicating pathway-specific selection on thermal sensitivity. Relative mass increments decreased linearly with increasing temperature and were higher under direct development than diapause. Contrary to predictions, population phenology did not explain trait variation or thermal sensitivity, but our experimental design probably lacks power for finding subtle phenology effects. We demonstrate adaptive differentiation in thermal reaction norms among alternative phenotypes, and suggest that the consequences of an environmentally dependent developmental switch primarily drive the evolution of alternative thermal reaction norms in P. napi. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family.

PubMed

Dos Santos, Helena G; Siltberg-Liberles, Jessica

2016-09-19

One of the largest multigene families in Metazoa are the tyrosine kinases (TKs). These are important multifunctional proteins that have evolved as dynamic switches that perform tyrosine phosphorylation and other noncatalytic activities regulated by various allosteric mechanisms. TKs interact with each other and with other molecules, ultimately activating and inhibiting different signaling pathways. TKs are implicated in cancer and almost 30 FDA-approved TK inhibitors are available. However, specific binding is a challenge when targeting an active site that has been conserved in multiple protein paralogs for millions of years. A cassette domain (CD) containing SH3-SH2-Tyrosine Kinase domains reoccurs in vertebrate nonreceptor TKs. Although part of the CD function is shared between TKs, it also presents TK specific features. Here, the evolutionary dynamics of sequence, structure, and phosphorylation across the CD in 17 TK paralogs have been investigated in a large-scale study. We establish that TKs often have ortholog-specific structural disorder and phosphorylation patterns, while secondary structure elements, as expected, are highly conserved. Further, domain-specific differences are at play. Notably, we found the catalytic domain to fluctuate more in certain secondary structure elements than the regulatory domains. By elucidating how different properties evolve after gene duplications and which properties are specifically conserved within orthologs, the mechanistic understanding of protein evolution is enriched and regions supposedly critical for functional divergence across paralogs are highlighted. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Stochastic modeling and experimental analysis of phenotypic switching and survival of cancer cells under stress

NASA Astrophysics Data System (ADS)

Zamani Dahaj, Seyed Alireza; Kumar, Niraj; Sundaram, Bala; Celli, Jonathan; Kulkarni, Rahul

The phenotypic heterogeneity of cancer cells is critical to their survival under stress. A significant contribution to heterogeneity of cancer calls derives from the epithelial-mesenchymal transition (EMT), a conserved cellular program that is crucial for embryonic development. Several studies have investigated the role of EMT in growth of early stage tumors into invasive malignancies. Also, EMT has been closely associated with the acquisition of chemoresistance properties in cancer cells. Motivated by these studies, we analyze multi-phenotype stochastic models of the evolution of cancers cell populations under stress. We derive analytical results for time-dependent probability distributions that provide insights into the competing rates underlying phenotypic switching (e.g. during EMT) and the corresponding survival of cancer cells. Experimentally, we evaluate these model-based predictions by imaging human pancreatic cancer cell lines grown with and without cytotoxic agents and measure growth kinetics, survival, morphological changes and (terminal evaluation of) biomarkers with associated epithelial and mesenchymal phenotypes. The results derived suggest approaches for distinguishing between adaptation and selection scenarios for survival in the presence of external stresses.

The evolution of antipsychotic switch and polypharmacy in natural practice--a longitudinal perspective.

PubMed

Tsutsumi, Chisa; Uchida, Hiroyuki; Suzuki, Takefumi; Watanabe, Koichiro; Takeuchi, Hiroyoshi; Nakajima, Shinichiro; Kimura, Yoshie; Tsutsumi, Yuichiro; Ishii, Koichi; Imasaka, Yasushi; Kapur, Shitij

2011-08-01

Most patients with schizophrenia first start with a single antipsychotic, and yet most finally end up 'switching' or using 'polypharmacy'. The objective of this study was to examine the evolution of antipsychotic switch and polypharmacy in the real-world from a longitudinal perspective. A systematic review of longitudinal antipsychotic prescriptions in 300 patients with schizophrenia (ICD-10) for up to 2 years after their first visit to one of the 4 participating psychiatric clinics in Tokyo, Japan between January, 2007 and June, 2008, was conducted. Reasons for prescription change were also examined. The evolution of switching and polypharmacy was studied, and prescribed doses were compared to suggested dose ranges by the Texas Medication Algorithm Project (TMAP). 208 patients started their antipsychotic treatment with monotherapy. 34.1% of the patients gave up monotherapy with an initial antipsychotic to move to antipsychotic switch (27.4%) and/or polypharmacy (17.8%) within 2 years. The main reason for antipsychotic switch was 'ineffectiveness'; interestingly, this happened despite the fact that the monotherapy dose was below the recommended range in 47.4% of the antipsychotic switch. In a subgroup of 100 patients who started as antipsychotic-free, 2-year prevalence rates of switching and antipsychotic polypharmacy were 27.0% and 18.0%, respectively, and polypharmacy was resorted to after a median of 1 antipsychotic had been tried for 84 days (median). These findings raise a concern that physicians may perform an antipsychotic switch without exploring the entire dose range and resort to antipsychotic polypharmacy without trying an adequate number of antipsychotics. Copyright © 2011 Elsevier B.V. All rights reserved.

Switch Transcripts in Immunoglobulin Class Switching

NASA Astrophysics Data System (ADS)

Lorenz, Matthias; Jung, Steffen; Radbruch, Andreas

1995-03-01

B cells can exchange gene segments for the constant region of the immunoglobulin heavy chain, altering the class and effector function of the antibodies that they produce. Class switching is directed to distinct classes by cytokines, which induce transcription of the targeted DNA sequences. These transcripts are processed, resulting in spliced "switch" transcripts. Switch recombination can be directed to immunoglobulin G1 (IgG1) by the heterologous human metallothionein II_A promoter in mutant mice. Induction of the structurally conserved, spliced switch transcripts is sufficient to target switch recombination to IgG1, whereas transcription alone is not.

Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

NASA Astrophysics Data System (ADS)

Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

2011-09-01

Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

Conservation of Toll-like receptor signaling pathways in teleost fish

USGS Publications Warehouse

Purcell, M.K.; Smith, K.D.; Aderem, A.; Hood, L.; Winton, J.R.; Roach, J.C.

2006-01-01

In mammals, toll-like receptors (TLR) recognize ligands, including pathogen-associated molecular patterns (PAMPs), and respond with ligand-specific induction of genes. In this study, we establish evolutionary conservation in teleost fish of key components of the TLR-signaling pathway that act as switches for differential gene induction, including MYD88, TIRAP, TRIF, TRAF6, IRF3, and IRF7. We further explore this conservation with a molecular phylogenetic analysis of MYD88. To the extent that current genomic analysis can establish, each vertebrate has one ortholog to each of these genes. For molecular tree construction and phylogeny inference, we demonstrate a methodology for including genes with only partial primary sequences without disrupting the topology provided by the high-confidence full-length sequences. Conservation of the TLR-signaling molecules suggests that the basic program of gene regulation by the TLR-signaling pathway is conserved across vertebrates. To test this hypothesis, leukocytes from a model fish, rainbow trout (Oncorhynchus mykiss), were stimulated with known mammalian TLR agonists including: diacylated and triacylated forms of lipoprotein, flagellin, two forms of LPS, synthetic double-stranded RNA, and two imidazoquinoline compounds (loxoribine and R848). Trout leukocytes responded in vitro to a number of these agonists with distinct patterns of cytokine expression that correspond to mammalian responses. Our results support the key prediction from our phylogenetic analyses that strong selective pressure of pathogenic microbes has preserved both TLR recognition and signaling functions during vertebrate evolution.

An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia.

PubMed

Berney, Michael; Greening, Chris; Conrad, Ralf; Jacobs, William R; Cook, Gregory M

2014-08-05

Oxygen availability is a major factor and evolutionary force determining the metabolic strategy of bacteria colonizing an environmental niche. In the soil, conditions can switch rapidly between oxia and anoxia, forcing soil bacteria to remodel their energy metabolism accordingly. Mycobacterium is a dominant genus in the soil, and all its species are obligate aerobes. Here we show that an obligate aerobe, the soil actinomycete Mycobacterium smegmatis, adopts an anaerobe-type strategy by activating fermentative hydrogen production to adapt to hypoxia. This process is controlled by the two-component system DosR-DosS/DosT, an oxygen and redox sensor that is well conserved in mycobacteria. We show that DosR tightly regulates the two [NiFe]-hydrogenases: Hyd3 (MSMEG_3931-3928) and Hyd2 (MSMEG_2719-2718). Using genetic manipulation and high-sensitivity GC, we demonstrate that Hyd3 facilitates the evolution of H2 when oxygen is depleted. Combined activity of Hyd2 and Hyd3 was necessary to maintain an optimal NAD(+)/NADH ratio and enhanced adaptation to and survival of hypoxia. We demonstrate that fermentatively-produced hydrogen can be recycled when fumarate or oxygen become available, suggesting Mycobacterium smegmatis can switch between fermentation, anaerobic respiration, and aerobic respiration. Hydrogen metabolism enables this obligate aerobe to rapidly meet its energetic needs when switching between microoxic and anoxic conditions and provides a competitive advantage in low oxygen environments.

Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

PubMed Central

Gallie, Jenna; Libby, Eric; Bertels, Frederic; Remigi, Philippe; Jendresen, Christian B.; Ferguson, Gayle C.; Desprat, Nicolas; Buffing, Marieke F.; Sauer, Uwe; Beaumont, Hubertus J. E.; Martinussen, Jan; Kilstrup, Mogens; Rainey, Paul B.

2015-01-01

Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to provide empirical insight was delivered by an experiment in which populations of the bacterium Pseudomonas fluorescens SBW25 evolved, de novo, the ability to switch between two colony phenotypes. Here we unravel the molecular mechanism behind colony switching, revealing how a single nucleotide change in a gene enmeshed in central metabolism (carB) generates such a striking phenotype. We show that colony switching is underpinned by ON/OFF expression of capsules consisting of a colanic acid-like polymer. We use molecular genetics, biochemical analyses, and experimental evolution to establish that capsule switching results from perturbation of the pyrimidine biosynthetic pathway. Of central importance is a bifurcation point at which uracil triphosphate is partitioned towards either nucleotide metabolism or polymer production. This bifurcation marks a cell-fate decision point whereby cells with relatively high pyrimidine levels favour nucleotide metabolism (capsule OFF), while cells with lower pyrimidine levels divert resources towards polymer biosynthesis (capsule ON). This decision point is present and functional in the wild-type strain. Finally, we present a simple mathematical model demonstrating that the molecular components of the decision point are capable of producing switching. Despite its simple mutational cause, the connection between genotype and phenotype is complex and multidimensional, offering a rare glimpse of how noise in regulatory networks can provide opportunity for evolution. PMID:25763575

Chemical state evolution in ferroelectric films during tip-induced polarization and electroresistive switching

DOE PAGES

Ievlev, Anton V.; Maksymovych, Petro; Trassin, Morgan; ...

2016-10-11

Domain formation and ferroelectric switching is fundamentally inseparable from polarization screening, which on free surfaces can be realized via band bending and ionic adsorption. In the latter case, polarization switching is intrinsically coupled to the surface electrochemical phenomena, and the electrochemical stage can control kinetics and induce long-range interactions. However, despite extensive evidence towards the critical role of surface electrochemistry, little is known about the nature of the associated processes. Here we combine SPM tip induce polarization switching and secondary ion mass spectrometry to explore the evolution of chemical state of ferroelectric during switching. Surprisingly, we find that even pristinemore » surfaces contain ions (e.g. Cl -) that are not anticipated based on chemistry of the system and processing. In the ferroelectric switching regime, we find surprising changes in surface chemistry, including redistribution of base cations. Finally, at higher voltages in the electroforming regime significant surface deformation was observed and associated with a strong ion intermixing.« less

Evolution of low-aspect-ratio rectangular synthetic jets in a quiescent environment

NASA Astrophysics Data System (ADS)

Wang, Lei; Feng, Li-Hao; Wang, Jin-Jun; Li, Tian

2018-06-01

An experimental study was conducted on the evolution of low-aspect-ratio (AR) rectangular synthetic jets using time-resolved two-dimensional particle image velocimetry and stereoscopic particle image velocimetry. Five orifice ARs ranging from 1 to 5 were found to have an obvious effect on the axis switching of vortex rings and the near-field flow physics at a uniform Reynolds number of 166 and non-dimensional stroke length of 4.5. Compared with conventional continuous jets, rectangular synthetic jets displayed more times of axis switching and the first axis-switching location was closer to the jet exit. Two types of different streamwise vortices, SV-I and SV-II, were detected in the near field as the characteristic products of axis switching. Influenced by the axis switching and streamwise vortices, significant entrainment and mixing enhancement was demonstrated for low-AR rectangular synthetic jets.

A conserved post-transcriptional BMP2 switch in lung cells.

PubMed

Jiang, Shan; Fritz, David T; Rogers, Melissa B

2010-05-15

An ultra-conserved sequence in the bone morphogenetic protein 2 (BMP2) 3' untranslated region (UTR) markedly represses BMP2 expression in non-transformed lung cells. In contrast, the ultra-conserved sequence stimulates BMP2 expression in transformed lung cells. The ultra-conserved sequence functions as a post-transcriptional cis-regulatory switch. A common single-nucleotide polymorphism (SNP, rs15705, +A1123C), which has been shown to influence human morphology, disrupts a conserved element within the ultra-conserved sequence and altered reporter gene activity in non-transformed lung cells. This polymorphism changed the affinity of the BMP2 RNA for several proteins including nucleolin, which has an increased affinity for the C allele. Elevated BMP2 synthesis is associated with increased malignancy in mouse models of lung cancer and poor lung cancer patient prognosis. Understanding the cis- and trans-regulatory factors that control BMP2 synthesis is relevant to the initiation or progression of pathologies associated with abnormal BMP2 levels. (c) 2010 Wiley-Liss, Inc.

Modeling the Evolution of a Science Project in Software-Reliant System Acquisition Programs

DTIC Science & Technology

2013-07-24

might: • Limit worker burnout • Perform better regarding schedule 10 Software Technology Conference April 10, 2013 © 2013 Carnegie Mellon...University The Evolution of a Science Project Key Preliminary Findings -3 The tipping point contributes to the “90% Done” Syndrome Percentage...worker burnout - SP User Satisfaction SP increasing satisfaction indicated satisfaction + + B3 Moderating User Satisfaction overage switch demand switch

The beta-diversity of species interactions: Untangling the drivers of geographic variation in plant-pollinator diversity and function across scales.

PubMed

Burkle, Laura A; Myers, Jonathan A; Belote, R Travis

2016-01-01

Geographic patterns of biodiversity have long inspired interest in processes that shape the assembly, diversity, and dynamics of communities at different spatial scales. To study mechanisms of community assembly, ecologists often compare spatial variation in community composition (beta-diversity) across environmental and spatial gradients. These same patterns inspired evolutionary biologists to investigate how micro- and macro-evolutionary processes create gradients in biodiversity. Central to these perspectives are species interactions, which contribute to community assembly and geographic variation in evolutionary processes. However, studies of beta-diversity have predominantly focused on single trophic levels, resulting in gaps in our understanding of variation in species-interaction networks (interaction beta-diversity), especially at scales most relevant to evolutionary studies of geographic variation. We outline two challenges and their consequences in scaling-up studies of interaction beta-diversity from local to biogeographic scales using plant-pollinator interactions as a model system in ecology, evolution, and conservation. First, we highlight how variation in regional species pools may contribute to variation in interaction beta-diversity among biogeographic regions with dissimilar evolutionary history. Second, we highlight how pollinator behavior (host-switching) links ecological networks to geographic patterns of plant-pollinator interactions and evolutionary processes. Third, we outline key unanswered questions regarding the role of geographic variation in plant-pollinator interactions for conservation and ecosystem services (pollination) in changing environments. We conclude that the largest advances in the burgeoning field of interaction beta-diversity will come from studies that integrate frameworks in ecology, evolution, and conservation to understand the causes and consequences of interaction beta-diversity across scales. © 2016 Botanical Society of America.

Research Results

NASA Astrophysics Data System (ADS)

2012-12-01

Achievements in Sino-German Interdisciplinary Major Research Project Published by Small A Conserved Proline Switch on the Ribosome Facilitates the Recruitment and Binding of trGTPases Air Pollution Contributes in Sunshine Dimming in China Role of Lymphatic Trafficking and Biodistribution Soft Fibrin Gels Promote Selection and Growth of Tumorigenic Cells Targeted Therapy: The New Lease on Life for Acute Promyelocytic Leukemia, and Beyond The Structural Basis for the Sensing and Binding of Cyclic di-GMP by STING Research on Atomic-Scale Investigation of Li Storage Mechanism in Spinel Li4Ti5O12 NSFC Funded Project Made Significant Progress in Intelligent Nanomaterial and Device Palaeobotany and the Evolution of the Monsoon in China Non Heme System Asymmetric Epoxidation Reaction Made Progress Rapid Advancement of Immunology Study in China Chinese Experts Successfully Produced Transgenic Animals from Haploid Embryonic Stem Cells

Vertebrate sex-determining genes play musical chairs.

PubMed

Pan, Qiaowei; Anderson, Jennifer; Bertho, Sylvain; Herpin, Amaury; Wilson, Catherine; Postlethwait, John H; Schartl, Manfred; Guiguen, Yann

2016-01-01

Sexual reproduction is one of the most highly conserved processes in evolution. However, the genetic and cellular mechanisms making the decision of whether the undifferentiated gonad of animal embryos develops either towards male or female are manifold and quite diverse. In vertebrates, sex-determining mechanisms range from environmental to simple or complex genetic mechanisms and different mechanisms have evolved repeatedly and independently. In species with simple genetic sex-determination, master sex-determining genes lying on sex chromosomes drive the gonadal differentiation process by switching on a developmental program, which ultimately leads to testicular or ovarian differentiation. So far, very few sex-determining genes have been identified in vertebrates and apart from mammals and birds, these genes are apparently not conserved over a larger number of related orders, families, genera, or even species. To fill this knowledge gap and to better explore genetic sex-determination, we propose a strategy (RAD-Sex) that makes use of next-generation sequencing technology to identify genetic markers that define sex-specific segments of the male or female genome. Copyright © 2016 Académie des sciences. All rights reserved.

A conserved supergene locus controls colour pattern diversity in Heliconius butterflies.

PubMed

Joron, Mathieu; Papa, Riccardo; Beltrán, Margarita; Chamberlain, Nicola; Mavárez, Jesús; Baxter, Simon; Abanto, Moisés; Bermingham, Eldredge; Humphray, Sean J; Rogers, Jane; Beasley, Helen; Barlow, Karen; ffrench-Constant, Richard H; Mallet, James; McMillan, W Owen; Jiggins, Chris D

2006-10-01

We studied whether similar developmental genetic mechanisms are involved in both convergent and divergent evolution. Mimetic insects are known for their diversity of patterns as well as their remarkable evolutionary convergence, and they have played an important role in controversies over the respective roles of selection and constraints in adaptive evolution. Here we contrast three butterfly species, all classic examples of Müllerian mimicry. We used a genetic linkage map to show that a locus, Yb, which controls the presence of a yellow band in geographic races of Heliconius melpomene, maps precisely to the same location as the locus Cr, which has very similar phenotypic effects in its co-mimic H. erato. Furthermore, the same genomic location acts as a "supergene", determining multiple sympatric morphs in a third species, H. numata. H. numata is a species with a very different phenotypic appearance, whose many forms mimic different unrelated ithomiine butterflies in the genus Melinaea. Other unlinked colour pattern loci map to a homologous linkage group in the co-mimics H. melpomene and H. erato, but they are not involved in mimetic polymorphism in H. numata. Hence, a single region from the multilocus colour pattern architecture of H. melpomene and H. erato appears to have gained control of the entire wing-pattern variability in H. numata, presumably as a result of selection for mimetic "supergene" polymorphism without intermediates. Although we cannot at this stage confirm the homology of the loci segregating in the three species, our results imply that a conserved yet relatively unconstrained mechanism underlying pattern switching can affect mimicry in radically different ways. We also show that adaptive evolution, both convergent and diversifying, can occur by the repeated involvement of the same genomic regions.

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

PubMed

Li, Xinguo; Wu, Harry X; Southerton, Simon G

2010-06-21

Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

PubMed Central

2010-01-01

Background Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. Results The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conclusions Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution. PMID:20565927

Functional Conservation and Divergence of daf-22 Paralogs in Pristionchus pacificus Dauer Development.

PubMed

Markov, Gabriel V; Meyer, Jan M; Panda, Oishika; Artyukhin, Alexander B; Claaßen, Marc; Witte, Hanh; Schroeder, Frank C; Sommer, Ralf J

2016-10-01

Small-molecule signaling in nematode dauer formation has emerged as a major model to study chemical communication in development and evolution. Developmental arrest as nonfeeding and stress-resistant dauer larvae represents the major survival and dispersal strategy. Detailed studies in Caenorhabditis elegans and Pristionchus pacificus revealed that small-molecule communication changes rapidly in evolution resulting in extreme structural diversity of small-molecule compounds. In C. elegans, a blend of ascarosides constitutes the dauer pheromone, whereas the P. pacificus dauer pheromone includes additional paratosides and integrates building blocks from diverse primary metabolic pathways. Despite this complexity of small-molecule structures and functions, little is known about the biosynthesis of small molecules in nematodes outside C. elegans Here, we show that the genes encoding enzymes of the peroxisomal β-oxidation pathway involved in small-molecule biosynthesis evolve rapidly, including gene duplications and domain switching. The thiolase daf-22, the most downstream factor in C. elegans peroxisomal β-oxidation, has duplicated in P. pacificus, resulting in Ppa-daf-22.1, which still contains the sterol-carrier-protein (SCP) domain that was lost in C. elegans daf-22, and Ppa-daf-22.2. Using the CRISPR/Cas9 system, we induced mutations in both P. pacificus daf-22 genes and identified an unexpected complexity of functional conservation and divergence. Under well-fed conditions, ascaroside biosynthesis proceeds exclusively via Ppa-daf-22.1 In contrast, starvation conditions induce Ppa-daf-22.2 activity, resulting in the production of a specific subset of ascarosides. Gene expression studies indicate a reciprocal up-regulation of both Ppa-daf-22 genes, which is, however, independent of starvation. Thus, our study reveals an unexpected functional complexity of dauer development and evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Expanding the view on the evolution of the nematode dauer signalling pathways: refinement through gene gain and pathway co-option.

PubMed

Gilabert, Aude; Curran, David M; Harvey, Simon C; Wasmuth, James D

2016-06-27

Signalling pathways underlie development, behaviour and pathology. To understand patterns in the evolution of signalling pathways, we undertook a comprehensive investigation of the pathways that control the switch between growth and developmentally quiescent dauer in 24 species of nematodes spanning the phylum. Our analysis of 47 genes across these species indicates that the pathways and their interactions are not conserved throughout the Nematoda. For example, the TGF-β pathway was co-opted into dauer control relatively late in a lineage that led to the model species Caenorhabditis elegans. We show molecular adaptations described in C. elegans that are restricted to its genus or even just to the species. Similarly, our analyses both identify species where particular genes have been lost and situations where apparently incorrect orthologues have been identified. Our analysis also highlights the difficulties of working with genome sequences from non-model species as reliance on the published gene models would have significantly restricted our understanding of how signalling pathways evolve. Our approach therefore offers a robust standard operating procedure for genomic comparisons.

Regular and chaotic motions of the Chaplygin sleigh with periodically switched location of nonholonomic constraint

NASA Astrophysics Data System (ADS)

Kuznetsov, Sergey P.

2017-04-01

We consider motions of the Chaplygin sleigh on a plane supposing that the nonholonomic constraint is located periodically turn by turn at each of three legs supporting the sleigh. We assume that at switching on the constraint the respective element (“knife-edge”) is directed along the local velocity vector and becomes fixed relatively to the sleigh for a certain time interval till the next switch. Differential equations of the mathematical model are formulated and analytical derivation of a 2D map for the state transformation on the switching period is provided. The dynamics takes place with conservation of the mechanical energy. Numerical simulations show phenomena characteristic to nonholonomic systems with complex dynamics. In particular, on the energy surface attractors may occur responsible for regular sustained motions settling in domains of prevalent area compression by the map. In addition, chaotic and quasi-periodic regimes take place similar to those observed in conservative nonlinear dynamics.

On orbital allotments for geostationary satellites

NASA Technical Reports Server (NTRS)

Gonsalvez, David J. A.; Reilly, Charles H.; Mount-Campbell, Clark A.

1986-01-01

The following satellite synthesis problem is addressed: communication satellites are to be allotted positions on the geostationary arc so that interference does not exceed a given acceptable level by enforcing conservative pairwise satellite separation. A desired location is specified for each satellite, and the objective is to minimize the sum of the deviations between the satellites' prescribed and desired locations. Two mixed integer programming models for the satellite synthesis problem are presented. Four solution strategies, branch-and-bound, Benders' decomposition, linear programming with restricted basis entry, and a switching heuristic, are used to find solutions to example synthesis problems. Computational results indicate the switching algorithm yields solutions of good quality in reasonable execution times when compared to the other solution methods. It is demonstrated that the switching algorithm can be applied to synthesis problems with the objective of minimizing the largest deviation between a prescribed location and the corresponding desired location. Furthermore, it is shown that the switching heuristic can use no conservative, location-dependent satellite separations in order to satisfy interference criteria.

An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia

PubMed Central

Berney, Michael; Greening, Chris; Conrad, Ralf; Jacobs, William R.; Cook, Gregory M.

2014-01-01

Oxygen availability is a major factor and evolutionary force determining the metabolic strategy of bacteria colonizing an environmental niche. In the soil, conditions can switch rapidly between oxia and anoxia, forcing soil bacteria to remodel their energy metabolism accordingly. Mycobacterium is a dominant genus in the soil, and all its species are obligate aerobes. Here we show that an obligate aerobe, the soil actinomycete Mycobacterium smegmatis, adopts an anaerobe-type strategy by activating fermentative hydrogen production to adapt to hypoxia. This process is controlled by the two-component system DosR-DosS/DosT, an oxygen and redox sensor that is well conserved in mycobacteria. We show that DosR tightly regulates the two [NiFe]-hydrogenases: Hyd3 (MSMEG_3931-3928) and Hyd2 (MSMEG_2719-2718). Using genetic manipulation and high-sensitivity GC, we demonstrate that Hyd3 facilitates the evolution of H2 when oxygen is depleted. Combined activity of Hyd2 and Hyd3 was necessary to maintain an optimal NAD+/NADH ratio and enhanced adaptation to and survival of hypoxia. We demonstrate that fermentatively-produced hydrogen can be recycled when fumarate or oxygen become available, suggesting Mycobacterium smegmatis can switch between fermentation, anaerobic respiration, and aerobic respiration. Hydrogen metabolism enables this obligate aerobe to rapidly meet its energetic needs when switching between microoxic and anoxic conditions and provides a competitive advantage in low oxygen environments. PMID:25049411

Detection and characterization of multi-filament evolution during resistive switching

DOE PAGES

Mickel, Patrick R.; Lohn, Andrew J.; Marinella, Matthew J.

2014-08-05

We present resistive switching data in TaO x memristors displaying signatures of multi-filament switching modes, and develop a geometrically defined equivalent circuit to separate the individual resistances and powers dissipated in each filament. Using these resolved values, we compare the individual switching curves of each filament and demonstrate that the switching data of each filament collapse onto a single switching curve determined by the analytical steady-state resistive switching solution for filamentary switching. Analyzing our results in terms of this solution, we determine the switching temperature, heat flow, conductivity, and time evolving areas of each filament during resistive switching. Finally, wemore » discuss operational modes which may limit the formation of additional conducting filaments, potentially leading to increased device endurance.« less

Comparison of conservation metrics in a case study of lemurs.

PubMed

Gudde, Renske; Venditti, Chris

2016-12-01

Conservation planning is important to protect species from going extinct now that natural habitats are decreasing owing to human activity and climate change. However, there is considerable controversy in choosing appropriate metrics to weigh the value of species and geographic regions. For example, the added value of phylogenetic conservation-selection criteria remains disputed because high correlations between them and the nonphylogenetic criteria of species richness have been reported. We evaluated the commonly used conservation metrics species richness, endemism, phylogenetic diversity (PD), and phylogenetic endemism (PE) in a case study on lemurs of Madagascar. This enabled us to identify the conservation target of each metric and consider how they may be used in future conservation planning. We also devised a novel metric that uses a phylogeny scaled according to the rate of phenotypic evolution as a proxy for a species' ability to adapt to change. High rates of evolution may indicate generalization or specialization. Both specialization and low rates of evolution may result in an inability to adapt to changing environments. We examined conservation priorities by using the inverse of the rate of body mass evolution to account for species with low rates of evolution. In line with previous work, we found high correlations among species richness and PD (r = 0.96), and endemism and PE (r = 0.82) in Malagasy lemurs. Phylogenetic endemism in combination with rates of evolution and their inverse prioritized grid cells containing highly endemic and specialized lemurs at risk of extinction, such as Avahi occidentalis and Lepilemur edwardsi, 2 endangered lemurs with high rates of phenotypic evolution and low-quality diets, and Hapalemur aureus, a critically endangered species with a low rate of body mass evolution and a diet consisting of very high doses of cyanide. © 2016 Society for Conservation Biology.

76 FR 52854 - Energy Conservation Program: Energy Conservation Standards for Residential Clothes Dryers and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-24

... Equipment Price Forecasting in Energy Conservation Standards Analysis (76 FR 9696, Feb. 22, 2011), has not... with such switching (e.g., the need to install a new dedicated electrical outlet). 3. Energy Price Forecast AGA stated that DOE's use of the Annual Energy Outlook (AEO) 2010 Reference Case for energy prices...

Mechanical cause for acute left lung atelectasis after neonatal aortic arch repair with arterial switch operation: Conservative management.

PubMed

Maddali, Madan Mohan; Kandachar, Pranav Subbaraya; Al-Hanshi, Said; Al Ghafri, Mohammed; Valliattu, John

2017-01-01

Respiratory complications due to mechanical obstruction of the airways can occur following pediatric cardiac surgery. Clinically significant intrathoracic vascular compression of the airway can occur when extensive dissection and mobilization of arch and neck vessels is involved as in repair of interrupted aortic arch. This case report describes a neonate who underwent interrupted aortic arch repair along with an arterial switch operation and developed a left lung collapse immediately after tracheal extubation. Fiber-optic bronchoscopy revealed vascular compression as the real culprit. The child was successfully managed conservatively.

Autoinhibition and signaling by the switch II motif in the G-protein chaperone of a radical B12 enzyme.

PubMed

Lofgren, Michael; Koutmos, Markos; Banerjee, Ruma

2013-10-25

MeaB is an accessory GTPase protein involved in the assembly, protection, and reactivation of 5'-deoxyadenosyl cobalamin-dependent methylmalonyl-CoA mutase (MCM). Mutations in the human ortholog of MeaB result in methylmalonic aciduria, an inborn error of metabolism. G-proteins typically utilize conserved switch I and II motifs for signaling to effector proteins via conformational changes elicited by nucleotide binding and hydrolysis. Our recent discovery that MeaB utilizes an unusual switch III region for bidirectional signaling with MCM raised questions about the roles of the switch I and II motifs in MeaB. In this study, we addressed the functions of conserved switch II residues by performing alanine-scanning mutagenesis. Our results demonstrate that the GTPase activity of MeaB is autoinhibited by switch II and that this loop is important for coupling nucleotide-sensitive conformational changes in switch III to elicit the multiple chaperone functions of MeaB. Furthermore, we report the structure of MeaB·GDP crystallized in the presence of AlFx(-) to form the putative transition state analog, GDP·AlF4(-). The resulting crystal structure and its comparison with related G-proteins support the conclusion that the catalytic site of MeaB is incomplete in the absence of the GTPase-activating protein MCM and therefore unable to stabilize the transition state analog. Favoring an inactive conformation in the absence of the client MCM protein might represent a strategy for suppressing the intrinsic GTPase activity of MeaB in which the switch II loop plays an important role.

Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR.

PubMed

Ganis, Jared J; Hsia, Nelson; Trompouki, Eirini; de Jong, Jill L O; DiBiase, Anthony; Lambert, Janelle S; Jia, Zhiying; Sabo, Peter J; Weaver, Molly; Sandstrom, Richard; Stamatoyannopoulos, John A; Zhou, Yi; Zon, Leonard I

2012-06-15

Globin gene switching is a complex, highly regulated process allowing expression of distinct globin genes at specific developmental stages. Here, for the first time, we have characterized all of the zebrafish globins based on the completed genomic sequence. Two distinct chromosomal loci, termed major (chromosome 3) and minor (chromosome 12), harbor the globin genes containing α/β pairs in a 5'-3' to 3'-5' orientation. Both these loci share synteny with the mammalian α-globin locus. Zebrafish globin expression was assayed during development and demonstrated two globin switches, similar to human development. A conserved regulatory element, the locus control region (LCR), was revealed by analyzing DNase I hypersensitive sites, H3K4 trimethylation marks and GATA1 binding sites. Surprisingly, the position of these sites with relation to the globin genes is evolutionarily conserved, despite a lack of overall sequence conservation. Motifs within the zebrafish LCR include CACCC, GATA, and NFE2 sites, suggesting functional interactions with known transcription factors but not the same LCR architecture. Functional homology to the mammalian α-LCR MCS-R2 region was confirmed by robust and specific reporter expression in erythrocytes of transgenic zebrafish. Our studies provide a comprehensive characterization of the zebrafish globin loci and clarify the regulation of globin switching. Copyright © 2012 Elsevier Inc. All rights reserved.

Switching probability of all-perpendicular spin valve nanopillars

NASA Astrophysics Data System (ADS)

Tzoufras, M.

2018-05-01

In all-perpendicular spin valve nanopillars the probability density of the free-layer magnetization is independent of the azimuthal angle and its evolution equation simplifies considerably compared to the general, nonaxisymmetric geometry. Expansion of the time-dependent probability density to Legendre polynomials enables analytical integration of the evolution equation and yields a compact expression for the practically relevant switching probability. This approach is valid when the free layer behaves as a single-domain magnetic particle and it can be readily applied to fitting experimental data.

Reducing Glucose Variability Due to Meals and Postprandial Exercise in T1DM Using Switched LPV Control: In Silico Studies.

PubMed

Colmegna, Patricio H; Sánchez-Peña, Ricardo S; Gondhalekar, Ravi; Dassau, Eyal; Doyle, Francis J

2016-05-01

Time-varying dynamics is one of the main issues for achieving safe blood glucose control in type 1 diabetes mellitus (T1DM) patients. In addition, the typical disturbances considered for controller design are meals, which increase the glucose level, and physical activity (PA), which increases the subject's sensitivity to insulin. In previous works the authors have applied a linear parameter-varying (LPV) control technique to manage unannounced meals. A switched LPV controller that switches between 3 LPV controllers, each with a different level of aggressiveness, is designed to further cope with both unannounced meals and postprandial PA. Thus, the proposed control strategy has a "standard" mode, an "aggressive" mode, and a "conservative" mode. The "standard" mode is designed to be applied most of the time, while the "aggressive" mode is designed to deal only with hyperglycemia situations. On the other hand, the "conservative" mode is focused on postprandial PA control. An ad hoc simulator has been developed to test the proposed controller. This simulator is based on the distribution version of the UVA/Padova model and includes the effect of PA based on Schiavon.(1) The test results obtained when using this simulator indicate that the proposed control law substantially reduces the risk of hypoglycemia with the conservative strategy, while the risk of hyperglycemia is scarcely affected. It is demonstrated that the announcement, or anticipation, of exercise is indispensable for letting a mono-hormonal artificial pancreas deal with the consequences of postprandial PA. In view of this the proposed controller allows switching into a conservative mode when notified of PA by the user. © 2016 Diabetes Technology Society.

Strategy evolution driven by switching probabilities in structured multi-agent systems

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Chen, Zengqiang; Li, Zhiqi

2017-10-01

Evolutionary mechanism driving the commonly seen cooperation among unrelated individuals is puzzling. Related models for evolutionary games on graphs traditionally assume that players imitate their successful neighbours with higher benefits. Notably, an implicit assumption here is that players are always able to acquire the required pay-off information. To relax this restrictive assumption, a contact-based model has been proposed, where switching probabilities between strategies drive the strategy evolution. However, the explicit and quantified relation between a player's switching probability for her strategies and the number of her neighbours remains unknown. This is especially a key point in heterogeneously structured system, where players may differ in the numbers of their neighbours. Focusing on this, here we present an augmented model by introducing an attenuation coefficient and evaluate its influence on the evolution dynamics. Results show that the individual influence on others is negatively correlated with the contact numbers specified by the network topologies. Results further provide the conditions under which the coexisting strategies can be calculated analytically.

On the long-term fitness of cells in periodically switching environments.

PubMed

Pang, Ning-Ning; Tzeng, Wen-Jer

2008-01-01

Because all the cell populations are capable of making switches between different genetic expression states in response to the environmental change, Thattai and van Oudenaarden (Genetics 167, 523-530, 2004) have raised a very interesting question: In a constantly fluctuating environment, which type of cell population (heterogeneous or homogeneous) is fitter in the long term? This problem is very important to development and evolution biology. We thus take an extensive analysis about how the cell population evolves in a periodically switching environment either with symmetrical time-span or asymmetrical time-span. A complete picture of the phase diagrams for both cases is obtained. Furthermore, we find that the systems with time-dependent cellular transitions all collapse to the same set of dynamical equations with the modified parameters. Furthermore, we also explain in detail how the fitness problem bears much resemblance to the phenomenon, stochastic resonance, in physical sciences. Our results could be helpful for the biologists to design artificial evolution experiments and unveil the mystery of development and evolution.

Gene family size conservation is a good indicator of evolutionary rates.

PubMed

Chen, Feng-Chi; Chen, Chiuan-Jung; Li, Wen-Hsiung; Chuang, Trees-Juen

2010-08-01

The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

Designing non-Hermitian dynamics for conservative state evolution on the Bloch sphere

NASA Astrophysics Data System (ADS)

Yu, Sunkyu; Piao, Xianji; Park, Namkyoo

2018-03-01

An evolution on the Bloch sphere is the fundamental state transition, including optical polarization controls and qubit operations. Conventional evolution of a polarization state or qubit is implemented within a closed system that automatically satisfies energy conservation from the Hermitian formalism. Although particular forms of static non-Hermitian Hamiltonians, such as parity-time-symmetric Hamiltonians, allow conservative states in an open system, the criteria for the energy conservation in a dynamical open system have not been fully explored. Here, we derive the condition of conservative state evolution in open-system dynamics and its inverse design method, by developing the non-Hermitian modification of the Larmor precession equation. We show that the geometrically designed locus on the Bloch sphere can be realized by different forms of dynamics, leading to the isolocus family of non-Hermitian dynamics. This increased degree of freedom allows the complementary phenomena of error-robust and highly sensitive evolutions on the Bloch sphere, which could be applicable to stable polarizers, quantum gates, and optimized sensors in dynamical open systems.

Pace of Coreceptor Tropism Switch in HIV-1-Infected Individuals after Recent Infection.

PubMed

Arif, Muhammad Shoaib; Hunter, James; Léda, Ana Rachel; Zukurov, Jean Paulo Lopes; Samer, Sadia; Camargo, Michelle; Galinskas, Juliana; Kallás, Esper Georges; Komninakis, Shirley Vasconcelos; Janini, Luiz Mario; Sucupira, Maria Cecilia; Diaz, Ricardo Sobhie

2017-10-01

HIV-1 entry into target cells influences several aspects of HIV-1 pathogenesis, including viral tropism, HIV-1 transmission and disease progression, and response to entry inhibitors. The evolution from CCR5- to CXCR4-using strains in a given human host is still unpredictable. Here we analyzed timing and predictors for coreceptor evolution among recently HIV-1-infected individuals. Proviral DNA was longitudinally evaluated in 66 individuals using Geno2pheno [coreceptor] Demographics, viral load, CD4 + and CD8 + T cell counts, CCR5Δ32 polymorphisms, GB virus C (GBV-C) coinfection, and HLA profiles were also evaluated. Ultradeep sequencing was performed on initial samples from 11 selected individuals. A tropism switch from CCR5- to CXCR4-using strains was identified in 9/49 (18.4%) individuals. Only a low baseline false-positive rate (FPR) was found to be a significant tropism switch predictor. No minor CXCR4-using variants were identified in initial samples of 4 of 5 R5/non-R5 switchers. Logistic regression analysis showed that patients with an FPR of >40.6% at baseline presented a stable FPR over time whereas lower FPRs tend to progressively decay, leading to emergence of CXCR4-using strains, with a mean evolution time of 27.29 months (range, 8.90 to 64.62). An FPR threshold above 40.6% determined by logistic regression analysis may make it unnecessary to further determine tropism for prediction of disease progression related to emergence of X4 strains or use of CCR5 antagonists. The detection of variants with intermediate FPRs and progressive FPR decay over time not only strengthens the power of Geno2pheno in predicting HIV tropism but also indirectly confirms a continuous evolution from earlier R5 variants toward CXCR4-using strains. IMPORTANCE The introduction of CCR5 antagonists in the antiretroviral arsenal has sparked interest in coreceptors utilized by HIV-1. Despite concentrated efforts, viral and human host features predicting tropism switch are still poorly understood. Limited longitudinal data are available to assess the influence that these factors have on predicting tropism switch and disease progression. The present study describes longitudinal tropism evolution in a group of recently HIV-infected individuals to determine the prevalence and potential correlates of tropism switch. We demonstrated here that a low baseline FPR determined by the Geno2pheno [coreceptor] algorithm can predict tropism evolution from CCR5 to CXCR4 coreceptor use. Copyright © 2017 American Society for Microbiology.

Reputation-based partner choice promotes cooperation in social networks

NASA Astrophysics Data System (ADS)

Fu, Feng; Hauert, Christoph; Nowak, Martin A.; Wang, Long

2008-08-01

We investigate the cooperation dynamics attributed to the interplay between the evolution of individual strategies and evolution of individual partnerships. We focus on the effect of reputation on an individual’s partner-switching process. We assume that individuals can either change their strategies by imitating their partners or adjust their partnerships based on local information about reputations. We manipulate the partner switching in two ways; that is, individuals can switch from the lowest reputation partners, either to their partners’ partners who have the highest reputation (i.e., ordering in partnership) or to others randomly chosen from the entire population (i.e., randomness in partnership). We show that when individuals are able to alter their behavioral strategies and their social interaction partnerships on the basis of reputation, cooperation can prevail. We find that the larger temptation to defect and the denser the partner network, the more frequently individuals need to shift their partnerships in order for cooperation to thrive. Furthermore, an increasing tendency of switching to partners’ partners is more likely to lead to a higher level of cooperation. We show that when reputation is absent in such partner-switching processes, cooperation is much less favored than that of the reputation involved. Moreover, we investigate the effect of discounting an individual’s reputation on the evolution of cooperation. Our results highlight the importance of the consideration of reputation (indirect reciprocity) on the promotion of cooperation when individuals can adjust their partnerships.

Investigating the Effect of Voltage-Switching on Low-Energy Task Scheduling in Hard Real-Time Systems

DTIC Science & Technology

2005-01-01

We investigate the effect of voltage-switching on task execution times and energy consumption for dual-speed hard real - time systems , and present a...scheduling algorithm and apply it to two real-life task sets. Our results show that energy can be conserved in embedded real - time systems using energy...aware task scheduling. We also show that switching times have a significant effect on the energy consumed in hard real - time systems .

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution.

PubMed

Janky, Rekin's; van Helden, Jacques

2008-01-23

The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints) has become a common strategy to predict cis-acting regulatory elements. Several software tools are routinely used to raise hypotheses about regulation. However, these tools are generally used as black boxes, with default parameters. A systematic evaluation of optimal parameters for a footprint discovery strategy can bring a sizeable improvement to the predictions. We evaluate the performances of a footprint discovery approach based on the detection of over-represented spaced motifs. This method is particularly suitable for (but not restricted to) Bacteria, since such motifs are typically bound by factors containing a Helix-Turn-Helix domain. We evaluated footprint discovery in 368 Escherichia coli K12 genes with annotated sites, under 40 different combinations of parameters (taxonomical level, background model, organism-specific filtering, operon inference). Motifs are assessed both at the levels of correctness and significance. We further report a detailed analysis of 181 bacterial orthologs of the LexA repressor. Distinct motifs are detected at various taxonomical levels, including the 7 previously characterized taxon-specific motifs. In addition, we highlight a significantly stronger conservation of half-motifs in Actinobacteria, relative to Firmicutes, suggesting an intermediate state in specificity switching between the two Gram-positive phyla, and thereby revealing the on-going evolution of LexA auto-regulation. The footprint discovery method proposed here shows excellent results with E. coli and can readily be extended to predict cis-acting regulatory signals and propose testable hypotheses in bacterial genomes for which nothing is known about regulation.

Voltage- and current-activated metal-insulator transition in VO2-based electrical switches: a lifetime operation analysis.

PubMed

Crunteanu, Aurelian; Givernaud, Julien; Leroy, Jonathan; Mardivirin, David; Champeaux, Corinne; Orlianges, Jean-Christophe; Catherinot, Alain; Blondy, Pierre

2010-12-01

Vanadium dioxide is an intensively studied material that undergoes a temperature-induced metal-insulator phase transition accompanied by a large change in electrical resistivity. Electrical switches based on this material show promising properties in terms of speed and broadband operation. The exploration of the failure behavior and reliability of such devices is very important in view of their integration in practical electronic circuits. We performed systematic lifetime investigations of two-terminal switches based on the electrical activation of the metal-insulator transition in VO 2 thin films. The devices were integrated in coplanar microwave waveguides (CPWs) in series configuration. We detected the evolution of a 10 GHz microwave signal transmitted through the CPW, modulated by the activation of the VO 2 switches in both voltage- and current-controlled modes. We demonstrated enhanced lifetime operation of current-controlled VO 2 -based switching (more than 260 million cycles without failure) compared with the voltage-activated mode (breakdown at around 16 million activation cycles). The evolution of the electrical self-oscillations of a VO 2 -based switch induced in the current-operated mode is a subtle indicator of the material properties modification and can be used to monitor its behavior under various external stresses in sensor applications.

Soliton switching in a site-dependent ferromagnet

NASA Astrophysics Data System (ADS)

Senjudarvannan, R.; Sathishkumar, P.; Vijayalakshmi, S.

2017-02-01

Switching of soliton in a ferromagnetic medium offers the possibility of developing a new innovative approach for information storage technologies. The nonlinear spin dynamics of a site-dependent Heisenberg ferromagnetic spin chain with Gilbert damping under the influence of external magnetic field is expressed in the form of the Landau-Lifshitz-Gilbert equation in the classical continuum limit. The corresponding evolution equation is developed through stereographic projection technique by projecting the unit sphere of spin onto a complex plane. The exact soliton solutions are constructed by solving the associated evolution equation through the modified extended tanh-function method. The impact of damping and external magnetic field on the magnetic soliton under the invariant inhomogeneity is investigated and finally, the magnetization switching in the form of shape changing solitons are demonstrated.

The evolution of resource adaptation: how generalist and specialist consumers evolve.

PubMed

Ma, Junling; Levin, Simon A

2006-07-01

Why and how specialist and generalist strategies evolve are important questions in evolutionary ecology. In this paper, with the method of adaptive dynamics and evolutionary branching, we identify conditions that select for specialist and generalist strategies. Generally, generalist strategies evolve if there is a switching benefit; specialists evolve if there is a switching cost. If the switching cost is large, specialists always evolve. If the switching cost is small, even though the consumer will first evolve toward a generalist strategy, it will eventually branch into two specialists.

Analytical solution of the transient temperature profile in gain medium of passively Q-switched microchip laser.

PubMed

Han, Xiahui; Li, Jianlang

2014-11-01

The transient temperature evolution in the gain medium of a continuous wave (CW) end-pumped passively Q-switched microchip (PQSM) laser is analyzed. By approximating the time-dependent population inversion density as a sawtooth function of time and treating the time-dependent pump absorption of a CW end-pumped PQSM laser as the superposition of an infinite series of short pumping pulses, the analytical expressions of transient temperature evolution and distribution in the gain medium for four- and three-level laser systems, respectively, are given. These analytical solutions are applied to evaluate the transient temperature evolution and distribution in the gain medium of CW end-pumped PQSM Nd:YAG and Yb:YAG lasers.

Switching from Computer to Microcomputer Architecture Education

ERIC Educational Resources Information Center

Bolanakis, Dimosthenis E.; Kotsis, Konstantinos T.; Laopoulos, Theodore

2010-01-01

In the last decades, the technological and scientific evolution of the computing discipline has been widely affecting research in software engineering education, which nowadays advocates more enlightened and liberal ideas. This article reviews cross-disciplinary research on a computer architecture class in consideration of its switching to…

Overlapping activation-induced cytidine deaminase hotspot motifs in Ig class-switch recombination

PubMed Central

Han, Li; Masani, Shahnaz; Yu, Kefei

2011-01-01

Ig class-switch recombination (CSR) is directed by the long and repetitive switch regions and requires activation-induced cytidine deaminase (AID). One of the conserved switch-region sequence motifs (AGCT) is a preferred site for AID-mediated DNA-cytosine deamination. By using somatic gene targeting and recombinase-mediated cassette exchange, we established a cell line-based CSR assay that allows manipulation of switch sequences at the endogenous locus. We show that AGCT is only one of a family of four WGCW motifs in the switch region that can facilitate CSR. We go on to show that it is the overlap of AID hotspots at WGCW sites on the top and bottom strands that is critical. This finding leads to a much clearer model for the difference between CSR and somatic hypermutation. PMID:21709240

Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches

PubMed Central

Krobath, Heinrich; Chan, Hue Sun

2016-01-01

Deciphering the effects of nonsynonymous mutations on protein structure is central to many areas of biomedical research and is of fundamental importance to the study of molecular evolution. Much of the investigation of protein evolution has focused on mutations that leave a protein’s folded structure essentially unchanged. However, to evolve novel folds of proteins, mutations that lead to large conformational modifications have to be involved. Unraveling the basic biophysics of such mutations is a challenge to theory, especially when only one or two amino acid substitutions cause a large-scale conformational switch. Among the few such mutational switches identified experimentally, the one between the GA all-α and GB α+β folds is extensively characterized; but all-atom simulations using fully transferrable potentials have not been able to account for this striking switching behavior. Here we introduce an explicit-chain model that combines structure-based native biases for multiple alternative structures with a general physical atomic force field, and apply this construct to twelve mutants spanning the sequence variation between GA and GB. In agreement with experiment, we observe conformational switching from GA to GB upon a single L45Y substitution in the GA98 mutant. In line with the latent evolutionary potential concept, our model shows a gradual sequence-dependent change in fold preference in the mutants before this switch. Our analysis also indicates that a sharp GA/GB switch may arise from the orientation dependence of aromatic π-interactions. These findings provide physical insights toward rationalizing, predicting and designing evolutionary conformational switches. PMID:27253392

Long-Term Evolution of the Electrical Stimulation Levels for Cochlear Implant Patients

PubMed Central

Vargas, Jose Luis; Sainz, Manuel; Roldan, Cristina; de la Torre, Angel

2012-01-01

Objectives The stimulation levels programmed in cochlear implant systems are affected by an evolution since the first switch-on of the processor. This study was designed to evaluate the changes in stimulation levels over time and the relationship between post-implantation physiological changes and with the hearing experience provided by the continuous use of the cochlear implant. Methods Sixty-two patients, ranging in age from 4 to 68 years at the moment of implantation participated in this study. All subjects were implanted with the 12 channels COMBI 40+ cochlear implant at San Cecilio University Hospital, Granada, Spain. Hearing loss etiology and progression characteristics varied across subjects. Results The analyzed programming maps show that the stimulation levels suffer a fast evolution during the first weeks after the first switch-on of the processor. Then, the evolution becomes slower and the programming parameters tend to be stable at about 6 months after the first switch-on. The evolution of the stimulation levels implies an increment of the electrical dynamic range, which is increased from 15.4 to 20.7 dB and improves the intensity resolution. A significant increment of the sensitivity to acoustic stimuli is also observed. For some patients, we have also observed transitory changes in the electrode impedances associated to secretory otitis media, which cause important changes in the programming maps. Conclusion We have studied the long-term evolution of the stimulation levels in cochlear implant patients. Our results show the importance of systematic measurements of the electrode impedances before the revision of the programming map. This report also highlights that the evolution of the programming maps is an important factor to be considered in order to determine an adequate calendar fitting of the cochlear implant processor. PMID:23205223

Evolution of SUMO Function and Chain Formation in Insects.

PubMed

Ureña, Enric; Pirone, Lucia; Chafino, Silvia; Pérez, Coralia; Sutherland, James D; Lang, Valérie; Rodriguez, Manuel S; Lopitz-Otsoa, Fernando; Blanco, Francisco J; Barrio, Rosa; Martín, David

2016-02-01

SUMOylation, the covalent binding of Small Ubiquitin-like Modifier (SUMO) to target proteins, is a posttranslational modification that regulates critical cellular processes in eukaryotes. In insects, SUMOylation has been studied in holometabolous species, particularly in the dipteran Drosophila melanogaster, which contains a single SUMO gene (smt3). This has led to the assumption that insects contain a single SUMO gene. However, the analysis of insect genomes shows that basal insects contain two SUMO genes, orthologous to vertebrate SUMO1 and SUMO2/3. Our phylogenetical analysis reveals that the SUMO gene has been duplicated giving rise to SUMO1 and SUMO2/3 families early in Metazoan evolution, and that later in insect evolution the SUMO1 gene has been lost after the Hymenoptera divergence. To explore the consequences of this loss, we have examined the characteristics and different biological functions of the two SUMO genes (SUMO1 and SUMO3) in the hemimetabolous cockroach Blattella germanica and compared them with those of Drosophila Smt3. Here, we show that the metamorphic role of the SUMO genes is evolutionary conserved in insects, although there has been a regulatory switch from SUMO1 in basal insects to SUMO3 in more derived ones. We also show that, unlike vertebrates, insect SUMO3 proteins cannot form polySUMO chains due to the loss of critical lysine residues within the N-terminal part of the protein. Furthermore, the formation of polySUMO chains by expression of ectopic human SUMO3 has a deleterious effect in Drosophila. These findings contribute to the understanding of the functional consequences of the evolution of SUMO genes. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A New Calorimetry Design for Assessing Proposed Technologies in Low Energy Power Production

DTIC Science & Technology

2012-12-01

an induction coil, some connectors, switches, insulation materials, and stainless steel and plastic tubing. Water from a common faucet was used as...5. First version of the calorimeter The water exits the faucet and splits via two switches to two tubing structures, which finally both end in the...3 1. Conservation of Mass ..........................................................................3 2

Time-programmable drug dosing allows the manipulation, suppression and reversal of antibiotic drug resistance in vitro

NASA Astrophysics Data System (ADS)

Yoshida, Mari; Reyes, Sabrina Galiñanes; Tsuda, Soichiro; Horinouchi, Takaaki; Furusawa, Chikara; Cronin, Leroy

2017-06-01

Multi-drug strategies have been attempted to prolong the efficacy of existing antibiotics, but with limited success. Here we show that the evolution of multi-drug-resistant Escherichia coli can be manipulated in vitro by administering pairs of antibiotics and switching between them in ON/OFF manner. Using a multiplexed cell culture system, we find that switching between certain combinations of antibiotics completely suppresses the development of resistance to one of the antibiotics. Using this data, we develop a simple deterministic model, which allows us to predict the fate of multi-drug evolution in this system. Furthermore, we are able to reverse established drug resistance based on the model prediction by modulating antibiotic selection stresses. Our results support the idea that the development of antibiotic resistance may be potentially controlled via continuous switching of drugs.

Synchronization in dynamical networks with unconstrained structure switching

NASA Astrophysics Data System (ADS)

del Genio, Charo I.; Romance, Miguel; Criado, Regino; Boccaletti, Stefano

2015-12-01

We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the structure is determined indirectly from a carefully built transformation of the eigenvector matrices of the coupling Laplacians, which are guaranteed to change smoothly in time. In turn, this allows one to extend the master stability function formalism, which can be used to assess the stability of a synchronized state. This approach is independent from the particular topologies that the network visits, and is not restricted to commuting structures. Also, it does not depend on the time scale of the evolution, which can be faster than, comparable to, or even secular with respect to the dynamics of the units.

Exploiting the hidden symmetry of spinning black holes: conservation laws and numerical tests

NASA Astrophysics Data System (ADS)

Witzany, Vojtěch

2018-01-01

The Kerr black hole is stationary and axisymmetric, which leads to conservation of energy and azimuthal angular momentum along the orbits of free test particles in its vicinity, but also to conservation laws for the evolution of continuum matter fields. However, the Kerr space-time possesses an additional 'hidden symmetry', which exhibits itself in an unexpected conserved quantity along geodesics known as the Carter constant. We investigate the possibility of using this hidden symmetry to obtain conservation laws and other identities that could be used to test astrophysical simulations of the evolution of matter fields near spinning black holes. After deriving such identities, we set up a simple numerical toy model on which we demonstrate how they can detect the violations of evolution equations in a numerical simulation. Even though one of the expressions we derive is in the form of a conservation law, we end up recommending an equivalent but simpler expression that is not in the form of a conservation law for practical implementation.

Space-time evolution of ejected plasma for the triggering of gas switch

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

Liu, Shanhong, E-mail: liushanhong108098@163.com; Liu, Xuandong; Shen, Xi

2016-06-15

Ejected plasma has been widely applied to the discharge process of gas spark switches as a trigger technology, and the development process of ejected plasma has a direct and important effect on the discharge characteristics of gas switches. In this paper, both the injection characteristics and space-time evolution of ejected plasma for the triggering of gas spark switch with different stored energies, pulse polarities, and pressures are studied. The discharge characteristics and breakdown process of a gas switch ignited by ejected plasma under different working coefficients are also discussed briefly. The results show that stored energy has significant influence onmore » the characteristics of ejected plasma. With the increase of stored energy, the propulsion mode of ejected plasma in the axial direction transforms from “plasmoid” to “plasma flow,” and the distribution of the ejected plasma goes through “cloud,” “core-cloud,” and “branch” in sequence. The velocity of ejected plasma under negative pulse polarity is obviously higher than that under positive pulse polarity, especially at the very beginning time. The radial dimensions of ejected plasma under two kinds of pulse polarities follow the similar varying pattern over time, which increase first and then decrease, assuming an inverted “U”-shaped curve. With the increase of pressure, the velocity of ejected plasma significantly decreases and the “branch” channels droop earlier. Applying the ejected plasma to the triggering of a gas switch, the switch can be triggered reliably in a much wide working coefficient range of 10%–90%. With the increase of working coefficient, the breakdown process of the switch translates from slow working mode to fast working mode, and the delay time reduces from tens of μs to hundreds of ns.« less

Evolution of a Fluctuating Population in a Randomly Switching Environment.

PubMed

Wienand, Karl; Frey, Erwin; Mobilia, Mauro

2017-10-13

Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity. Assuming that one strain grows slightly faster than the other, we consider two scenarios-one of pure resource competition, and one in which one strain provides a public good-and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population's fixation properties and size distribution. By analytical means and simulations, we show that these coupled sources of noise can significantly enhance the fixation probability of the slower-growing species. We also show that the population size distribution can be unimodal, bimodal, or multimodal and undergoes noise-induced transitions between these regimes when the rate of switching matches the population's growth rate.

Evolution of a Fluctuating Population in a Randomly Switching Environment

NASA Astrophysics Data System (ADS)

Wienand, Karl; Frey, Erwin; Mobilia, Mauro

2017-10-01

Environment plays a fundamental role in the competition for resources, and hence in the evolution of populations. Here, we study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity. Assuming that one strain grows slightly faster than the other, we consider two scenarios—one of pure resource competition, and one in which one strain provides a public good—and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population's fixation properties and size distribution. By analytical means and simulations, we show that these coupled sources of noise can significantly enhance the fixation probability of the slower-growing species. We also show that the population size distribution can be unimodal, bimodal, or multimodal and undergoes noise-induced transitions between these regimes when the rate of switching matches the population's growth rate.

Convergent, modular expression of ebony and tan in the mimetic wing patterns of Heliconius butterflies.

PubMed

Ferguson, Laura C; Maroja, Luana; Jiggins, Chris D

2011-12-01

The evolution of pigmentation in vertebrates and flies has involved repeated divergence at a small number of genes related to melanin synthesis. Here, we study insect melanin synthesis genes in Heliconius butterflies, a group characterised by its diversity of wing patterns consisting of black (melanin), and yellow and red (ommochrome) pigmented scales. Consistent with their respective biochemical roles in Drosophila melanogaster, ebony is upregulated in non-melanic wing regions destined to be pigmented red whilst tan is upregulated in melanic regions. Wing regions destined to be pigmented yellow, however, are downregulated for both genes. This pattern is conserved across multiple divergent and convergent phenotypes within the Heliconii, suggesting a conserved mechanism for the development of black, red and yellow pattern elements across the genus. Linkage mapping of five melanin biosynthesis genes showed that, in contrast to other organisms, these genes do not control pattern polymorphism. Thus, the pigmentation genes themselves are not the locus of evolutionary change but lie downstream of a wing pattern regulatory factor. The results suggest a modular system in which particular combinations of genes are switched on whenever red, yellow or black pattern elements are favoured by natural selection for diverse and mimetic wing patterns. © Springer-Verlag 2011

Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans

PubMed Central

King, Justin J.; Amemiya, Chris T.; Hsu, Ellen

2017-01-01

ABSTRACT Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties. PMID:28716949

Short template switch events explain mutation clusters in the human genome.

PubMed

Löytynoja, Ari; Goldman, Nick

2017-06-01

Resequencing efforts are uncovering the extent of genetic variation in humans and provide data to study the evolutionary processes shaping our genome. One recurring puzzle in both intra- and inter-species studies is the high frequency of complex mutations comprising multiple nearby base substitutions or insertion-deletions. We devised a generalized mutation model of template switching during replication that extends existing models of genome rearrangement and used this to study the role of template switch events in the origin of short mutation clusters. Applied to the human genome, our model detects thousands of template switch events during the evolution of human and chimp from their common ancestor and hundreds of events between two independently sequenced human genomes. Although many of these are consistent with a template switch mechanism previously proposed for bacteria, our model also identifies new types of mutations that create short inversions, some flanked by paired inverted repeats. The local template switch process can create numerous complex mutation patterns, including hairpin loop structures, and explains multinucleotide mutations and compensatory substitutions without invoking positive selection, speculative mechanisms, or implausible coincidence. Clustered sequence differences are challenging for current mapping and variant calling methods, and we show that many erroneous variant annotations exist in human reference data. Local template switch events may have been neglected as an explanation for complex mutations because of biases in commonly used analyses. Incorporation of our model into reference-based analysis pipelines and comparisons of de novo assembled genomes will lead to improved understanding of genome variation and evolution. © 2017 Löytynoja and Goldman; Published by Cold Spring Harbor Laboratory Press.

Microstructure evolution characteristics induced by oxygen vacancy generation in anatase TiO2 based resistive switching devices

NASA Astrophysics Data System (ADS)

Liu, Chen; Gao, Bin; Huang, Peng; Kang, Jinfeng

2017-03-01

In this work, first principle calculations are employed to study the microstructure characteristics of the anatase TiO2 resistive switching material associated with the generation of oxygen vacancy (V o) based nanofilaments during the switching process. The calculations indicate that both the magnéli phase Ti4O7 and V o-defect phase of anatase TiO2 may be formed with the generation of oxygen vacancies during the forming and SET processes. Based on the calculations, a new physical insight is proposed to clarify the microstructure evolution characteristics of the anatase TiO2 resistive switching material and the correlation with resistive switching behaviors. During the forming or SET process, the anatase TiO2 is first excited to a transition state with the generation of oxygen vacancies, then fully relaxes to a stable V o-defect state. This V o-defect state may either recover to the original state with the recombination of the oxygen vacancies, which causes the reversible resistive switching behavior, or further transform to a much more stable state—the magnéli phase Ti4O7, through a phase transition process with the generation of many more oxygen vacancies. The phase transition from V o- defective anatase phase to magnéli phase Ti4O7 causes the failure of the resistive switching due to the significantly reduced possibility of the reversible phase transition from the magnéli phase to the anatase phase, compared with the possibility of the recombination from the V o-defective anatase.

Inertia in strategy switching transforms the strategy evolution.

PubMed

Zhang, Yanling; Fu, Feng; Wu, Te; Xie, Guangming; Wang, Long

2011-12-01

A recent experimental study [Traulsen et al., Proc. Natl. Acad. Sci. 107, 2962 (2010)] shows that human strategy updating involves both direct payoff comparison and the cost of switching strategy, which is equivalent to inertia. However, it remains largely unclear how such a predisposed inertia affects 2 × 2 games in a well-mixed population of finite size. To address this issue, the "inertia bonus" (strategy switching cost) is added to the learner payoff in the Fermi process. We find how inertia quantitatively shapes the stationary distribution and that stochastic stability under inertia exhibits three regimes, with each covering seven regions in the plane spanned by two inertia parameters. We also obtain the extended "1/3" rule with inertia and the speed criterion with inertia; these two findings hold for a population above two. We illustrate the above results in the framework of the Prisoner's Dilemma game. As inertia varies, two intriguing stationary distributions emerge: the probability of coexistence state is maximized, or those of two full states are simultaneously peaked. Our results may provide useful insights into how the inertia of changing status quo acts on the strategy evolution and, in particular, the evolution of cooperation.

Deconstruction of the Ras switching cycle through saturation mutagenesis

PubMed Central

Bandaru, Pradeep; Shah, Neel H; Bhattacharyya, Moitrayee; Barton, John P; Kondo, Yasushi; Cofsky, Joshua C; Gee, Christine L; Chakraborty, Arup K; Kortemme, Tanja; Ranganathan, Rama; Kuriyan, John

2017-01-01

Ras proteins are highly conserved signaling molecules that exhibit regulated, nucleotide-dependent switching between active and inactive states. The high conservation of Ras requires mechanistic explanation, especially given the general mutational tolerance of proteins. Here, we use deep mutational scanning, biochemical analysis and molecular simulations to understand constraints on Ras sequence. Ras exhibits global sensitivity to mutation when regulated by a GTPase activating protein and a nucleotide exchange factor. Removing the regulators shifts the distribution of mutational effects to be largely neutral, and reveals hotspots of activating mutations in residues that restrain Ras dynamics and promote the inactive state. Evolutionary analysis, combined with structural and mutational data, argue that Ras has co-evolved with its regulators in the vertebrate lineage. Overall, our results show that sequence conservation in Ras depends strongly on the biochemical network in which it operates, providing a framework for understanding the origin of global selection pressures on proteins. DOI: http://dx.doi.org/10.7554/eLife.27810.001 PMID:28686159

Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions

PubMed Central

Kumawat, Amit; Chakrabarty, Suman; Kulkarni, Kiran

2017-01-01

Ras superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of “sub-states” such as state 1 & state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound “OFF” state have very similar conformations, whereas the GTP bound “ON” state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the γ-phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors. PMID:28374773

Nucleotide Dependent Switching in Rho GTPase: Conformational Heterogeneity and Competing Molecular Interactions

NASA Astrophysics Data System (ADS)

Kumawat, Amit; Chakrabarty, Suman; Kulkarni, Kiran

2017-04-01

Ras superfamily of GTPases regulate myriad cellular processes through a conserved nucleotide (GTP/GDP) dependent switching mechanism. Unlike Ras family of GTPases, for the Rho GTPases, there is no clear evidence for the existence of “sub-states” such as state 1 & state 2 in the GTP bound form. To explore the nucleotide dependent conformational space of the Switch I loop and also to look for existence of state 1 like conformations in Rho GTPases, atomistic molecular dynamics and metadynamics simulations on RhoA were performed. These studies demonstrate that both the nucleotide-free state and the GDP bound “OFF” state have very similar conformations, whereas the GTP bound “ON” state has unique conformations with signatures of two intermediate states. The conformational free energy landscape for these systems suggests the presence of multiple intermediate states. Interestingly, the energetic penalty of exposing the non-polar residues in the GTP bound form is counter balanced by the favourable hydrogen bonded interactions between the γ-phosphate group of GTP with the highly conserved Tyr34 and Thr37 residues. These competing molecular interactions lead to a tuneable energy landscape of the Switch I conformation, which can undergo significant changes based on the local environment including changes upon binding to effectors.

Comparative genomics of the mimicry switch in Papilio dardanus.

PubMed

Timmermans, Martijn J T N; Baxter, Simon W; Clark, Rebecca; Heckel, David G; Vogel, Heiko; Collins, Steve; Papanicolaou, Alexie; Fukova, Iva; Joron, Mathieu; Thompson, Martin J; Jiggins, Chris D; ffrench-Constant, Richard H; Vogler, Alfried P

2014-07-22

The African Mocker Swallowtail, Papilio dardanus, is a textbook example in evolutionary genetics. Classical breeding experiments have shown that wing pattern variation in this polymorphic Batesian mimic is determined by the polyallelic H locus that controls a set of distinct mimetic phenotypes. Using bacterial artificial chromosome (BAC) sequencing, recombination analyses and comparative genomics, we show that H co-segregates with an interval of less than 500 kb that is collinear with two other Lepidoptera genomes and contains 24 genes, including the transcription factor genes engrailed (en) and invected (inv). H is located in a region of conserved gene order, which argues against any role for genomic translocations in the evolution of a hypothesized multi-gene mimicry locus. Natural populations of P. dardanus show significant associations of specific morphs with single nucleotide polymorphisms (SNPs), centred on en. In addition, SNP variation in the H region reveals evidence of non-neutral molecular evolution in the en gene alone. We find evidence for a duplication potentially driving physical constraints on recombination in the lamborni morph. Absence of perfect linkage disequilibrium between different genes in the other morphs suggests that H is limited to nucleotide positions in the regulatory and coding regions of en. Our results therefore support the hypothesis that a single gene underlies wing pattern variation in P. dardanus.

Potential role of acetyl-CoA synthetase (acs) and malate dehydrogenase (mae) in the evolution of the acetate switch in Bacteria and Archaea

USGS Publications Warehouse

Barnhart, Elliott P.; McClure, Marcella A.; Johnson, Kiki; Cleveland, Sean; Hunt, Kristopher A.; Fields, Matthew W.

2015-01-01

Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- and ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. These results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.

Potential Role of Acetyl-CoA Synthetase (acs) and Malate Dehydrogenase (mae) in the Evolution of the Acetate Switch in Bacteria and Archaea

DOE PAGES

Barnhart, Elliott P.; McClure, Marcella A.; Johnson, Kiki; ...

2015-08-03

Although many Archaea have AMP-Acs (acetyl-coenzyme A synthetase) and ADP-Acs, the extant methanogenic genus Methanosarcina is the only identified Archaeal genus that can utilize acetate via acetate kinase (Ack) and phosphotransacetylase (Pta). Despite the importance of ack as the potential urkinase in the ASKHA phosphotransferase superfamily, an origin hypothesis does not exist for the acetate kinase in Bacteria, Archaea, or Eukarya. Here we demonstrate that Archaeal AMP-Acs and ADP-Acs contain paralogous ATPase motifs previously identified in Ack, which demonstrate a novel relation between these proteins in Archaea. The identification of ATPase motif conservation and resulting structural features in AMP- andmore » ADP-acetyl-CoA synthetase proteins in this study expand the ASKHA superfamily to include acetyl-CoA synthetase. Additional phylogenetic analysis showed that Pta and MaeB sequences had a common ancestor, and that the Pta lineage within the halophilc archaea was an ancestral lineage. Lastly, these results suggested that divergence of a duplicated maeB within an ancient halophilic, archaeal lineage formed a putative pta ancestor. These results provide a potential scenario for the establishment of the Ack/Pta pathway and provide novel insight into the evolution of acetate metabolism for all three domains of life.« less

SPECIAL ISSUE ON OPTICAL PROCESSING OF INFORMATION: Reversible logic elements as a new field of application of optical solitons

NASA Astrophysics Data System (ADS)

Maimistov, Andrei I.

1995-10-01

An analysis is made of the fundamental concepts of conservative logic. It is shown that the existing optical soliton switches can be converted into logic gates which act as conservative logic elements. A logic device of this type, based on a nonlinear fibre-optic directional coupler, is considered. Polarised solitons are used in this coupler. This use of solitons leads in a natural way to the desirability of developing conservative triple-valued logic.

A Model of Substitution Trajectories in Sequence Space and Long-Term Protein Evolution

PubMed Central

Usmanova, Dinara R.; Ferretti, Luca; Povolotskaya, Inna S.; Vlasov, Peter K.; Kondrashov, Fyodor A.

2015-01-01

The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution. PMID:25415964

Switch I-dependent allosteric signaling in a G-protein chaperone-B12 enzyme complex.

PubMed

Campanello, Gregory C; Lofgren, Michael; Yokom, Adam L; Southworth, Daniel R; Banerjee, Ruma

2017-10-27

G-proteins regulate various processes ranging from DNA replication and protein synthesis to cytoskeletal dynamics and cofactor assimilation and serve as models for uncovering strategies deployed for allosteric signal transduction. MeaB is a multifunctional G-protein chaperone, which gates loading of the active 5'-deoxyadenosylcobalamin cofactor onto methylmalonyl-CoA mutase (MCM) and precludes loading of inactive cofactor forms. MeaB also safeguards MCM, which uses radical chemistry, against inactivation and rescues MCM inactivated during catalytic turnover by using the GTP-binding energy to offload inactive cofactor. The conserved switch I and II signaling motifs used by G-proteins are predicted to mediate allosteric regulation in response to nucleotide binding and hydrolysis in MeaB. Herein, we targeted conserved residues in the MeaB switch I motif to interrogate the function of this loop. Unexpectedly, the switch I mutations had only modest effects on GTP binding and on GTPase activity and did not perturb stability of the MCM-MeaB complex. However, these mutations disrupted multiple MeaB chaperone functions, including cofactor editing, loading, and offloading. Hence, although residues in the switch I motif are not essential for catalysis, they are important for allosteric regulation. Furthermore, single-particle EM analysis revealed, for the first time, the overall architecture of the MCM-MeaB complex, which exhibits a 2:1 stoichiometry. These EM studies also demonstrate that the complex exhibits considerable conformational flexibility. In conclusion, the switch I element does not significantly stabilize the MCM-MeaB complex or influence the affinity of MeaB for GTP but is required for transducing signals between MeaB and MCM. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Switching LPV Control with Double-Layer LPV Model for Aero-Engines

NASA Astrophysics Data System (ADS)

Tang, Lili; Huang, Jinquan; Pan, Muxuan

2017-11-01

To cover the whole range of operating conditions of aero-engine, a double-layer LPV model is built so as to take into account of the variability due to the flight altitude, Mach number and the rotational speed. With this framework, the problem of designing LPV state-feedback robust controller that guarantees desired bounds on both H_∞ and H_2 performances is considered. Besides this, to reduce the conservativeness caused by a single LPV controller of the whole flight envelope and the common Lyapunov function method, a new method is proposed to design a family of LPV switching controllers. The switching LPV controllers can ensure that the closed-loop system remains stable in the sense of Lyapunov under arbitrary switching logic. Meanwhile, the switching LPV controllers can ensure the parameters change smoothly. The validity and performance of the theoretical results are demonstrated through a numerical example.

Reversible switching between pressure-induced amorphization and thermal-driven recrystallization in VO2(B) nanosheets

PubMed Central

Wang, Yonggang; Zhu, Jinlong; Yang, Wenge; Wen, Ting; Pravica, Michael; Liu, Zhenxian; Hou, Mingqiang; Fei, Yingwei; Kang, Lei; Lin, Zheshuai; Jin, Changqing; Zhao, Yusheng

2016-01-01

Pressure-induced amorphization (PIA) and thermal-driven recrystallization have been observed in many crystalline materials. However, controllable switching between PIA and a metastable phase has not been described yet, due to the challenge to establish feasible switching methods to control the pressure and temperature precisely. Here, we demonstrate a reversible switching between PIA and thermally-driven recrystallization of VO2(B) nanosheets. Comprehensive in situ experiments are performed to establish the precise conditions of the reversible phase transformations, which are normally hindered but occur with stimuli beyond the energy barrier. Spectral evidence and theoretical calculations reveal the pressure–structure relationship and the role of flexible VOx polyhedra in the structural switching process. Anomalous resistivity evolution and the participation of spin in the reversible phase transition are observed for the first time. Our findings have significant implications for the design of phase switching devices and the exploration of hidden amorphous materials. PMID:27426219

Reversible switching between pressure-induced amorphization and thermal-driven recrystallization in VO2(B) nanosheets.

PubMed

Wang, Yonggang; Zhu, Jinlong; Yang, Wenge; Wen, Ting; Pravica, Michael; Liu, Zhenxian; Hou, Mingqiang; Fei, Yingwei; Kang, Lei; Lin, Zheshuai; Jin, Changqing; Zhao, Yusheng

2016-07-18

Pressure-induced amorphization (PIA) and thermal-driven recrystallization have been observed in many crystalline materials. However, controllable switching between PIA and a metastable phase has not been described yet, due to the challenge to establish feasible switching methods to control the pressure and temperature precisely. Here, we demonstrate a reversible switching between PIA and thermally-driven recrystallization of VO2(B) nanosheets. Comprehensive in situ experiments are performed to establish the precise conditions of the reversible phase transformations, which are normally hindered but occur with stimuli beyond the energy barrier. Spectral evidence and theoretical calculations reveal the pressure-structure relationship and the role of flexible VOx polyhedra in the structural switching process. Anomalous resistivity evolution and the participation of spin in the reversible phase transition are observed for the first time. Our findings have significant implications for the design of phase switching devices and the exploration of hidden amorphous materials.

Patterns of co-speciation and host switching in primate malaria parasites.

PubMed

Garamszegi, László Zsolt

2009-05-22

The evolutionary history of many parasites is dependent on the evolution of their hosts, leading to an association between host and parasite phylogenies. However, frequent host switches across broad phylogenetic distances may weaken this close evolutionary link, especially when vectors are involved in parasites transmission, as is the case for malaria pathogens. Several studies suggested that the evolution of the primate-infective malaria lineages may be constrained by the phylogenetic relationships of their hosts, and that lateral switches between distantly related hosts may have been occurred. However, no systematic analysis has been quantified the degree of phylogenetic association between primates and their malaria parasites. Here phylogenetic approaches have been used to discriminate statistically between events due to co-divergence, duplication, extinction and host switches that can potentially cause historical association between Plasmodium parasites and their primate hosts. A Bayesian reconstruction of parasite phylogeny based on genetic information for six genes served as basis for the analyses, which could account for uncertainties about the evolutionary hypotheses of malaria parasites. Related lineages of primate-infective Plasmodium tend to infect hosts within the same taxonomic family. Different analyses testing for congruence between host and parasite phylogenies unanimously revealed a significant association between the corresponding evolutionary trees. The most important factor that resulted in this association was host switching, but depending on the parasite phylogeny considered, co-speciation and duplication may have also played some additional role. Sorting seemed to be a relatively infrequent event, and can occur only under extreme co-evolutionary scenarios. The concordance between host and parasite phylogenies is heterogeneous: while the evolution of some malaria pathogens is strongly dependent on the phylogenetic history of their primate hosts, the congruent evolution is less emphasized for other parasite lineages (e.g. for human malaria parasites). Estimation of ancestral states of host use along the phylogenetic tree of parasites revealed that lateral transfers across distantly related hosts were likely to occur in several cases. Parasites cannot infect all available hosts, and they should preferentially infect hosts that provide a similar environment for reproduction. Marginally significant evidence suggested that there might be a consistent variation within host ranges in terms of physiology. The evolution of primate malarias is constrained by the phylogenetic associations of their hosts. Some parasites can preserve a great flexibility to infect hosts across a large phylogenetic distance, thus host switching can be an important factor in mediating host ranges observed in nature. Due to this inherent flexibility and the potential exposure to various vectors, the emergence of new malaria disease in primates including humans cannot be predicted from the phylogeny of parasites.

Monte Carlo simulation of a simple gene network yields new evolutionary insights.

PubMed

Andrecut, M; Cloud, D; Kauffman, S A

2008-02-07

Monte Carlo simulations of a genetic toggle switch show that its behavior can be more complex than analytic models would suggest. We show here that as a result of the interplay between frequent and infrequent reaction events, such a switch can have more stable states than an analytic model would predict, and that the number and character of these states depend to a large extent on the propensity of transcription factors to bind to and dissociate from promoters. The effects of gene duplications differ even more; in analytic models, these seem to result in the disappearance of bi-stability and thus a loss of the switching function, but a Monte Carlo simulation shows that they can result in the appearance of new stable states without the loss of old ones, and thus in an increase of the complexity of the switch's behavior which may facilitate the evolution of new cellular functions. These differences are of interest with respect to the evolution of gene networks, particularly in clonal lines of cancer cells, where the duplication of active genes is an extremely common event, and often seems to result in the appearance of viable new cellular phenotypes.

The evolution of reputation-based partner-switching behaviors with a cost

PubMed Central

Li, Yixiao

2014-01-01

Humans constantly adjust their social relationships and choose new partners of good reputations, thereby promoting the evolution of cooperation. Individuals have to pay a cost to build a reputation, obtain others' information and then make partnership adjustments, yet the conditions under which such costly behaviors are able to evolve remain to be explored. In this model, I assume that individuals have to pay a cost to adjust their partnerships. Furthermore, whether an individual can adjust his partnership based on reputation is determined by his strategic preference, which is updated via coevolution. Using the metaphor of a public goods game where the collective benefit is shared among all members of a group, the coupling dynamics of cooperation and partnership adjustment were numerically simulated. Partner-switching behavior cannot evolve in a public goods game with a low amplification factor. However, such an effect can be exempted by raising the productivity of public goods or the frequency of partnership adjustment. Moreover, costly partner-switching behavior is remarkably promoted by the condition that the mechanism of reputation evaluation considers its prosociality. A mechanism of reputation evaluation that praises both cooperative and partner-switching behaviors allows them to coevolve. PMID:25091006

The evolution of reputation-based partner-switching behaviors with a cost

NASA Astrophysics Data System (ADS)

Li, Yixiao

2014-08-01

Humans constantly adjust their social relationships and choose new partners of good reputations, thereby promoting the evolution of cooperation. Individuals have to pay a cost to build a reputation, obtain others' information and then make partnership adjustments, yet the conditions under which such costly behaviors are able to evolve remain to be explored. In this model, I assume that individuals have to pay a cost to adjust their partnerships. Furthermore, whether an individual can adjust his partnership based on reputation is determined by his strategic preference, which is updated via coevolution. Using the metaphor of a public goods game where the collective benefit is shared among all members of a group, the coupling dynamics of cooperation and partnership adjustment were numerically simulated. Partner-switching behavior cannot evolve in a public goods game with a low amplification factor. However, such an effect can be exempted by raising the productivity of public goods or the frequency of partnership adjustment. Moreover, costly partner-switching behavior is remarkably promoted by the condition that the mechanism of reputation evaluation considers its prosociality. A mechanism of reputation evaluation that praises both cooperative and partner-switching behaviors allows them to coevolve.

Partner switching promotes cooperation among myopic agents on a geographical plane

NASA Astrophysics Data System (ADS)

Li, Yixiao; Min, Yong; Zhu, Xiaodong; Cao, Jie

2013-02-01

We study the coupling dynamics between the evolution of cooperation and the evolution of partnership network on a geographical plane. While agents play networked prisoner’s dilemma games, they can dynamically adjust their partnerships based on local information about reputation. We incorporate geographical features into the process of the agent’s partner switching and investigate the corresponding effects. At each time step of the coevolution, a random agent can either update his strategy by imitation or adjust his partnership by switching from the lowest reputation partner to the highest reputation one among his neighbors. We differentiate two types of neighbors: geographical neighbors (i.e., the set of agents who are close to the focal agent in terms of geographical distance) and connectivity neighbors (i.e., the set of agents who are close to the focal agent in the partnership network in terms of geodesic distance). We find that switching to either geographical neighbors or connectivity neighbors enhances cooperation greatly in a wide parameter range. Cooperation can be favored in a much stricter condition when agents switch to connectivity neighbors more frequently. However, an increasing tendency of reconnecting to geographical neighbors shortens the geographical distance between a pair of partners on average. When agents consider the cost of geographical distance in adjusting the partnership, they are prone to reconnect to geographical neighbors.

Genomics of sex determination.

PubMed

Zhang, Jisen; Boualem, Adnane; Bendahmane, Abdelhafid; Ming, Ray

2014-04-01

Sex determination is a major switch in the evolutionary history of angiosperm, resulting 11% monoecious and dioecious species. The genomic sequences of papaya sex chromosomes unveiled the molecular basis of recombination suppression in the sex determination region, and candidate genes for sex determination. Identification and analyses of sex determination genes in cucurbits and maize demonstrated conservation of sex determination mechanism in one lineage and divergence between the two systems. Epigenetic control and hormonal influence of sex determination were elucidated in both plants and animals. Intensive investigation of potential sex determination genes in model species will improve our understanding of sex determination gene network. Such network will in turn accelerate the identification of sex determination genes in dioecious species with sex chromosomes, which are burdensome due to no recombination in sex determining regions. The sex determination genes in dioecious species are crucial for understanding the origin of dioecy and sex chromosomes, particularly in their early stage of evolution. Copyright © 2014 Elsevier Ltd. All rights reserved.

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence

PubMed Central

Zhang, Linlin

2017-01-01

The optix gene has been implicated in butterfly wing pattern adaptation by genetic association, mapping, and expression studies. The actual developmental function of this gene has remained unclear, however. Here we used CRISPR/Cas9 genome editing to show that optix plays a fundamental role in nymphalid butterfly wing pattern development, where it is required for determination of all chromatic coloration. optix knockouts in four species show complete replacement of color pigments with melanins, with corresponding changes in pigment-related gene expression, resulting in black and gray butterflies. We also show that optix simultaneously acts as a switch gene for blue structural iridescence in some butterflies, demonstrating simple regulatory coordination of structural and pigmentary coloration. Remarkably, these optix knockouts phenocopy the recurring “black and blue” wing pattern archetype that has arisen on many independent occasions in butterflies. Here we demonstrate a simple genetic basis for structural coloration, and show that optix plays a deeply conserved role in butterfly wing pattern development. PMID:28923944

Single master regulatory gene coordinates the evolution and development of butterfly color and iridescence.

PubMed

Zhang, Linlin; Mazo-Vargas, Anyi; Reed, Robert D

2017-10-03

The optix gene has been implicated in butterfly wing pattern adaptation by genetic association, mapping, and expression studies. The actual developmental function of this gene has remained unclear, however. Here we used CRISPR/Cas9 genome editing to show that optix plays a fundamental role in nymphalid butterfly wing pattern development, where it is required for determination of all chromatic coloration. optix knockouts in four species show complete replacement of color pigments with melanins, with corresponding changes in pigment-related gene expression, resulting in black and gray butterflies. We also show that optix simultaneously acts as a switch gene for blue structural iridescence in some butterflies, demonstrating simple regulatory coordination of structural and pigmentary coloration. Remarkably, these optix knockouts phenocopy the recurring "black and blue" wing pattern archetype that has arisen on many independent occasions in butterflies. Here we demonstrate a simple genetic basis for structural coloration, and show that optix plays a deeply conserved role in butterfly wing pattern development.

Flux quench in a system of interacting spinless fermions in one dimension

NASA Astrophysics Data System (ADS)

Nakagawa, Yuya O.; Misguich, Grégoire; Oshikawa, Masaki

2016-05-01

We study a quantum quench in a one-dimensional spinless fermion model (equivalent to the XXZ spin chain), where a magnetic flux is suddenly switched off. This quench is equivalent to imposing a pulse of electric field and therefore generates an initial particle current. This current is not a conserved quantity in the presence of a lattice and interactions, and we investigate numerically its time evolution after the quench, using the infinite time-evolving block decimation method. For repulsive interactions or large initial flux, we find oscillations that are governed by excitations deep inside the Fermi sea. At long times we observe that the current remains nonvanishing in the gapless cases, whereas it decays to zero in the gapped cases. Although the linear response theory (valid for a weak flux) predicts the same long-time limit of the current for repulsive and attractive interactions (relation with the zero-temperature Drude weight), larger nonlinearities are observed in the case of repulsive interactions compared with that of the attractive case.

Evolution and Conservation of Plant NLR Functions

PubMed Central

Jacob, Florence; Vernaldi, Saskia; Maekawa, Takaki

2013-01-01

In plants and animals, nucleotide-binding domain and leucine-rich repeats (NLR)-containing proteins play pivotal roles in innate immunity. Despite their similar biological functions and protein architecture, comparative genome-wide analyses of NLRs and genes encoding NLR-like proteins suggest that plant and animal NLRs have independently arisen in evolution. Furthermore, the demonstration of interfamily transfer of plant NLR functions from their original species to phylogenetically distant species implies evolutionary conservation of the underlying immune principle across plant taxonomy. In this review we discuss plant NLR evolution and summarize recent insights into plant NLR-signaling mechanisms, which might constitute evolutionarily conserved NLR-mediated immune mechanisms. PMID:24093022

SWITCH user's manual

NASA Technical Reports Server (NTRS)

1987-01-01

The planning program, SWITCH, and its surrounding changed-goal-replanning program, Runaround, are described. The evolution of SWITCH and Runaround from an earlier planner, DEVISER, is recounted. SWITCH's plan representation, and its process of building a plan by backward chaining with strict chronological backtracking, are described. A guide for writing knowledge base files is provided, as are narrative guides for installing the program, running it, and interacting with it while it is running. Some utility functions are documented. For the sake of completeness, a narrative guide to the experimental discrepancy-replanning feature is provided. Appendices contain knowledge base files for a blocksworld domain, and a DRIBBLE file illustrating the output from, and user interaction with, the program in that domain.

Switching the mode of metabolism in the yeast Saccharomyces cerevisiae

PubMed Central

Otterstedt, Karin; Larsson, Christer; Bill, Roslyn M; Ståhlberg, Anders; Boles, Eckhard; Hohmann, Stefan; Gustafsson, Lena

2004-01-01

The biochemistry of most metabolic pathways is conserved from bacteria to humans, although the control mechanisms are adapted to the needs of each cell type. Oxygen depletion commonly controls the switch from respiration to fermentation. However, Saccharomyces cerevisiae also controls that switch in response to the external glucose level. We have generated an S. cerevisiae strain in which glucose uptake is dependent on a chimeric hexose transporter mediating reduced sugar uptake. This strain shows a fully respiratory metabolism also at high glucose levels as seen for aerobic organisms, and switches to fermentation only when oxygen is lacking. These observations illustrate that manipulating a single step can alter the mode of metabolism. The novel yeast strain is an excellent tool to study the mechanisms underlying glucose-induced signal transduction. PMID:15071495

LMI-based adaptive reliable H∞ static output feedback control against switched actuator failures

NASA Astrophysics Data System (ADS)

An, Liwei; Zhai, Ding; Dong, Jiuxiang; Zhang, Qingling

2017-08-01

This paper investigates the H∞ static output feedback (SOF) control problem for switched linear system under arbitrary switching, where the actuator failure models are considered to depend on switching signal. An active reliable control scheme is developed by combination of linear matrix inequality (LMI) method and adaptive mechanism. First, by exploiting variable substitution and Finsler's lemma, new LMI conditions are given for designing the SOF controller. Compared to the existing results, the proposed design conditions are more relaxed and can be applied to a wider class of no-fault linear systems. Then a novel adaptive mechanism is established, where the inverses of switched failure scaling factors are estimated online to accommodate the effects of actuator failure on systems. Two main difficulties arise: first is how to design the switched adaptive laws to prevent the missing of estimating information due to switching; second is how to construct a common Lyapunov function based on a switched estimate error term. It is shown that the new method can give less conservative results than that for the traditional control design with fixed gain matrices. Finally, simulation results on the HiMAT aircraft are given to show the effectiveness of the proposed approaches.

Evolution of households’ responses to the groundwater arsenic crisis in Bangladesh: information on environmental health risks can have increasing behavioral impact over time

PubMed Central

Balasubramanya, Soumya; Pfaff, Alexander; Bennear, Lori; Tarozzi, Alessandro; Ahmed, Kazi Matin; Schoenfeld, Amy; van Geen, Alexander

2014-01-01

A national campaign of well testing through 2003 enabled households in rural Bangladesh to switch, at least for drinking, from high-arsenic wells to neighboring lower-arsenic wells. We study the well-switching dynamics over time by re-interviewing, in 2008, a randomly selected subset of households in the Araihazar region who had been interviewed in 2005. Contrary to concerns that the impact of arsenic information on switching behavior would erode over time, we find that not only was 2003–2005 switching highly persistent but also new switching by 2008 doubled the share of households at unsafe wells who had switched. The passage of time also had a cost: 22% of households did not recall test results by 2008. The loss of arsenic knowledge led to staying at unsafe wells and switching from safe wells. Our results support ongoing well testing for arsenic to reinforce this beneficial information. PMID:25383015

Influence of switches and crossings on wheel profile evolution in freight vehicles

NASA Astrophysics Data System (ADS)

Casanueva, Carlos; Doulgerakis, Emmanouil; Jönsson, Per-Anders; Stichel, Sebastian

2014-05-01

Wheel reprofiling costs for freight vehicles are a major issue in Sweden, reducing the profitability of freight traffic operations and therefore hindering the modal shift needed for achieving reduced emissions. In order to understand the damage modes in freight vehicles, uniform wear prediction with Archard's wear law has been studied in a two-axle timber transport wagon, and simulation results have been compared to measurements. Challenges of wheel wear prediction in freight wagons are discussed, including the influence of block brakes and switches and crossings. The latter have a major influence on the profile evolution of this case study, so specific simulations are performed and a thorough discussion is carried out.

Evolution of Signaling in a Multi-Robot System: Categorization and Communication

NASA Astrophysics Data System (ADS)

Ampatzis, Christos; Tuci, Elio; Trianni, Vito; Dorigo, Marco

We use Evolutionary Robotics to design robot controllers in which decision-making mechanisms to switch from solitary to social behavior are integrated with the mechanisms that underpin the sensory-motor repertoire of the robots. In particular, we study the evolution of behavioral and communicative skills in a categorization task. The individual decision-making structures are based on the integration over time of sensory information. The mechanisms for switching from solitary to social behavior and the ways in which the robots can affect each other's behavior are not predetermined by the experimenter, but are aspects of our model designed by artificial evolution. Our results show that evolved robots manage to cooperate and collectively discriminate between different environments by developing a simple communication protocol based on sound signaling. Communication emerges in the absence of explicit selective pressure coded in the fitness function. The evolution of communication is neither trivial nor obvious; for a meaningful signaling system to evolve, evolution must produce both appropriate signals and appropriate reactions to signals. The use of communication proves to be adaptive for the group, even if, in principle, non-cooperating robots can be equally successful with cooperating robots.

Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks

PubMed Central

Pechmann, Sebastian; Frydman, Judith

2014-01-01

Evolution is driven by mutations, which lead to new protein functions but come at a cost to protein stability. Non-conservative substitutions are of interest in this regard because they may most profoundly affect both function and stability. Accordingly, organisms must balance the benefit of accepting advantageous substitutions with the possible cost of deleterious effects on protein folding and stability. We here examine factors that systematically promote non-conservative mutations at the proteome level. Intrinsically disordered regions in proteins play pivotal roles in protein interactions, but many questions regarding their evolution remain unanswered. Similarly, whether and how molecular chaperones, which have been shown to buffer destabilizing mutations in individual proteins, generally provide robustness during proteome evolution remains unclear. To this end, we introduce an evolutionary parameter λ that directly estimates the rate of non-conservative substitutions. Our analysis of λ in Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens sequences reveals how co- and post-translationally acting chaperones differentially promote non-conservative substitutions in their substrates, likely through buffering of their destabilizing effects. We further find that λ serves well to quantify the evolution of intrinsically disordered proteins even though the unstructured, thus generally variable regions in proteins are often flanked by very conserved sequences. Crucially, we show that both intrinsically disordered proteins and highly re-wired proteins in protein interaction networks, which have evolved new interactions and functions, exhibit a higher λ at the expense of enhanced chaperone assistance. Our findings thus highlight an intricate interplay of molecular chaperones and protein disorder in the evolvability of protein networks. Our results illuminate the role of chaperones in enabling protein evolution, and underline the importance of the cellular context and integrated approaches for understanding proteome evolution. We feel that the development of λ may be a valuable addition to the toolbox applied to understand the molecular basis of evolution. PMID:24968255

Mosaic Structure and Molecular Evolution of the Leukotoxin Operon (lktCABD) in Mannheimia (Pasteurella) haemolytica, Mannheimia glucosida, and Pasteurella trehalosi

PubMed Central

Davies, Robert L.; Campbell, Susan; Whittam, Thomas S.

2002-01-01

The mosaic structure and molecular evolution of the leukotoxin operon (lktCABD) was investigated by nucleotide sequence comparison of the lktC, lktB, and lktD genes in 23 Mannheimia (Pasteurella) haemolytica, 6 Mannheimia glucosida, and 4 Pasteurella trehalosi strains. Sequence variation in the lktA gene has been described previously (R. L. Davies et al., J. Bacteriol. 183:1394–1404, 2001). The leukotoxin operon of M. haemolytica has a complex mosaic structure and has been derived by extensive inter- and intraspecies horizontal DNA transfer and intragenic recombination events. However, the pattern of recombination varies throughout the operon and among the different evolutionary lineages of M. haemolytica. The lktA and lktB genes have the most complex mosaic structures with segments derived from up to four different sources, including M. glucosida and P. trehalosi. In contrast, the lktD gene is highly conserved in M. haemolytica. The lktC, lktA, and lktB genes of strains representing the major ovine lineages contain recombinant segments derived from bovine or bovine-like serotype A2 strains. These findings support the previous conclusion that host switching of bovine A2 strains from cattle to sheep has played a major role in the evolution of the leukotoxin operon in ovine strains of M. haemolytica. Homologous segments of donor and recipient alleles are identical, or nearly identical, indicating that the recombinational exchanges occurred relatively recent in evolutionary terms. The 5′ and 3′ ends of the operon are highly conserved in M. haemolytica, which suggests that multiple horizontal exchanges of the complete operon have occurred by a common mechanism such as transduction. Although the lktA and lktB genes both have complex mosaic structures and high nucleotide substitution rates, the amino acid diversity of LktB is significantly lower than that of LktA due to a higher degree of evolutionary constraint against amino acid replacement. The recombinational exchanges within the leukotoxin operon have had greatest effect on LktA and probably provide an adaptive advantage against the host antibody response by generating novel antigenic variation at surface-exposed sites. PMID:11741868

CryoSat Ice Processor: Known Processor Anomalies and Potential Future Product Evolutions

NASA Astrophysics Data System (ADS)

Mannan, R.; Webb, E.; Hall, A.; Bouffard, J.; Femenias, P.; Parrinello, T.; Bouffard, J.; Brockley, D.; Baker, S.; Scagliola, M.; Urien, S.

2016-08-01

Launched in 2010, CryoSat was designed to measure changes in polar sea ice thickness and ice sheet elevation. To reach this goal the CryoSat data products have to meet the highest performance standards and are subjected to a continual cycle of improvement achieved through upgrades to the Instrument Processing Facilities (IPFs). Following the switch to the Baseline-C Ice IPFs there are already planned evolutions for the next processing Baseline, based on recommendations from the Scientific Community, Expert Support Laboratory (ESL), Quality Control (QC) Centres and Validation campaigns. Some of the proposed evolutions, to be discussed with the scientific community, include the activation of freeboard computation in SARin mode, the potential operation of SARin mode over flat-to-slope transitory land ice areas, further tuning of the land ice retracker, the switch to NetCDF format and the resolution of anomalies arising in Baseline-C. This paper describes some of the anomalies known to affect Baseline-C in addition to potential evolutions that are planned and foreseen for Baseline-D.

An Evolutionary Perspective on Yeast Mating-Type Switching

PubMed Central

Hanson, Sara J.; Wolfe, Kenneth H.

2017-01-01

Cell differentiation in yeast species is controlled by a reversible, programmed DNA-rearrangement process called mating-type switching. Switching is achieved by two functionally similar but structurally distinct processes in the budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. In both species, haploid cells possess one active and two silent copies of the mating-type locus (a three-cassette structure), the active locus is cleaved, and synthesis-dependent strand annealing is used to replace it with a copy of a silent locus encoding the opposite mating-type information. Each species has its own set of components responsible for regulating these processes. In this review, we summarize knowledge about the function and evolution of mating-type switching components in these species, including mechanisms of heterochromatin formation, MAT locus cleavage, donor bias, lineage tracking, and environmental regulation of switching. We compare switching in these well-studied species to others such as Kluyveromyces lactis and the methylotrophic yeasts Ogataea polymorpha and Komagataella phaffii. We focus on some key questions: Which cells switch mating type? What molecular apparatus is required for switching? Where did it come from? And what is the evolutionary purpose of switching? PMID:28476860

Comparative developmental analysis of Drosophila and Tribolium reveals conserved and diverged roles of abrupt in insect wing evolution.

PubMed

Ravisankar, Padmapriyadarshini; Lai, Yi-Ting; Sambrani, Nagraj; Tomoyasu, Yoshinori

2016-01-15

Morphological innovation is a fundamental process in evolution, yet its molecular basis is still elusive. Acquisition of elytra, highly modified beetle forewings, is an important innovation that has driven the successful radiation of beetles. Our RNAi screening for candidate genes has identified abrupt (ab) as a potential key player in elytron evolution. In this study, we performed a series of RNA interference (RNAi) experiments in both Tribolium and Drosophila to understand the contributions of ab to the evolution of beetle elytra. We found that (i) ab is essential for proper wing vein patterning both in Tribolium and Drosophila, (ii) ab has gained a novel function in determining the unique elytron shape in the beetle lineage, (iii) unlike Hippo and Insulin, other shape determining pathways, the shape determining function of ab is specific to the elytron and not required in the hindwing, (iv) ab has a previously undescribed role in the Notch signal-associated wing formation processes, which appears to be conserved between beetles and flies. These data suggest that ab has gained a new function during elytron evolution in beetles without compromising the conserved wing-related functions. Gaining a new function without losing evolutionarily conserved functions may be a key theme in the evolution of morphologically novel structures. Copyright © 2015 Elsevier Inc. All rights reserved.

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.

PubMed

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A; McHardy, Alice C; Embley, T Martin; Prosser, James I; Macqueen, Daniel J

2015-07-28

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400-700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum.

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

PubMed Central

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A.; McHardy, Alice C.; Embley, T. Martin; Prosser, James I.; Macqueen, Daniel J.

2015-01-01

The Thaumarchaeota is an abundant and ubiquitous phylum of archaea that plays a major role in the global nitrogen cycle. Previous analyses of the ammonia monooxygenase gene amoA suggest that pH is an important driver of niche specialization in these organisms. Although the ecological distribution and ecophysiology of extant Thaumarchaeota have been studied extensively, the evolutionary rise of these prokaryotes to ecological dominance in many habitats remains poorly understood. To characterize processes leading to their diversification, we investigated coevolutionary relationships between amoA, a conserved marker gene for Thaumarchaeota, and soil characteristics, by using deep sequencing and comprehensive environmental data in Bayesian comparative phylogenetics. These analyses reveal a large and rapid increase in diversification rates during early thaumarchaeotal evolution; this finding was verified by independent analyses of 16S rRNA. Our findings suggest that the entire Thaumarchaeota diversification regime was strikingly coupled to pH adaptation but less clearly correlated with several other tested environmental factors. Interestingly, the early radiation event coincided with a period of pH adaptation that enabled the terrestrial Thaumarchaeota ancestor to initially move from neutral to more acidic and alkaline conditions. In contrast to classic evolutionary models, whereby niches become rapidly filled after adaptive radiation, global diversification rates have remained stably high in Thaumarchaeota during the past 400–700 million years, suggesting an ongoing high rate of niche formation or switching for these microbes. Our study highlights the enduring importance of environmental adaptation during thaumarchaeotal evolution and, to our knowledge, is the first to link evolutionary diversification to environmental adaptation in a prokaryotic phylum. PMID:26170282

Identification of a Transcriptionally Forward α Gene and Two υ Genes within the Pigeon (Columba livia) IgH Gene Locus.

PubMed

Huang, Tian; Wang, Xifeng; Si, Run; Chi, Hao; Han, Binyue; Han, Haitang; Cao, Gengsheng; Zhao, Yaofeng

2018-06-01

Compared with mammals, the bird Ig genetic system relies on gene conversion to create an Ab repertoire, with inversion of the IgA-encoding gene and very few cases of Ig subclass diversification. Although gene conversion has been studied intensively, class-switch recombination, a mechanism by which the IgH C region is exchanged, has rarely been investigated in birds. In this study, based on the published genome of pigeon ( Columba livia ) and high-throughput transcriptome sequencing of immune-related tissues, we identified a transcriptionally forward α gene and found that the pigeon IgH gene locus is arranged as μ-α-υ1-υ2. In this article, we show that both DNA deletion and inversion may result from IgA and IgY class switching, and similar junction patterns were observed for both types of class-switch recombination. We also identified two subclasses of υ genes in pigeon, which share low sequence identity. Phylogenetic analysis suggests that divergence of the two pigeon υ genes occurred during the early stage of bird evolution. The data obtained in this study provide new insight into class-switch recombination and Ig gene evolution in birds. Copyright © 2018 by The American Association of Immunologists, Inc.

The structural coupling between ATPase activation and recovery stroke in the myosin II motor

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

Koppole, Sampath; Smith, Jeremy C; Fischer, S.

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates {approx} 65{sup o}. Simultaneous with this 'recovery stroke', myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 {angstrom}-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transitionmore » at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.« less

The structural coupling between ATPase activation and recovery stroke in the myosin II motor.

PubMed

Koppole, Sampath; Smith, Jeremy C; Fischer, Stefan

2007-07-01

Before the myosin motor head can perform the next power stroke, it undergoes a large conformational transition in which the converter domain, bearing the lever arm, rotates approximately 65 degrees . Simultaneous with this "recovery stroke," myosin activates its ATPase function by closing the Switch-2 loop over the bound ATP. This coupling between the motions of the converter domain and of the 40 A-distant Switch-2 loop is essential to avoid unproductive ATP hydrolysis. The coupling mechanism is determined here by finding a series of optimized intermediates between crystallographic end structures of the recovery stroke (Dictyostelium discoideum), yielding movies of the transition at atomic detail. The successive formation of two hydrogen bonds by the Switch-2 loop is correlated with the successive see-saw motions of the relay and SH1 helices that hold the converter domain. SH1 helix and Switch-2 loop communicate via a highly conserved loop that wedges against the SH1-helix upon Switch-2 closing.

The beginning of kinesin's force-generating cycle visualized at 9-Å resolution

PubMed Central

Sindelar, Charles V.; Downing, Kenneth H.

2007-01-01

We have used cryo-electron microscopy of kinesin-decorated microtubules to resolve the structure of the motor protein kinesin's crucial nucleotide response elements, switch I and the switch II helix, in kinesin's poorly understood nucleotide-free state. Both of the switch elements undergo conformational change relative to the microtubule-free state. The changes in switch I suggest a role for it in “ejecting” adenosine diphosphate when kinesin initially binds to the microtubule. The switch II helix has an N-terminal extension, apparently stabilized by conserved microtubule contacts, implying a microtubule activation mechanism that could convey the state of the bound nucleotide to kinesin's putative force-delivering element (the “neck linker”). In deriving this structure, we have adapted an image-processing technique, single-particle reconstruction, for analyzing decorated microtubules. The resulting reconstruction visualizes the asymmetric seam present in native, 13-protofilament microtubules, and this method will provide an avenue to higher-resolution characterization of a variety of microtubule- binding proteins, as well as the microtubule itself. PMID:17470637

Alpha3, a transposable element that promotes host sexual reproduction.

PubMed

Barsoum, Emad; Martinez, Paula; Aström, Stefan U

2010-01-01

Theoretical models predict that selfish DNA elements require host sex to persist in a population. Therefore, a transposon that induces sex would strongly favor its own spread. We demonstrate that a protein homologous to transposases, called alpha3, was essential for mating type switch in Kluyveromyces lactis. Mutational analysis showed that amino acids conserved among transposases were essential for its function. During switching, sequences in the 5' and 3' flanking regions of the alpha3 gene were joined, forming a DNA circle, showing that alpha3 mobilized from the genome. The sequences encompassing the alpha3 gene circle junctions in the mating type alpha (MATalpha) locus were essential for switching from MATalpha to MATa, suggesting that alpha3 mobilization was a coupled event. Switching also required a DNA-binding protein, Mating type switch 1 (Mts1), whose binding sites in MATalpha were important. Expression of Mts1 was repressed in MATa/MATalpha diploids and by nutrients, limiting switching to haploids in low-nutrient conditions. A hairpin-capped DNA double-strand break (DSB) was observed in the MATa locus in mre11 mutant strains, indicating that mating type switch was induced by MAT-specific DSBs. This study provides empirical evidence for selfish DNA promoting host sexual reproduction by mediating mating type switch.

Nanoscopic studies of domain structure dynamics in ferroelectric La:HfO2 capacitors

NASA Astrophysics Data System (ADS)

Buragohain, P.; Richter, C.; Schenk, T.; Lu, H.; Mikolajick, T.; Schroeder, U.; Gruverman, A.

2018-05-01

Visualization of domain structure evolution under an electrical bias has been carried out in ferroelectric La:HfO2 capacitors by a combination of Piezoresponse Force Microscopy (PFM) and pulse switching techniques to study the nanoscopic mechanism of polarization reversal and the wake-up process. It has been directly shown that the main mechanism behind the transformation of the polarization hysteretic behavior and an increase in the remanent polarization value upon the alternating current cycling is electrically induced domain de-pinning. PFM imaging and local spectroscopy revealed asymmetric switching in the La:HfO2 capacitors due to a significant imprint likely caused by the different boundary conditions at the top and bottom interfaces. Domain switching kinetics can be well-described by the nucleation limited switching model characterized by a broad distribution of the local switching times. It has been found that the domain velocity varies significantly throughout the switching process indicating strong interaction with structural defects.

Reversible switching between pressure-induced amorphization and thermal-driven recrystallization in VO2(B) nanosheets

DOE PAGES

Wang, Yonggang; Zhu, Jinlong; Yang, Wenge; ...

2016-07-18

Pressure-induced amorphization (PIA) and thermal-driven recrystallization have been observed in many crystalline materials. However, controllable switching between PIA and a metastable phase has not been described yet, due to the challenge to establish feasible switching methods to control the pressure and temperature precisely. Here, we demonstrate a reversible switching between PIA and thermally-driven recrystallization of VO 2(B) nanosheets. Comprehensive in situ experiments are performed to establish the precise conditions of the reversible phase transformations, which are normally hindered but occur with stimuli beyond the energy barrier. Spectral evidence and theoretical calculations reveal the pressure–structure relationship and the role of flexiblemore » VO x polyhedra in the structural switching process. Anomalous resistivity evolution and the participation of spin in the reversible phase transition are observed for the first time. Our findings have significant implications for the design of phase switching devices and the exploration of hidden amorphous materials.« less

Conservative ecological and evolutionary patterns in liverwort–fungal symbioses

PubMed Central

Bidartondo, Martin I.; Duckett, Jeffrey G.

2010-01-01

Liverworts, the most ancient group of land plants, form a range of intimate associations with fungi that may be analogous to the mycorrhizas of vascular plants. Most thalloid liverworts contain arbuscular mycorrhizal glomeromycete fungi similar to most vascular plants. In contrast, a range of leafy liverwort genera and one simple thalloid liverwort family (the Aneuraceae) have switched to basidiomycete fungi. These liverwort switches away from glomeromycete fungi may be expected to parallel switches undergone by vascular plants that target diverse lineages of basidiomycete fungi to form ectomycorrhizas. To test this hypothesis, we used a cultivation-independent approach to examine the basidiomycete fungi associated with liverworts in varied worldwide locations by generating fungal DNA sequence data from over 200 field collections of over 30 species. Here we show that eight leafy liverwort genera predominantly and consistently associate with members of the Sebacina vermifera species complex and that Aneuraceae thalloid liverworts associate nearly exclusively with Tulasnella species. Furthermore, within sites where multiple liverwort species co-occur, they almost never share the same fungi. Our analyses reveal a strikingly conservative ecological and evolutionary pattern of liverwort symbioses with basidiomycete fungi that is unlike that of vascular plant mycorrhizas. PMID:19812075

A least-squares parameter estimation algorithm for switched hammerstein systems with applications to the VOR

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.; Kearney, Robert E.; Galiana, Henrietta L.

2005-01-01

A "Multimode" or "switched" system is one that switches between various modes of operation. When a switch occurs from one mode to another, a discontinuity may result followed by a smooth evolution under the new regime. Characterizing the switching behavior of these systems is not well understood and, therefore, identification of multimode systems typically requires a preprocessing step to classify the observed data according to a mode of operation. A further consequence of the switched nature of these systems is that data available for parameter estimation of any subsystem may be inadequate. As such, identification and parameter estimation of multimode systems remains an unresolved problem. In this paper, we 1) show that the NARMAX model structure can be used to describe the impulsive-smooth behavior of switched systems, 2) propose a modified extended least squares (MELS) algorithm to estimate the coefficients of such models, and 3) demonstrate its applicability to simulated and real data from the Vestibulo-Ocular Reflex (VOR). The approach will also allow the identification of other nonlinear bio-systems, suspected of containing "hard" nonlinearities.

How MIKC* MADS-box genes originated and evidence for their conserved function throughout the evolution of vascular plant gametophytes.

PubMed

Kwantes, Michiel; Liebsch, Daniela; Verelst, Wim

2012-01-01

Land plants have a remarkable life cycle that alternates between a diploid sporophytic and a haploid gametophytic generation, both of which are multicellular and changed drastically during evolution. Classical MIKC MADS-domain (MIKCC) transcription factors are famous for their role in sporophytic development and are considered crucial for its evolution. About the regulation of gametophyte development, in contrast, little is known. Recent evidence indicated that the closely related MIKC* MADS-domain proteins are important for the functioning of the Arabidopsis thaliana male gametophyte (pollen). Furthermore, also in bryophytes, several MIKC* genes are expressed in the haploid generation. Therefore, that MIKC* genes have a similar role in the evolution of the gametophytic phase as MIKCC genes have in the sporophyte is a tempting hypothesis. To get a comprehensive view of the involvement of MIKC* genes in gametophyte evolution, we isolated them from a broad variety of vascular plants, including the lycophyte Selaginella moellendorffii, the fern Ceratopteris richardii, and representatives of several flowering plant lineages. Phylogenetic analysis revealed an extraordinary conservation not found in MIKCC genes. Moreover, expression and interaction studies suggest that a conserved and characteristic network operates in the gametophytes of all tested model organisms. Additionally, we found that MIKC* genes probably evolved from an ancestral MIKCC-like gene by a duplication in the Keratin-like region. We propose that this event facilitated the independent evolution of MIKC* and MIKCC protein networks and argue that whereas MIKCC genes diversified and attained new functions, MIKC* genes retained a conserved role in the gametophyte during land plant evolution.

Stepwise artificial evolution of a plant disease resistance gene.

PubMed

Harris, C Jake; Slootweg, Erik J; Goverse, Aska; Baulcombe, David C

2013-12-24

Genes encoding plant nucleotide-binding leucine-rich repeat (NB-LRR) proteins confer dominant resistance to diverse pathogens. The wild-type potato NB-LRR protein Rx confers resistance against a single strain of potato virus X (PVX), whereas LRR mutants protect against both a second PVX strain and the distantly related poplar mosaic virus (PopMV). In one of the Rx mutants there was a cost to the broad-spectrum resistance because the response to PopMV was transformed from a mild disease on plants carrying wild-type Rx to a trailing necrosis that killed the plant. To explore the use of secondary mutagenesis to eliminate this cost of broad-spectrum resistance, we performed random mutagenesis of the N-terminal domains of this broad-recognition version of Rx and isolated four mutants with a stronger response against the PopMV coat protein due to enhanced activation sensitivity. These mutations are located close to the nucleotide-binding pocket, a highly conserved structure that likely controls the "switch" between active and inactive NB-LRR conformations. Stable transgenic plants expressing one of these versions of Rx are resistant to the strains of PVX and the PopMV that previously caused trailing necrosis. We conclude from this work that artificial evolution of NB-LRR disease resistance genes in crops can be enhanced by modification of both activation and recognition phases, to both accentuate the positive and eliminate the negative aspects of disease resistance.

Recent Advance on Mesoporous Silica Nanoparticles-Based Controlled Release System: Intelligent Switches Open up New Horizon

PubMed Central

Sun, Ruijuan; Wang, Wenqian; Wen, Yongqiang; Zhang, Xueji

2015-01-01

Mesoporous silica nanoparticle (MSN)-based intelligent transport systems have attracted many researchers’ attention due to the characteristics of uniform pore and particle size distribution, good biocompatibility, high surface area, and versatile functionalization, which have led to their widespread application in diverse areas. In the past two decades, many kinds of smart controlled release systems were prepared with the development of brilliant nano-switches. This article reviews and discusses the advantages of MSN-based controlled release systems. Meanwhile, the switching mechanisms based on different types of stimulus response are systematically analyzed and summarized. Additionally, the application fields of these devices are further discussed. Obviously, the recent evolution of smart nano-switches promoted the upgrading of the controlled release system from the simple “separated” switch to the reversible, multifunctional, complicated logical switches and selective switches. Especially the free-blockage switches, which are based on hydrophobic/hydrophilic conversion, have been proposed and designed in the last two years. The prospects and directions of this research field are also briefly addressed, which could be better used to promote the further development of this field to meet the needs of mankind. PMID:28347110

Energy Conservation Designed into HDR's New Building

ERIC Educational Resources Information Center

Jenkins, Larry

1974-01-01

A new building has been engineered by its engineer-owner tenants with provisions for two gas-oil hot water generators and for an electric boiler, so that operating personnel could switch to whatever fuel is available. (Author/MLF)

National energy conservation

NASA Technical Reports Server (NTRS)

1975-01-01

A set of energy conservation actions that cut across all sectors of the economy were analyzed so that all actions under consideration be analyzed systematically and as a whole. The actions considered were as follows: (1) roll back the price of newly discovered oil, (2) freeze gasoline production for 3 years at 1972 levels, (3) mandate automobile mileage improvements, (4) require industry to improve energy efficiency, (5) require manufacture of household appliances with greater efficiency, (6) force conversion of many power plants from gas and oil to coal. The results showed that considerable gas and oil would be saved by forcing switches to coal. However, the large scale switch to coal was shown to require greatly increased outputs from many other industries that in turn require more energy. It was estimated that nearly 2.5 quads of additional coal were needed to produce these additional requirements. Also, the indirect requirements would create more jobs.

Co-option of the hormone-signalling module dafachronic acid-DAF-12 in nematode evolution.

PubMed

Bento, Gilberto; Ogawa, Akira; Sommer, Ralf J

2010-07-22

Morphological novelties are lineage-specific traits that serve new functions. Developmental polyphenisms have been proposed to be facilitators of phenotypic evolution, but little is known about the interplay between the associated genetic and environmental factors. Here, we study two alternative morphologies in the mouth of the nematode Pristionchus pacificus and the formation of teeth-like structures that are associated with bacteriovorous feeding and predatory behaviour on fungi and other worms. These teeth-like denticles represent an evolutionary novelty, which is restricted to some members of the nematode family Diplogastridae but is absent from Caenorhabditis elegans and related nematodes. We show that the mouth dimorphism is a polyphenism that is controlled by starvation and the co-option of an endocrine switch mechanism. Mutations in the nuclear hormone receptor DAF-12 and application of its ligand, the sterol hormone dafachronic acid, strongly influence this switch mechanism. The dafachronic acid-DAF-12 module has been shown to control the formation of arrested dauer larvae in both C. elegans and P. pacificus, as well as related life-history decisions in distantly related nematodes. The comparison of dauer formation and mouth morphology switch reveals that different thresholds of dafachronic acid signalling provide specificity. This study shows how hormonal signalling acts by coupling environmental change and genetic regulation and identifies dafachronic acid as a key hormone in nematode evolution.

Oxygen-ion-migration-modulated bipolar resistive switching and complementary resistive switching in tungsten/indium tin oxide/gold memory device

NASA Astrophysics Data System (ADS)

Wu, Xinghui; Zhang, Qiuhui; Cui, Nana; Xu, Weiwei; Wang, Kefu; Jiang, Wei; Xu, Qixing

2018-06-01

In this paper, we report our investigation of room-temperature-fabricated tungsten/indium tin oxide/gold (W/ITO/Au) resistive random access memory (RRAM), which exhibits asymmetric bipolar resistive switching (BRS) behavior. The device displays good write/erase endurance and data retention properties. The device shows complementary resistive switching (CRS) characteristics after controlling the compliance current. A WO x layer electrically formed at the W/ITO in the forming process. Mobile oxygen ions within ITO migrate toward the electrode/ITO interface and produce a semiconductor-like layer that acts as a free-carrier barrier. The CRS characteristic here can be elucidated in light of the evolution of an asymmetric free-carrier blocking layer at the electrode/ITO interface.

Adaptive Output-Feedback Neural Control of Switched Uncertain Nonlinear Systems With Average Dwell Time.

PubMed

Long, Lijun; Zhao, Jun

2015-07-01

This paper investigates the problem of adaptive neural tracking control via output-feedback for a class of switched uncertain nonlinear systems without the measurements of the system states. The unknown control signals are approximated directly by neural networks. A novel adaptive neural control technique for the problem studied is set up by exploiting the average dwell time method and backstepping. A switched filter and different update laws are designed to reduce the conservativeness caused by adoption of a common observer and a common update law for all subsystems. The proposed controllers of subsystems guarantee that all closed-loop signals remain bounded under a class of switching signals with average dwell time, while the output tracking error converges to a small neighborhood of the origin. As an application of the proposed design method, adaptive output feedback neural tracking controllers for a mass-spring-damper system are constructed.

Fundamental studies on initiation and evolution of multi-channel discharges and their application to next generation pulsed power machines.

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

Schwarz, Jens; Savage, Mark E.; Lucero, Diego Jose

Future pulsed power systems may rely on linear transformer driver (LTD) technology. The LTD's will be the building blocks for a driver that can deliver higher current than the Z-Machine. The LTD's would require tens of thousands of low inductance ( %3C 85nH), high voltage (200 kV DC) switches with high reliability and long lifetime ( 10 4 shots). Sandia's Z-Machine employs 36 megavolt class switches that are laser triggered by a single channel discharge. This is feasible for tens of switches but the high inductance and short switch life- time associated with the single channel discharge are undesirable formore » future machines. Thus the fundamental problem is how to lower inductance and losses while increasing switch life- time and reliability. These goals can be achieved by increasing the number of current-carrying channels. The rail gap switch is ideal for this purpose. Although those switches have been extensively studied during the past decades, each effort has only characterized a particular switch. There is no comprehensive understanding of the underlying physics that would allow predictive capability for arbitrary switch geometry. We have studied rail gap switches via an extensive suite of advanced diagnostics in synergy with theoretical physics and advanced modeling capability. Design and topology of multichannel switches as they relate to discharge dynamics are investigated. This involves electrically and optically triggered rail gaps, as well as discrete multi-site switch concepts.« less

Identification and characterization of a member of Rab subfamily, Rab8, from Clonorchis sinensis.

PubMed

Liang, Pei; He, Lei; Yu, Jinyun; Xie, Zhizhi; Chen, Xueqing; Mao, Qiang; Liang, Chi; Huang, Yan; Lu, Gang; Yu, Xinbing

2015-05-01

The Rabs act as a binary molecular switch that utilizes the conformational changes associated with the GTP/GDP cycle to elicit responses from target proteins. It regulates a broad spectrum of cellular processes including cell proliferation, cytoskeletal assembly, and intracellular membrane trafficking in eukaryotes. The Rab8 from Clonorchis sinensis (CsRab8) was composed of 199 amino acids. The deduced amino acid sequence shared above 50% identities with other species from trematode, tapeworm, mammal, insecta, nematode, and reptile, respectively. The homologous analysis of sequences showed the conservative domains: G1 box (GDSGVGKS), G2 box (T), G3 box (DTAG), G4 box (GNKCDL), and G5 box. In addition, the structure modeling had also shown other functional domains: GTP/Mg(2+) binding sites, switch I region, and switch II region. A phylogenic tree analysis indicated that the CsRab8 was clustered with the Rab from Schistosoma japonicum, and trematode and tapeworm came from the same branch, which was different from an evolutional branch built by other species, such as mammal animal, insecta, nematode, and reptile. The recombinant CsRab8 protein was expressed in Escherichia coli and the purified protein was a soluble molecule by 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis. CsRab8 was identified as a component of excretory/secretory products of C. sinensis by western blot analysis. The transcriptional level of CsRab8 at metacercaria stage was the highest at the four stages and higher by 56.49-folds than that at adult worm, 1.23-folds than that at excysted metacercaria, and 2.69-folds than that at egg stage. Immunohistochemical localization analysis showed that CsRab8 was specifically distributed in the tegument, vitellarium, eggs, and testicle of adult worms, and detected on the vitellarium and tegument of metacercaria. Combined with the results, CsRab8 is indispensable for survival and development of parasites, especially for regulating excretory/secretory products secretion.

Evolutionary Plasticity of AmrZ Regulation in Pseudomonas

PubMed Central

Dougherty, Kevin; Diaz, Beatriz; Murillo, Rachel

2018-01-01

ABSTRACT amrZ encodes a master regulator protein conserved across pseudomonads, which can be either a positive or negative regulator of swimming motility depending on the species examined. To better understand plasticity in the regulatory function of AmrZ, we characterized the mode of regulation for this protein for two different motility-related phenotypes in Pseudomonas stutzeri. As in Pseudomonas syringae, AmrZ functions as a positive regulator of swimming motility within P. stutzeri, which suggests that the functions of this protein with regard to swimming motility have switched at least twice across pseudomonads. Shifts in mode of regulation cannot be explained by changes in AmrZ sequence alone. We further show that AmrZ acts as a positive regulator of colony spreading within this strain and that this regulation is at least partially independent of swimming motility. Closer investigation of mechanistic shifts in dual-function regulators like AmrZ could provide unique insights into how transcriptional pathways are rewired between closely related species. IMPORTANCE Microbes often display finely tuned patterns of gene regulation across different environments, with major regulatory changes controlled by a small group of “master” regulators within each cell. AmrZ is a master regulator of gene expression across pseudomonads and can be either a positive or negative regulator for a variety of pathways depending on the strain and genomic context. Here, we demonstrate that the phenotypic outcomes of regulation of swimming motility by AmrZ have switched at least twice independently in pseudomonads, so that AmrZ promotes increased swimming motility in P. stutzeri and P. syringae but represses this phenotype in Pseudomonas fluorescens and Pseudomonas aeruginosa. Since examples of switches in regulatory mode are relatively rare, further investigation into the mechanisms underlying shifts in regulator function for AmrZ could provide unique insights into the evolution of bacterial regulatory proteins. PMID:29669886

Stability analysis for uncertain switched neural networks with time-varying delay.

PubMed

Shen, Wenwen; Zeng, Zhigang; Wang, Leimin

2016-11-01

In this paper, stability for a class of uncertain switched neural networks with time-varying delay is investigated. By exploring the mode-dependent properties of each subsystem, all the subsystems are categorized into stable and unstable ones. Based on Lyapunov-like function method and average dwell time technique, some delay-dependent sufficient conditions are derived to guarantee the exponential stability of considered uncertain switched neural networks. Compared with general results, our proposed approach distinguishes the stable and unstable subsystems rather than viewing all subsystems as being stable, thus getting less conservative criteria. Finally, two numerical examples are provided to show the validity and the advantages of the obtained results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantifying and Disaggregating Consumer Purchasing Behavior for Energy Systems Modeling

EPA Science Inventory

Consumer behaviors such as energy conservation, adoption of more efficient technologies, and fuel switching represent significant potential for greenhouse gas mitigation. Current efforts to model future energy outcomes have tended to use simplified economic assumptions ...

Phylogenetic distribution of plant snoRNA families.

PubMed

Patra Bhattacharya, Deblina; Canzler, Sebastian; Kehr, Stephanie; Hertel, Jana; Grosse, Ivo; Stadler, Peter F

2016-11-24

Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.

Switched-Observer-Based Adaptive Neural Control of MIMO Switched Nonlinear Systems With Unknown Control Gains.

PubMed

Long, Lijun; Zhao, Jun

2017-07-01

In this paper, the problem of adaptive neural output-feedback control is addressed for a class of multi-input multioutput (MIMO) switched uncertain nonlinear systems with unknown control gains. Neural networks (NNs) are used to approximate unknown nonlinear functions. In order to avoid the conservativeness caused by adoption of a common observer for all subsystems, an MIMO NN switched observer is designed to estimate unmeasurable states. A new switched observer-based adaptive neural control technique for the problem studied is then provided by exploiting the classical average dwell time (ADT) method and the backstepping method and the Nussbaum gain technique. It effectively handles the obstacle about the coexistence of multiple Nussbaum-type function terms, and improves the classical ADT method, since the exponential decline property of Lyapunov functions for individual subsystems is no longer satisfied. It is shown that the technique proposed is able to guarantee semiglobal uniformly ultimately boundedness of all the signals in the closed-loop system under a class of switching signals with ADT, and the tracking errors converge to a small neighborhood of the origin. The effectiveness of the approach proposed is illustrated by its application to a two inverted pendulum system.

Conceptual design of a 0.1 W magnetic refrigerator for operation between 10 K and 2 K

NASA Technical Reports Server (NTRS)

Helvensteijn, Ben P. M.; Kashani, Ali

1990-01-01

The design of a magnetic refrigerator for space applications is discussed. The refrigerator is to operate in the temperature range of 10 K-2 K, at a 2 K cooling power of 0.10 W. As in other magnetic refrigerators operating in this temperature range GGG has been selected as the refrigerant. Crucial to the design of the magnetic refrigerator are the heat switches at both the hot and cold ends of the GGG pill. The 2 K heat switch utilizes a narrow He II filled gap. The 10 K heat switch is based on a narrow helium gas gap. For each switch, the helium in the gap is cycled by means of activated carbon pumps. The design concentrates on reducing the switching times of the pumps and the switches as a whole. A single stage system (one magnet; one refrigerant pill) is being developed. Continuous cooling requires the fully stationary system to have at least two stages running parallel/out of phase with each other. In order to conserve energy, it is intended to recycle the magnetic energy between the magnets. To this purpose, converter networks designed for superconducting magnetic energy storage are being studied.

Using temperature-switching approach to evaluate the ELDRS of bipolar devices

NASA Astrophysics Data System (ADS)

Li, Xiaolong; Lu, Wu; Wang, Xin; Guo, Qi; Yu, Xin; He, Chengfa; Sun, Jing; Liu, Mohan; Yao, Shuai; Wei, Xinyu

2017-12-01

Enhanced low-dose rate sensitivity (ELDRS) exhibited at low-dose rates (LDRs) by most bipolar devices is considered as one of the main concerns for spacecraft reliability. In this work, a time-saving and conservative approach - temperature-switching approach (TSA) - to simulate the ELDRS of bipolar devices is presented. Good agreement is observed between the predictive curve obtained with the TSA and the LDR data, and TSA provides us with a new insight into the test technique for ELDRS. Additionally, the mechanisms of TSA are analyzed in this paper.

Developmental plasticity and the evolution of parasitism in an unusual nematode, Parastrongyloides trichosuri.

PubMed

Stasiuk, Susan J; Scott, Maxwell J; Grant, Warwick N

2012-01-03

Parasitism is an important life history strategy in many metazoan taxa. This is particularly true of the Phylum Nematoda, in which parasitism has evolved independently at least nine times. The apparent ease with which parasitism has evolved amongst nematodes may, in part, be due to a feature of nematode development acting as a pre-adaptation for the transition from a free-living to a parasitic life history. One candidate pre-adaptive feature for evolution in terrestrial nematodes is the dauer larva, a developmentally arrested morph formed in response to environmental signals. We investigated the role of dauer development in the nematode, Parastrongyloides trichosuri, which has retained a complete free-living life cycle in addition to a life cycle as a mammalian gastrointestinal parasite. We show that the developmental switch between these life histories is sensitive to the same environmental cues as dauer arrest in free-living nematodes, including sensitivity to a chemical cue produced by the free-living stages. Furthermore, we show that genetic variation for the sensitivity of the cue(s) exists in natural populations of P. trichosuri, such that we derived inbred lines that were largely insensitive to the cue and other lines that were supersensitive to the cue. For this parasitic clade, and perhaps more widely in the phylum, the evolution of parasitism co-opted the dauer switch of a free-living ancestor. This lends direct support to the hypothesis that the switch to developmental arrest in the dauer larva acted as a pre-adaptation for the evolution of parasitism, and suggests that the sensory transduction machinery downstream of the cue may have been similarly co-opted and modified.

Developmental plasticity and the evolution of parasitism in an unusual nematode, Parastrongyloides trichosuri

PubMed Central

2012-01-01

Background Parasitism is an important life history strategy in many metazoan taxa. This is particularly true of the Phylum Nematoda, in which parasitism has evolved independently at least nine times. The apparent ease with which parasitism has evolved amongst nematodes may, in part, be due to a feature of nematode development acting as a pre-adaptation for the transition from a free-living to a parasitic life history. One candidate pre-adaptive feature for evolution in terrestrial nematodes is the dauer larva, a developmentally arrested morph formed in response to environmental signals. Results We investigated the role of dauer development in the nematode, Parastrongyloides trichosuri, which has retained a complete free-living life cycle in addition to a life cycle as a mammalian gastrointestinal parasite. We show that the developmental switch between these life histories is sensitive to the same environmental cues as dauer arrest in free-living nematodes, including sensitivity to a chemical cue produced by the free-living stages. Furthermore, we show that genetic variation for the sensitivity of the cue(s) exists in natural populations of P. trichosuri, such that we derived inbred lines that were largely insensitive to the cue and other lines that were supersensitive to the cue. Conclusions For this parasitic clade, and perhaps more widely in the phylum, the evolution of parasitism co-opted the dauer switch of a free-living ancestor. This lends direct support to the hypothesis that the switch to developmental arrest in the dauer larva acted as a pre-adaptation for the evolution of parasitism, and suggests that the sensory transduction machinery downstream of the cue may have been similarly co-opted and modified. PMID:22214222

Redox switching and oxygen evolution at oxidized metal and metal oxide electrodes: iron in base.

PubMed

Lyons, Michael E G; Doyle, Richard L; Brandon, Michael P

2011-12-28

Outstanding issues regarding the film formation, redox switching characteristics and the oxygen evolution reaction (OER) electrocatalytic behaviour of multicycled iron oxyhydroxide films in aqueous alkaline solution have been revisited. The oxide is grown using a repetitive potential multicycling technique, and the mechanism of the latter hydrous oxide formation process has been discussed. A duplex layer model of the oxide/solution interphase region is proposed. The acid/base behaviour of the hydrous oxide and the microdispersed nature of the latter material has been emphasised. The hydrous oxide is considered as a porous assembly of interlinked octahedrally coordinated anionic metal oxyhydroxide surfaquo complexes which form an open network structure. The latter contains considerable quantities of water molecules which facilitate hydroxide ion discharge at the metal site during active oxygen evolution, and also charge compensating cations. The dynamics of redox switching has been quantified via analysis of the cyclic voltammetry response as a function of potential sweep rate using the Laviron-Aoki electron hopping diffusion model by analogy with redox polymer modified electrodes. Steady state Tafel plot analysis has been used to elucidate the kinetics and mechanism of oxygen evolution. Tafel slope values of ca. 60 mV dec(-1) and ca. 120 mV dec(-1) are found at low and high overpotentials respectively, whereas the reaction order with respect to hydroxide ion activity changes from ca. 3/2 to ca. 1 as the potential is increased. These observations are rationalised in terms of a kinetic scheme involving Temkin adsorption and the rate determining formation of a physisorbed hydrogen peroxide intermediate on the oxide surface. The dual Tafel slope behaviour is ascribed to the potential dependence of the surface coverage of adsorbed intermediates.

Vestigialization of an Allosteric Switch: Genetic and Structural Mechanisms for the Evolution of Constitutive Activity in a Steroid Hormone Receptor

PubMed Central

Bridgham, Jamie T.; Keay, June; Ortlund, Eric A.; Thornton, Joseph W.

2014-01-01

An important goal in molecular evolution is to understand the genetic and physical mechanisms by which protein functions evolve and, in turn, to characterize how a protein's physical architecture influences its evolution. Here we dissect the mechanisms for an evolutionary shift in function in the mollusk ortholog of the steroid hormone receptors (SRs), a family of biologically essential transcription factors. In vertebrates, the activity of SRs allosterically depends on binding a hormonal ligand; in mollusks, however, the SR ortholog (called ER, because of high sequence similarity to vertebrate estrogen receptors) activates transcription in the absence of ligand and does not respond to steroid hormones. To understand how this shift in regulation evolved, we combined evolutionary, structural, and functional analyses. We first determined the X-ray crystal structure of the ER of the Pacific oyster Crassostrea gigas (CgER), and found that its ligand pocket is filled with bulky residues that prevent ligand occupancy. To understand the genetic basis for the evolution of mollusk ERs' unique functions, we resurrected an ancient SR progenitor and characterized the effect of historical amino acid replacements on its functions. We found that reintroducing just two ancient replacements from the lineage leading to mollusk ERs recapitulates the evolution of full constitutive activity and the loss of ligand activation. These substitutions stabilize interactions among key helices, causing the allosteric switch to become “stuck” in the active conformation and making activation independent of ligand binding. Subsequent changes filled the ligand pocket without further affecting activity; by degrading the allosteric switch, these substitutions vestigialized elements of the protein's architecture required for ligand regulation and made reversal to the ancestral function more complex. These findings show how the physical architecture of allostery enabled a few large-effect mutations to trigger a profound evolutionary change in the protein's function and shaped the genetics of evolutionary reversibility. PMID:24415950

The Red Queen and the seed bank: pathogen resistance of ex situ and in situ conserved barley.

PubMed

Jensen, Helen R; Dreiseitl, Antonín; Sadiki, Mohammed; Schoen, Daniel J

2012-06-01

Plant geneticists have proposed that the dynamic conservation of crop plants in farm environments (in situ conservation) is complementary to static conservation in seed banks (ex situ conservation) because it may help to ensure adaptation to changing conditions. Here, we test whether collections of a traditional variety of Moroccan barley (Hordeum vulgare ssp. vulgare) conserved ex situ showed differences in qualitative and quantitative resistance to the endemic fungal pathogen, Blumeria graminis f.sp. hordei, compared to collections that were continuously cultivated in situ. In detached-leaf assays for qualitative resistance, there were some significant differences between in situ and ex situ conserved collections from the same localities. Some ex situ conserved collections showed lower resistance levels, while others showed higher resistance levels than their in situ conserved counterparts. In field trials for quantitative resistance, similar results were observed, with the highest resistance observed in situ. Overall, this study identifies some cases where the Red Queen appears to drive the evolution of increased resistance in situ. However, in situ conservation does not always result in improved adaptation to pathogen virulence, suggesting a more complex evolutionary scenario, consistent with several published examples of plant-pathogen co-evolution in wild systems.

Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.

PubMed

Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting

2017-09-12

Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little is known about the conservation of tissue-specific genome-wide DNA methylation patterns. Using a comparative epigenomics approach, we identified and compared the tissue-specific DNA methylation patterns of rat against those of mouse and human across three shared tissue types. We confirmed that tissue-specific differentially methylated regions are strongly associated with tissue-specific regulatory elements. Comparisons between species revealed that at a minimum 11-37% of tissue-specific DNA methylation patterns are conserved, a phenomenon that we define as epigenetic conservation. Conserved DNA methylation is accompanied by conservation of other epigenetic marks including histone modifications. Although a significant amount of locus-specific methylation is epigenetically conserved, the majority of tissue-specific DNA methylation is not conserved across the species and tissue types that we investigated. Examination of the genetic underpinning of epigenetic conservation suggests that primary sequence conservation is a driving force behind epigenetic conservation. In contrast, evolutionary dynamics of tissue-specific DNA methylation are best explained by the maintenance or turnover of binding sites for important transcription factors. Our study extends the limited literature of comparative epigenomics and suggests a new paradigm for epigenetic conservation without genetic conservation through analysis of transcription factor binding sites.

Neural network for control of rearrangeable Clos networks.

PubMed

Park, Y K; Cherkassky, V

1994-09-01

Rapid evolution in the field of communication networks requires high speed switching technologies. This involves a high degree of parallelism in switching control and routing performed at the hardware level. The multistage crossbar networks have always been attractive to switch designers. In this paper a neural network approach to controlling a three-stage Clos network in real time is proposed. This controller provides optimal routing of communication traffic requests on a call-by-call basis by rearranging existing connections, with a minimum length of rearrangement sequence so that a new blocked call request can be accommodated. The proposed neural network controller uses Paull's rearrangement algorithm, along with the special (least used) switch selection rule in order to minimize the length of rearrangement sequences. The functional behavior of our model is verified by simulations and it is shown that the convergence time required for finding an optimal solution is constant, regardless of the switching network size. The performance is evaluated for random traffic with various traffic loads. Simulation results show that applying the least used switch selection rule increases the efficiency in switch rearrangements, reducing the network convergence time. The implementation aspects are also discussed to show the feasibility of the proposed approach.

Evolutionary prisoner's dilemma games on the network with punishment and opportunistic partner switching

NASA Astrophysics Data System (ADS)

Takesue, H.

2018-02-01

Punishment and partner switching are two well-studied mechanisms that support the evolution of cooperation. Observation of human behaviour suggests that the extent to which punishment is adopted depends on the usage of alternative mechanisms, including partner switching. In this study, we investigate the combined effect of punishment and partner switching in evolutionary prisoner's dilemma games conducted on a network. In the model, agents are located on the network and participate in the prisoner's dilemma games with punishment. In addition, they can opportunistically switch interaction partners to improve their payoff. Our Monte Carlo simulation showed that a large frequency of punishers is required to suppress defectors when the frequency of partner switching is low. In contrast, cooperation is the most abundant strategy when the frequency of partner switching is high regardless of the strength of punishment. Interestingly, cooperators become abundant not because they avoid the cost of inflicting punishment and earn a larger average payoff per game but rather because they have more numerous opportunities to be referred to as a role agent by defectors. Our results imply that the fluidity of social relationships has a profound effect on the adopted strategy in maintaining cooperation.

Increased Automobile Fuel Efficiency and Synthetic Fuels: Alternatives for Reducing Oil Imports

DOT National Transportation Integrated Search

1982-09-01

This report assesses and compares increased automobile fuel efficiency and synthetic fuels production with respect to their potential to reduce conventional oil consumption, and their costs and impacts. Conservation and fuel switching as a means of r...

Studies on transient characteristics of unipolar resistive switching processes in TiO2 thin film grown by atomic layer deposition

NASA Astrophysics Data System (ADS)

Sahu, Vikas Kumar; Das, Amit K.; Ajimsha, R. S.; Misra, P.

2018-05-01

The transient characteristics of resistive switching processes have been investigated in TiO2 thin films grown by atomic layer deposition (ALD) to study the temporal evolution of the switching processes and measure the switching times. The reset and set switching times of unipolar Au/TiO2/Pt devices were found to be ~250 µs and 180 ns, respectively in the voltage windows of 0.5–0.9 V for reset and 1.9–4.8 V for set switching processes, obtained from quasi-static measurements. The reset switching time decreased exponentially with increasing amplitude of applied reset voltage pulse, while the set switching time remained insensitive to the amplitude of the set voltage pulse. A fast reset process with a switching time of ~400 ns was achieved by applying a reset voltage of ~1.8 V, higher than that of the quasi-static reset voltage window but below the set voltage window. The sluggish reset process in TiO2 thin film and the dependence of the reset switching time on the amplitude of the applied voltage pulse was understood on the basis of a self-accelerated thermal dissolution model of conducting filaments (CFs), where a higher temperature of the CFs owing to enhanced Joule heating at a higher applied voltage imposes faster diffusion of oxygen vacancies, resulting in a shorter reset switching time. Our results clearly indicate that fast resistive switching with switching times in hundreds of nanoseconds can be achieved in ALD-grown TiO2 thin films. This may find applications in fast non-volatile unipolar resistive switching memories.

Single molecules can operate as primitive biological sensors, switches and oscillators.

PubMed

Hernansaiz-Ballesteros, Rosa D; Cardelli, Luca; Csikász-Nagy, Attila

2018-06-18

Switch-like and oscillatory dynamical systems are widely observed in biology. We investigate the simplest biological switch that is composed of a single molecule that can be autocatalytically converted between two opposing activity forms. We test how this simple network can keep its switching behaviour under perturbations in the system. We show that this molecule can work as a robust bistable system, even for alterations in the reactions that drive the switching between various conformations. We propose that this single molecule system could work as a primitive biological sensor and show by steady state analysis of a mathematical model of the system that it could switch between possible states for changes in environmental signals. Particularly, we show that a single molecule phosphorylation-dephosphorylation switch could work as a nucleotide or energy sensor. We also notice that a given set of reductions in the reaction network can lead to the emergence of oscillatory behaviour. We propose that evolution could have converted this switch into a single molecule oscillator, which could have been used as a primitive timekeeper. We discuss how the structure of the simplest known circadian clock regulatory system, found in cyanobacteria, resembles the proposed single molecule oscillator. Besides, we speculate if such minimal systems could have existed in an RNA world.

Fidelity of northern pine snakes (Pituophis m. melanoleucus) to natural and artificial hibernation sites in the New Jersey Pine Barrens.

PubMed

Zappalorti, Robert T; Burger, Joanna; Burkett, David W; Schneider, David W; McCort, Matthew P; Golden, David M

2014-01-01

Environmental managers require information on whether human-made hibernacula are used by rare snakes before constructing large numbers of them as mitigation measures. Fidelity of northern pine snakes (Pituophis m. melanoleucus) was examined in a 6-year study in the New Jersey Pine Barrens to determine whether they used natural and artificial hibernacula equally. Pine snakes used both artificial (human-made) and natural (snake-adapted) hibernacula. Most natural hibernacula were in abandoned burrows of large mammals. Occupancy rates were similar between natural and artificial hibernacula. Only 6 of 27 radio-tracked snakes did not shift hibernacula between years, whereas 78% shifted sites at least once, and fidelity from one year to the next was 42%. For snakes that switched hibernacula (n = 21), one switched among artificial hibernacula, 14 (65%) switched among natural hibernacula, and 6 (29%) switched from artificial to natural hibernacula. Data indicate that most pine snakes switch among hibernacula, mainly selecting natural hibernacula, suggesting that artificial dens are used, but protecting natural hibernacula should be a higher conservation priority.

Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

PubMed

Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

2016-06-01

Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract. © 2016 WILEY Periodicals, Inc.

The genetics of reproductive organ morphology in two Petunia species with contrasting pollination syndromes.

PubMed

Hermann, Katrin; Klahre, Ulrich; Venail, Julien; Brandenburg, Anna; Kuhlemeier, Cris

2015-05-01

Switches between pollination syndromes have happened frequently during angiosperm evolution. Using QTL mapping and reciprocal introgressions, we show that changes in reproductive organ morphology have a simple genetic basis. In animal-pollinated plants, flowers have evolved to optimize pollination efficiency by different pollinator guilds and hence reproductive success. The two Petunia species, P. axillaris and P. exserta, display pollination syndromes adapted to moth or hummingbird pollination. For the floral traits color and scent, genetic loci of large phenotypic effect have been well documented. However, such large-effect loci may be typical for shifts in simple biochemical traits, whereas the evolution of morphological traits may involve multiple mutations of small phenotypic effect. Here, we performed a quantitative trait locus (QTL) analysis of floral morphology, followed by an in-depth study of pistil and stamen morphology and the introgression of individual QTL into reciprocal parental backgrounds. Two QTLs, on chromosomes II and V, are sufficient to explain the interspecific difference in pistil and stamen length. Since most of the difference in organ length is caused by differences in cell number, genes underlying these QTLs are likely to be involved in cell cycle regulation. Interestingly, conservation of the locus on chromosome II in a different P. axillaris subspecies suggests that the evolution of organ elongation was initiated on chromosome II in adaptation to different pollinators. We recently showed that QTLs for pistil and stamen length on chromosome II are tightly linked to QTLs for petal color and volatile emission. Linkage of multiple traits will enable major phenotypic change within a few generations in hybridizing populations. Thus, the genomic architecture of pollination syndromes in Petunia allows for rapid responses to changing pollinator availability.

Nanocrystalline Si pathway induced unipolar resistive switching behavior from annealed Si-rich SiNx/SiNy multilayers

NASA Astrophysics Data System (ADS)

Jiang, Xiaofan; Ma, Zhongyuan; Yang, Huafeng; Yu, Jie; Wang, Wen; Zhang, Wenping; Li, Wei; Xu, Jun; Xu, Ling; Chen, Kunji; Huang, Xinfan; Feng, Duan

2014-09-01

Adding a resistive switching functionality to a silicon microelectronic chip is a new challenge in materials research. Here, we demonstrate that unipolar and electrode-independent resistive switching effects can be realized in the annealed Si-rich SiNx/SiNy multilayers with high on/off ratio of 109. High resolution transmission electron microscopy reveals that for the high resistance state broken pathways composed of discrete nanocrystalline silicon (nc-Si) exist in the Si nitride multilayers. While for the low resistance state the discrete nc-Si regions is connected, forming continuous nc-Si pathways. Based on the analysis of the temperature dependent I-V characteristics and HRTEM photos, we found that the break-and-bridge evolution of nc-Si pathway is the origin of resistive switching memory behavior. Our findings provide insights into the mechanism of the resistive switching behavior in nc-Si films, opening a way for it to be utilized as a material in Si-based memories.

Chromosome rearrangements via template switching between diverged repeated sequences

PubMed Central

Anand, Ranjith P.; Tsaponina, Olga; Greenwell, Patricia W.; Lee, Cheng-Sheng; Du, Wei; Petes, Thomas D.

2014-01-01

Recent high-resolution genome analyses of cancer and other diseases have revealed the occurrence of microhomology-mediated chromosome rearrangements and copy number changes. Although some of these rearrangements appear to involve nonhomologous end-joining, many must have involved mechanisms requiring new DNA synthesis. Models such as microhomology-mediated break-induced replication (MM-BIR) have been invoked to explain these rearrangements. We examined BIR and template switching between highly diverged sequences in Saccharomyces cerevisiae, induced during repair of a site-specific double-strand break (DSB). Our data show that such template switches are robust mechanisms that give rise to complex rearrangements. Template switches between highly divergent sequences appear to be mechanistically distinct from the initial strand invasions that establish BIR. In particular, such jumps are less constrained by sequence divergence and exhibit a different pattern of microhomology junctions. BIR traversing repeated DNA sequences frequently results in complex translocations analogous to those seen in mammalian cells. These results suggest that template switching among repeated genes is a potent driver of genome instability and evolution. PMID:25367035

Stochastic switching of TiO2-based memristive devices with identical initial memory states

PubMed Central

2014-01-01

In this work, we show that identical TiO2-based memristive devices that possess the same initial resistive states are only phenomenologically similar as their internal structures may vary significantly, which could render quite dissimilar switching dynamics. We experimentally demonstrated that the resistive switching of practical devices with similar initial states could occur at different programming stimuli cycles. We argue that similar memory states can be transcribed via numerous distinct active core states through the dissimilar reduced TiO2-x filamentary distributions. Our hypothesis was finally verified via simulated results of the memory state evolution, by taking into account dissimilar initial filamentary distribution. PMID:24994953

Resistive switching behavior in oxygen ion irradiated TiO2-x films

NASA Astrophysics Data System (ADS)

Barman, A.; Saini, C. P.; Sarkar, P. K.; Bhattacharjee, G.; Bhattacharya, G.; Srivastava, S.; Satpati, B.; Kanjilal, D.; Ghosh, S. K.; Dhar, S.; Kanjilal, A.

2018-02-01

The room temperature resistive switching behavior in 50 keV O+-ion irradiated TiO2-x layers at an ion fluence of 5  ×  1016 ions cm-2 is reported. A clear transformation from columnar to layered polycrystalline films is revealed by transmission electron microscopy with increasing ion fluence, while the complementary electron energy loss spectroscopy suggests an evolution of oxygen vacancy (OV) in TiO2-x matrix. This is further verified by determining electron density with the help of x-ray reflectivity. Both local and device current-voltage measurements illustrate that the ion-beam induced OVs play a key role in bistable resistive switching mechanism.

Toward next-generation optical networks: a network operator perspective based on experimental tests and economic analysis

NASA Astrophysics Data System (ADS)

Xiao, Xiaojun; Du, Chunsheng; Zhou, Rongsheng

2004-04-01

As a result of data traffic"s exponential growth, network is currently evolving from fixed circuit switched services to dynamic packet switched services, which has brought unprecedented changes to the existing transport infrastructure. It is generally agreed that automatic switched optical network (ASON) is one of the promising solutions for the next generation optical networks. In this paper, we present the results of our experimental tests and economic analysis on ASON. The intention of this paper is to present our perspective, in terms of evolution strategy toward ASON, on next generation optical networks. It is shown through experimental tests that the performance of current Pre-standard ASON enabled equipments satisfies the basic requirements of network operators and is ready for initial deployment. The results of the economic analysis show that network operators can be benefit from the deployment of ASON from three sides. Firstly, ASON can reduce the CAPEX for network expanding by integrating multiple ADM & DCS into one box. Secondly, ASON can reduce the OPEX for network operation by introducing automatic resource control scheme. Finally, ASON can increase margin revenue by providing new optical network services such as Bandwidth on Demand, optical VPN etc. Finally, the evolution strategy is proposed as our perspective toward next generation optical networks. We hope the evolution strategy introduced may be helpful for the network operators to gracefully migrate their fixed ring based legacy networks to next generation dynamic mesh based network.

Evolution of an arsenal: structural and functional diversification of the venom system in the advanced snakes (Caenophidia).

PubMed

Fry, Bryan G; Scheib, Holger; van der Weerd, Louise; Young, Bruce; McNaughtan, Judith; Ramjan, S F Ryan; Vidal, Nicolas; Poelmann, Robert E; Norman, Janette A

2008-02-01

Venom is a key innovation underlying the evolution of advanced snakes (Caenophidia). Despite this, very little is known about venom system structural diversification, toxin recruitment event timings, or toxin molecular evolution. A multidisciplinary approach was used to examine the diversification of the venom system and associated toxins across the full range of the approximately 100 million-year-old advanced snake clade with a particular emphasis upon families that have not secondarily evolved a front-fanged venom system ( approximately 80% of the 2500 species). Analysis of cDNA libraries revealed complex venom transcriptomes containing multiple toxin types including three finger toxins, cobra venom factor, cysteine-rich secretory protein, hyaluronidase, kallikrein, kunitz, lectin, matrix metalloprotease, phospholipase A(2), snake venom metalloprotease/a disintegrin and metalloprotease, and waprin. High levels of sequence diversity were observed, including mutations in structural and functional residues, changes in cysteine spacing, and major deletions/truncations. Morphological analysis comprising gross dissection, histology, and magnetic resonance imaging also demonstrated extensive modification of the venom system architecture in non-front-fanged snakes in contrast to the conserved structure of the venom system within the independently evolved front-fanged elapid or viperid snakes. Further, a reduction in the size and complexity of the venom system was observed in species in which constriction has been secondarily evolved as the preferred method of prey capture or dietary preference has switched from live prey to eggs or to slugs/snails. Investigation of the timing of toxin recruitment events across the entire advanced snake radiation indicates that the evolution of advanced venom systems in three front-fanged lineages is associated with recruitment of new toxin types or explosive diversification of existing toxin types. These results support the role of venom as a key evolutionary innovation in the diversification of advanced snakes and identify a potential role for non-front-fanged venom toxins as a rich source for lead compounds for drug design and development.

Time-evolution of quantum systems via a complex nonlinear Riccati equation. I. Conservative systems with time-independent Hamiltonian

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

Cruz, Hans, E-mail: hans@ciencias.unam.mx; Schuch, Dieter; Castaños, Octavio, E-mail: ocasta@nucleares.unam.mx

2015-09-15

The sensitivity of the evolution of quantum uncertainties to the choice of the initial conditions is shown via a complex nonlinear Riccati equation leading to a reformulation of quantum dynamics. This sensitivity is demonstrated for systems with exact analytic solutions with the form of Gaussian wave packets. In particular, one-dimensional conservative systems with at most quadratic Hamiltonians are studied.

Evolution of Nova-Dependent Splicing Regulation in the Brain

PubMed Central

Živin, Marko; Darnell, Robert B

2007-01-01

A large number of alternative exons are spliced with tissue-specific patterns, but little is known about how such patterns have evolved. Here, we study the conservation of the neuron-specific splicing factors Nova1 and Nova2 and of the alternatively spliced exons they regulate in mouse brain. Whereas Nova RNA binding domains are 94% identical across vertebrate species, Nova-dependent splicing silencer and enhancer elements (YCAY clusters) show much greater divergence, as less than 50% of mouse YCAY clusters are conserved at orthologous positions in the zebrafish genome. To study the relation between the evolution of tissue-specific splicing and YCAY clusters, we compared the brain-specific splicing of Nova-regulated exons in zebrafish, chicken, and mouse. The presence of YCAY clusters in lower vertebrates invariably predicted conservation of brain-specific splicing across species, whereas their absence in lower vertebrates correlated with a loss of alternative splicing. We hypothesize that evolution of Nova-regulated splicing in higher vertebrates proceeds mainly through changes in cis-acting elements, that tissue-specific splicing might in some cases evolve in a single step corresponding to evolution of a YCAY cluster, and that the conservation level of YCAY clusters relates to the functions encoded by the regulated RNAs. PMID:17937501

Conserved noncoding sequences conserve biological networks and influence genome evolution.

PubMed

Xie, Jianbo; Qian, Kecheng; Si, Jingna; Xiao, Liang; Ci, Dong; Zhang, Deqiang

2018-05-01

Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection remains limited. Here, we used a combination of DNA methylome analysis, microarray expression analyses, and functional annotation to study these sequences in the model tree Populus trichocarpa. Methylation in CG contexts and non-CG contexts was lower in CNSs, particularly CNSs in the 5'-upstream regions of genes, compared with other sites in the genome. We observed that CNSs are enriched in genes with transcription and binding functions, and this also associated with syntenic genes and those from whole-genome duplications, suggesting that cis-regulatory sequences play a key role in genome evolution. We detected a significant positive correlation between CNS number and protein interactions, suggesting that CNSs may have roles in the evolution and maintenance of biological networks. The divergence of CNSs indicates that duplication-degeneration-complementation drives the subfunctionalization of a proportion of duplicated genes from whole-genome duplication. Furthermore, population genomics confirmed that most CNSs are under strong purifying selection and only a small subset of CNSs shows evidence of adaptive evolution. These findings provide a foundation for future studies exploring these key genomic features in the maintenance of biological networks, local adaptation, and transcription.

E-field induced resistive switch in metal/praseodymium calcium manganite interfaces: A model for future nonvolatile memory devices

NASA Astrophysics Data System (ADS)

Das, Nilanjan

Among the various candidates for non-volatile random access memory (RAM), interfacial resistive switch in Ag/Pr0.7Ca0.3 MnO3 (PCMO) configuration has drawn major attention in recent years due to its potential as a high storage density (˜ terabyte) device. However, the diverse nature of the resistive switch in different systems makes the development of a unifying model for its underlying physics very difficult. This dissertation will address both issues, namely, characterization of switches for device applications and development of a system-independent generic model, in detail. In our work, we have studied the properties electric pulse induced interfacial switch in electrode/PCMO system. A very fast speed ("write speed") of 100 ns, threshold ("programming voltage") as low as 2 V (for micro electrodes), and non-volatility ("data retention") of switched states have been achieved. A clear distinction between fast switch and sub-threshold slow quasistatic-dc switch has been made. Results obtained from time-dependence studies and impedance spectroscopy suggest that defect creation/annihilation, such as broken bonds (under very high field at interface, 107V/cm), is likely the mechanism for the sub-micros fast switching. On the other hand, slow accumulative process, such as electromigration of point defects, are responsible for the subthreshold quasi-dc switch. Scanning probe imaging has revealed the nanoscale inhomogeneity of the switched surfaces, essential for observing a resistive switch. Evolution of such structures has been observed under surface pre-training. Device scalability has been tested by creating reversible modification of surface conductivities with atomic force microscopy, thus creating the "nano-switch" (limited to a region of 10--100 nm).

Switching from computer to microcomputer architecture education

NASA Astrophysics Data System (ADS)

Bolanakis, Dimosthenis E.; Kotsis, Konstantinos T.; Laopoulos, Theodore

2010-03-01

In the last decades, the technological and scientific evolution of the computing discipline has been widely affecting research in software engineering education, which nowadays advocates more enlightened and liberal ideas. This article reviews cross-disciplinary research on a computer architecture class in consideration of its switching to microcomputer architecture. The authors present their strategies towards a successful crossing of boundaries between engineering disciplines. This communication aims at providing a different aspect on professional courses that are, nowadays, addressed at the expense of traditional courses.

Conservation of tubulin-binding sequences in TRPV1 throughout evolution.

PubMed

Sardar, Puspendu; Kumar, Abhishek; Bhandari, Anita; Goswami, Chandan

2012-01-01

Transient Receptor Potential Vanilloid sub type 1 (TRPV1), commonly known as capsaicin receptor can detect multiple stimuli ranging from noxious compounds, low pH, temperature as well as electromagnetic wave at different ranges. In addition, this receptor is involved in multiple physiological and sensory processes. Therefore, functions of TRPV1 have direct influences on adaptation and further evolution also. Availability of various eukaryotic genomic sequences in public domain facilitates us in studying the molecular evolution of TRPV1 protein and the respective conservation of certain domains, motifs and interacting regions that are functionally important. Using statistical and bioinformatics tools, our analysis reveals that TRPV1 has evolved about ∼420 million years ago (MYA). Our analysis reveals that specific regions, domains and motifs of TRPV1 has gone through different selection pressure and thus have different levels of conservation. We found that among all, TRP box is the most conserved and thus have functional significance. Our results also indicate that the tubulin binding sequences (TBS) have evolutionary significance as these stretch sequences are more conserved than many other essential regions of TRPV1. The overall distribution of positively charged residues within the TBS motifs is conserved throughout evolution. In silico analysis reveals that the TBS-1 and TBS-2 of TRPV1 can form helical structures and may play important role in TRPV1 function. Our analysis identifies the regions of TRPV1, which are important for structure-function relationship. This analysis indicates that tubulin binding sequence-1 (TBS-1) near the TRP-box forms a potential helix and the tubulin interactions with TRPV1 via TBS-1 have evolutionary significance. This interaction may be required for the proper channel function and regulation and may also have significance in the context of Taxol®-induced neuropathy.

Toward the Darwinian transition: Switching between distributed and speciated states in a simple model of early life.

PubMed

Arnoldt, Hinrich; Strogatz, Steven H; Timme, Marc

2015-01-01

It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable direction out of early collective evolution, potentially enabling the start of individuality and vertical Darwinian evolution.

Coherence Evolution and Transfer Supplemented by Sender's Initial-State Restoring

NASA Astrophysics Data System (ADS)

Fel'dman, E. B.; Zenchuk, A. I.

2017-12-01

The evolution of quantum coherences comes with a set of conservation laws provided that the Hamiltonian governing this evolution conserves the spin-excitation number. At that, coherences do not intertwist during the evolution. Using the transmission line and the receiver in the initial ground state we can transfer the coherences to the receiver without interaction between them, although the matrix elements contributing to each particular coherence intertwist in the receiver's state. Therefore we propose a tool based on the unitary transformation at the receiver side to untwist these elements and thus restore (at least partially) the structure of the sender's initial density matrix. A communication line with two-qubit sender and receiver is considered as an example of implementation of this technique.

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.

Study of selected phenotype switching strategies in time varying environment

NASA Astrophysics Data System (ADS)

Horvath, Denis; Brutovsky, Branislav

2016-03-01

Population heterogeneity plays an important role across many research, as well as the real-world, problems. The population heterogeneity relates to the ability of a population to cope with an environment change (or uncertainty) preventing its extinction. However, this ability is not always desirable as can be exemplified by an intratumor heterogeneity which positively correlates with the development of resistance to therapy. Causation of population heterogeneity is therefore in biology and medicine an intensively studied topic. In this paper the evolution of a specific strategy of population diversification, the phenotype switching, is studied at a conceptual level. The presented simulation model studies evolution of a large population of asexual organisms in a time-varying environment represented by a stochastic Markov process. Each organism disposes with a stochastic or nonlinear deterministic switching strategy realized by discrete-time models with evolvable parameters. We demonstrate that under rapidly varying exogenous conditions organisms operate in the vicinity of the bet-hedging strategy, while the deterministic patterns become relevant as the environmental variations are less frequent. Statistical characterization of the steady state regimes of the populations is done using the Hellinger and Kullback-Leibler functional distances and the Hamming distance.

Platform-Switching for Cemented Versus Screwed Fixed Dental Prostheses: Reliability and Failure Modes: An In Vitro Study.

PubMed

Anchieta, Rodolfo Brunieira; Machado, Lucas Silveira; Hirata, Ronaldo; Bonfante, Estevam Augusto; Coelho, Paulo G

2016-08-01

The aim of this study was to evaluate the probability of survival of cemented and screwed three-unit implant-supported fixed dental prostheses (ISFDP) using different implant-abutment horizontal matching configurations (regular vs switching platforms). One hundred and sixty-eight implants with internal hexagon connection (4 mm diameter, 10 mm length, Emfils; Colosso Evolution System, Itú, SP, Brazil) were selected for this study according to the horizontal implant-abutment matching configuration (regular or switching) and retention method and divided in four groups (n = 21 per group) as follows: 1) regular platform cemented (IRC); 2) or screw-retained (IRS); 3) switched-platform cemented (ISC); or 4) screw-retained (ISS). Regular and platform-switched abutments (Colosso evolution, 4 mm and 3.3 mm, respectively) were torqued, and 84 three-unit metal bridges were fabricated (first molar pontic). Implants were embedded in polymethyl-methacrylate resin and subjected to step-stress accelerated life testing in water. Weibull distribution was used to determine the probability of survival for a mission of 100,000 cycles at 400 N (90% two-sided confidence intervals). Polarized light and scanning electron microscopes were used for fractographic analysis. The β values of 0.50, 1.19, 1.25, and 1.95 for groups IRC, IRS, ISC, and ISS respectively, indicated that fatigue accelerated the failure for all groups, except IRC. The cement-retained groups presented significantly higher probability of survival (IRC - 98%, ISC - 59%) than screw-retained groups (IRS - 23% and ISS - 0%). Screw-retained FDPs exclusively failed by abutment-screw fractures, whereas cement-retained presented implant/screw/abutment fractures. The probability of survival of cement-retained ISFDP was higher than screw-retained, irrespective of implant-abutment horizontal configuration. © 2015 Wiley Periodicals, Inc.

Whole Genome Sequence Analysis of Mutations Accumulated in rad27Δ Yeast Strains with Defects in the Processing of Okazaki Fragments Indicates Template-Switching Events

PubMed Central

Omer, Sumita; Lavi, Bar; Mieczkowski, Piotr A.; Covo, Shay; Hazkani-Covo, Einat

2017-01-01

Okazaki fragments that are formed during lagging strand DNA synthesis include an initiating primer consisting of both RNA and DNA. The RNA fragment must be removed before the fragments are joined. In Saccharomyces cerevisiae, a key player in this process is the structure-specific flap endonuclease, Rad27p (human homolog FEN1). To obtain a genomic view of the mutational consequence of loss of RAD27, a S. cerevisiae rad27Δ strain was subcultured for 25 generations and sequenced using Illumina paired-end sequencing. Out of the 455 changes observed in 10 colonies isolated the two most common types of events were insertions or deletions (INDELs) in simple sequence repeats (SSRs) and INDELs mediated by short direct repeats. Surprisingly, we also detected a previously neglected class of 21 template-switching events. These events were presumably generated by quasi-palindrome to palindrome correction, as well as palindrome elongation. The formation of these events is best explained by folding back of the stalled nascent strand and resumption of DNA synthesis using the same nascent strand as a template. Evidence of quasi-palindrome to palindrome correction that could be generated by template switching appears also in yeast genome evolution. Out of the 455 events, 55 events appeared in multiple isolates; further analysis indicates that these loci are mutational hotspots. Since Rad27 acts on the lagging strand when the leading strand should not contain any gaps, we propose a mechanism favoring intramolecular strand switching over an intermolecular mechanism. We note that our results open new ways of understanding template switching that occurs during genome instability and evolution. PMID:28974572

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

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

Bradshaw, Niels; Levdikov, Vladimir M.; Zimanyi, Christina M.

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activitymore » in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site.« less

Adaptive Backstepping-Based Neural Tracking Control for MIMO Nonlinear Switched Systems Subject to Input Delays.

PubMed

Niu, Ben; Li, Lu

2018-06-01

This brief proposes a new neural-network (NN)-based adaptive output tracking control scheme for a class of disturbed multiple-input multiple-output uncertain nonlinear switched systems with input delays. By combining the universal approximation ability of radial basis function NNs and adaptive backstepping recursive design with an improved multiple Lyapunov function (MLF) scheme, a novel adaptive neural output tracking controller design method is presented for the switched system. The feature of the developed design is that different coordinate transformations are adopted to overcome the conservativeness caused by adopting a common coordinate transformation for all subsystems. It is shown that all the variables of the resulting closed-loop system are semiglobally uniformly ultimately bounded under a class of switching signals in the presence of MLF and that the system output can follow the desired reference signal. To demonstrate the practicability of the obtained result, an adaptive neural output tracking controller is designed for a mass-spring-damper system.

Intermittent metabolic switching, neuroplasticity and brain health

PubMed Central

Mattson, Mark P.; Moehl, Keelin; Ghena, Nathaniel; Schmaedick, Maggie; Cheng, Aiwu

2018-01-01

During evolution, individuals whose brains and bodies functioned well in a fasted state were successful in acquiring food, enabling their survival and reproduction. With fasting and extended exercise, liver glycogen stores are depleted and ketones are produced from adipose-cell-derived fatty acids. This metabolic switch in cellular fuel source is accompanied by cellular and molecular adaptations of neural networks in the brain that enhance their functionality and bolster their resistance to stress, injury and disease. Here, we consider how intermittent metabolic switching, repeating cycles of a metabolic challenge that induces ketosis (fasting and/or exercise) followed by a recovery period (eating, resting and sleeping), may optimize brain function and resilience throughout the lifespan, with a focus on the neuronal circuits involved in cognition and mood. Such metabolic switching impacts multiple signalling pathways that promote neuroplasticity and resistance of the brain to injury and disease. PMID:29321682

The Red Queen and the seed bank: pathogen resistance of ex situ and in situ conserved barley

PubMed Central

Jensen, Helen R; Dreiseitl, Antonín; Sadiki, Mohammed; Schoen, Daniel J

2012-01-01

Plant geneticists have proposed that the dynamic conservation of crop plants in farm environments (in situ conservation) is complementary to static conservation in seed banks (ex situ conservation) because it may help to ensure adaptation to changing conditions. Here, we test whether collections of a traditional variety of Moroccan barley (Hordeum vulgare ssp. vulgare) conserved ex situ showed differences in qualitative and quantitative resistance to the endemic fungal pathogen, Blumeria graminis f.sp. hordei, compared to collections that were continuously cultivated in situ. In detached-leaf assays for qualitative resistance, there were some significant differences between in situ and ex situ conserved collections from the same localities. Some ex situ conserved collections showed lower resistance levels, while others showed higher resistance levels than their in situ conserved counterparts. In field trials for quantitative resistance, similar results were observed, with the highest resistance observed in situ. Overall, this study identifies some cases where the Red Queen appears to drive the evolution of increased resistance in situ. However, in situ conservation does not always result in improved adaptation to pathogen virulence, suggesting a more complex evolutionary scenario, consistent with several published examples of plant–pathogen co-evolution in wild systems. PMID:25568056

Modern Science and Conservative Islam: An Uneasy Relationship

ERIC Educational Resources Information Center

Edis, Taner

2009-01-01

Familiar Western debates about religion, science, and science education have parallels in the Islamic world. There are difficulties reconciling conservative, traditional versions of Islam with modern science, particularly theories such as evolution. As a result, many conservative Muslim thinkers are drawn toward creationism, hopes of Islamizing…

On the primary variable switching technique for simulating unsaturated-saturated flows

NASA Astrophysics Data System (ADS)

Diersch, H.-J. G.; Perrochet, P.

Primary variable switching appears as a promising numerical technique for variably saturated flows. While the standard pressure-based form of the Richards equation can suffer from poor mass balance accuracy, the mixed form with its improved conservative properties can possess convergence difficulties for dry initial conditions. On the other hand, variable switching can overcome most of the stated numerical problems. The paper deals with variable switching for finite elements in two and three dimensions. The technique is incorporated in both an adaptive error-controlled predictor-corrector one-step Newton (PCOSN) iteration strategy and a target-based full Newton (TBFN) iteration scheme. Both schemes provide different behaviors with respect to accuracy and solution effort. Additionally, a simplified upstream weighting technique is used. Compared with conventional approaches the primary variable switching technique represents a fast and robust strategy for unsaturated problems with dry initial conditions. The impact of the primary variable switching technique is studied over a wide range of mostly 2D and partly difficult-to-solve problems (infiltration, drainage, perched water table, capillary barrier), where comparable results are available. It is shown that the TBFN iteration is an effective but error-prone procedure. TBFN sacrifices temporal accuracy in favor of accelerated convergence if aggressive time step sizes are chosen.

Clustering and Flow Conservation Monitoring Tool for Software Defined Networks.

PubMed

Puente Fernández, Jesús Antonio; García Villalba, Luis Javier; Kim, Tai-Hoon

2018-04-03

Prediction systems present some challenges on two fronts: the relation between video quality and observed session features and on the other hand, dynamics changes on the video quality. Software Defined Networks (SDN) is a new concept of network architecture that provides the separation of control plane (controller) and data plane (switches) in network devices. Due to the existence of the southbound interface, it is possible to deploy monitoring tools to obtain the network status and retrieve a statistics collection. Therefore, achieving the most accurate statistics depends on a strategy of monitoring and information requests of network devices. In this paper, we propose an enhanced algorithm for requesting statistics to measure the traffic flow in SDN networks. Such an algorithm is based on grouping network switches in clusters focusing on their number of ports to apply different monitoring techniques. Such grouping occurs by avoiding monitoring queries in network switches with common characteristics and then, by omitting redundant information. In this way, the present proposal decreases the number of monitoring queries to switches, improving the network traffic and preventing the switching overload. We have tested our optimization in a video streaming simulation using different types of videos. The experiments and comparison with traditional monitoring techniques demonstrate the feasibility of our proposal maintaining similar values decreasing the number of queries to the switches.

An efficient platform for genetic selection and screening of gene switches in Escherichia coli

PubMed Central

Muranaka, Norihito; Sharma, Vandana; Nomura, Yoko; Yokobayashi, Yohei

2009-01-01

Engineered gene switches and circuits that can sense various biochemical and physical signals, perform computation, and produce predictable outputs are expected to greatly advance our ability to program complex cellular behaviors. However, rational design of gene switches and circuits that function in living cells is challenging due to the complex intracellular milieu. Consequently, most successful designs of gene switches and circuits have relied, to some extent, on high-throughput screening and/or selection from combinatorial libraries of gene switch and circuit variants. In this study, we describe a generic and efficient platform for selection and screening of gene switches and circuits in Escherichia coli from large libraries. The single-gene dual selection marker tetA was translationally fused to green fluorescent protein (gfpuv) via a flexible peptide linker and used as a dual selection and screening marker for laboratory evolution of gene switches. Single-cycle (sequential positive and negative selections) enrichment efficiencies of >7000 were observed in mock selections of model libraries containing functional riboswitches in liquid culture. The technique was applied to optimize various parameters affecting the selection outcome, and to isolate novel thiamine pyrophosphate riboswitches from a complex library. Artificial riboswitches with excellent characteristics were isolated that exhibit up to 58-fold activation as measured by fluorescent reporter gene assay. PMID:19190095

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

PubMed

Bergman, C M; Kreitman, M

2001-08-01

Comparative genomic approaches to gene and cis-regulatory prediction are based on the principle that differential DNA sequence conservation reflects variation in functional constraint. Using this principle, we analyze noncoding sequence conservation in Drosophila for 40 loci with known or suspected cis-regulatory function encompassing >100 kb of DNA. We estimate the fraction of noncoding DNA conserved in both intergenic and intronic regions and describe the length distribution of ungapped conserved noncoding blocks. On average, 22%-26% of noncoding sequences surveyed are conserved in Drosophila, with median block length approximately 19 bp. We show that point substitution in conserved noncoding blocks exhibits transition bias as well as lineage effects in base composition, and occurs more than an order of magnitude more frequently than insertion/deletion (indel) substitution. Overall, patterns of noncoding DNA structure and evolution differ remarkably little between intergenic and intronic conserved blocks, suggesting that the effects of transcription per se contribute minimally to the constraints operating on these sequences. The results of this study have implications for the development of alignment and prediction algorithms specific to noncoding DNA, as well as for models of cis-regulatory DNA sequence evolution.

Precessional Switching of Thin Nanomagnets with Uniaxial Anisotropy

NASA Astrophysics Data System (ADS)

Devolder, Thibaut; Schumacher, Hans Werner; Chappert, Claude

This review describes the evolution of the magnetization of uniaxial thin magnets when subjected to fast-rising magnetic-field pulses. We report detailed "all-electrical" experimental investigations of precessional switching on soft uniaxial micrometer-sized thin magnets, and we discuss them using a comprehensive, mostly analytical framework. General criteria are derived for the analytical assessment of the switching ability of any arbitrary set of experimental parameters. For this, we start from the Landau-Lifshitz equation and first consider the precessional switching in a much idealized macrospin, easy-plane loss-free system. We then test the main outputs of this model with time-resolved experiments on advanced Magnetic Random Access Memories (MRAM) cells. Using applied fields above the anisotropy field H k , we prove the quasiperiodic nature of the magnetization trajectory and we demonstrate experimental conditions ensuring a sub-200 ps ballistic magnetization reversal. We then upgrade our model accuracy by taking into account the uniaxial anisotropy and the behavior in hard-axis fields of the order of H k . We derive a simple though reliable estimate of the switching speed; its limiting factors highlight the experimental poor switching reproducibility when close to the minimal hard-axis reversal field H k /2. The latter field does not correspond to the minimal energy cost of the reversal, whose prospective evolution in the future generations of MRAM is predicted. Small departures from the macrospin state are discussed. The effect of damping is modeled using perturbation theory. Finite damping alters the precessional motion periodicity and puts some constraints on the field rise time. A special focus is dedicated to the relaxation-dominated precessional switching: the minimal hard-axis field triggering the switching is shown to be above H k /2 by an extra field cost linked to the damping constant times the square root of M S H k . Finally, the selective addressing and the direct-write of a magnetic cell with combined easy-axis and hard-axis fields are studied. We introduce the concept of bounce and revisit the dynamical astroid to derive the related characteristic reversal durations and their margins. We propose a field timing that is immune to the delay jitter between the combined addressing fields. We finish by investigating briefly the challenges and the promises of the "precessional" strategy for future MRAM generations.

Interactions among Trypanosoma brucei RAD51 paralogues in DNA repair and antigenic variation

PubMed Central

Dobson, Rachel; Stockdale, Christopher; Lapsley, Craig; Wilkes, Jonathan; McCulloch, Richard

2011-01-01

Homologous recombination in Trypanosoma brucei is used for moving variant surface glycoprotein (VSG) genes into expression sites during immune evasion by antigenic variation. A major route for such VSG switching is gene conversion reactions in which RAD51, a universally conserved recombinase, catalyses homology-directed strand exchange. In any eukaryote, RAD51-directed strand exchange in vivo is mediated by further factors, including RAD51-related proteins termed Rad51 paralogues. These appear to be ubiquitously conserved, although their detailed roles in recombination remain unclear. In T. brucei, four putative RAD51 paralogue genes have been identified by sequence homology. Here we show that all four RAD51 paralogues act in DNA repair, recombination and RAD51 subnuclear dynamics, though not equivalently, while mutation of only one RAD51 paralogue gene significantly impedes VSG switching. We also show that the T. brucei RAD51 paralogues interact, and that the complexes they form may explain the distinct phenotypes of the mutants as well as observed expression interdependency. Finally, we document the Rad51 paralogues that are encoded by a wide range of protists, demonstrating that the Rad51 paralogue repertoire in T. brucei is unusually large among microbial eukaryotes and that one member of the protein family corresponds with a key, conserved eukaryotic Rad51 paralogue. PMID:21615552

75 FR 42579 - Energy Conservation Program for Consumer Products: Test Procedure for Microwave Ovens; Repeal of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-22

... the usable baking space. If there is a selector switch for selecting the mode of operation of the oven, set it for normal baking. If an oven permits baking by either forced convection by using a fan, or...

Evolution and Expression of Tissue Globins in Ray-Finned Fishes.

PubMed

Gallagher, Michael D; Macqueen, Daniel J

2017-01-01

The globin gene family encodes oxygen-binding hemeproteins conserved across the major branches of multicellular life. The origins and evolutionary histories of complete globin repertoires have been established for many vertebrates, but there remain major knowledge gaps for ray-finned fish. Therefore, we used phylogenetic, comparative genomic and gene expression analyses to discover and characterize canonical “non-blood” globin family members (i.e., myoglobin, cytoglobin, neuroglobin, globin-X, and globin-Y) across multiple ray-finned fish lineages, revealing novel gene duplicates (paralogs) conserved from whole genome duplication (WGD) and small-scale duplication events. Our key findings were that: (1) globin-X paralogs in teleosts have been retained from the teleost-specific WGD, (2) functional paralogs of cytoglobin, neuroglobin, and globin-X, but not myoglobin, have been conserved from the salmonid-specific WGD, (3) triplicate lineage-specific myoglobin paralogs are conserved in arowanas (Osteoglossiformes), which arose by tandem duplication and diverged under positive selection, (4) globin-Y is retained in multiple early branching fish lineages that diverged before teleosts, and (5) marked variation in tissue-specific expression of globin gene repertoires exists across ray-finned fish evolution, including several previously uncharacterized sites of expression. In this respect, our data provide an interesting link between myoglobin expression and the evolution of air breathing in teleosts. Together, our findings demonstrate great-unrecognized diversity in the repertoire and expression of nonblood globins that has arisen during ray-finned fish evolution.

Evolution of disorder in Mediator complex and its functional relevance

PubMed Central

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K.

2016-01-01

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. PMID:26590257

Single Cell Oncogenesis

NASA Astrophysics Data System (ADS)

Lu, Xin

It is believed that cancer originates from a single cell that has gone through generations of evolution of genetic and epigenetic changes that associate with the hallmarks of cancer. In some cancers such as various types of leukemia, cancer is clonal. Yet in other cancers like glioblastoma (GBM), there is tremendous tumor heterogeneity that is likely to be caused by simultaneous evolution of multiple subclones within the same tissue. It is obvious that understanding how a single cell develops into a clonal tumor upon genetic alterations, at molecular and cellular levels, holds the key to the real appreciation of tumor etiology and ultimate solution for therapeutics. Surprisingly very little is known about the process of spontaneous tumorigenesis from single cells in human or vertebrate animal models. The main reason is the lack of technology to track the natural process of single cell changes from a homeostatic state to a progressively cancerous state. Recently, we developed a patented compound, photoactivatable (''caged'') tamoxifen analogue 4-OHC and associated technique called optochemogenetic switch (OCG switch), which we believe opens the opportunity to address this urgent biological as well as clinical question about cancer. We propose to combine OCG switch with genetically engineered mouse models of head and neck squamous cell carcinoma and high grade astrocytoma (including GBM) to study how single cells, when transformed through acute loss of tumor suppressor genes PTEN and TP53 and gain of oncogenic KRAS, can develop into tumor colonies with cellular and molecular heterogeneity in these tissues. The abstract is for my invited talk in session ``Beyond Darwin: Evolution in Single Cells'' 3/18/2016 11:15 AM.

Nanocrystalline Si pathway induced unipolar resistive switching behavior from annealed Si-rich SiN{sub x}/SiN{sub y} multilayers

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

Jiang, Xiaofan; Ma, Zhongyuan, E-mail: zyma@nju.edu.cn; Yang, Huafeng

2014-09-28

Adding a resistive switching functionality to a silicon microelectronic chip is a new challenge in materials research. Here, we demonstrate that unipolar and electrode-independent resistive switching effects can be realized in the annealed Si-rich SiN{sub x}/SiN{sub y} multilayers with high on/off ratio of 10{sup 9}. High resolution transmission electron microscopy reveals that for the high resistance state broken pathways composed of discrete nanocrystalline silicon (nc-Si) exist in the Si nitride multilayers. While for the low resistance state the discrete nc-Si regions is connected, forming continuous nc-Si pathways. Based on the analysis of the temperature dependent I-V characteristics and HRTEM photos,more » we found that the break-and-bridge evolution of nc-Si pathway is the origin of resistive switching memory behavior. Our findings provide insights into the mechanism of the resistive switching behavior in nc-Si films, opening a way for it to be utilized as a material in Si-based memories.« less

Dynamic genetic conservation in the presence of invasive insect and pathogen threats to forest tree species of the United States

Treesearch

J.L. Koch; R.A. Sniezko

2017-01-01

Ex-situ genetic conservation focused on collection and storage of seed can play an important role in conserving the genetic diversity of species under grave threat by biotic organisms or a changing climate. However, ex-situ genetic conservation is primarily a static activity and does not allow for evolution of the species under a continuing,...

Developmental sources of conservation and variation in the evolution of the primate eye.

PubMed

Dyer, Michael A; Martins, Rodrigo; da Silva Filho, Manoel; Muniz, José Augusto P C; Silveira, Luiz Carlos L; Cepko, Constance L; Finlay, Barbara L

2009-06-02

Conserved developmental programs, such as the order of neurogenesis in the mammalian eye, suggest the presence of useful features for evolutionary stability and variability. The owl monkey, Aotus azarae, has developed a fully nocturnal retina in recent evolution. Description and quantification of cell cycle kinetics show that embryonic cytogenesis is extended in Aotus compared with the diurnal New World monkey Cebus apella. Combined with the conserved mammalian pattern of retinal cell specification, this single change in retinal progenitor cell proliferation can produce the multiple alterations of the nocturnal retina, including coordinated reduction in cone and ganglion cell numbers, increase in rod and rod bipolar numbers, and potentially loss of the fovea.

Exploring the Common Dynamics of Homologous Proteins. Application to the Globin Family

PubMed Central

Maguid, Sandra; Fernandez-Alberti, Sebastian; Ferrelli, Leticia; Echave, Julian

2005-01-01

We present a procedure to explore the global dynamics shared between members of the same protein family. The method allows the comparison of patterns of vibrational motion obtained by Gaussian network model analysis. After the identification of collective coordinates that were conserved during evolution, we quantify the common dynamics within a family. Representative vectors that describe these dynamics are defined using a singular value decomposition approach. As a test case, the globin heme-binding family is considered. The two lowest normal modes are shown to be conserved within this family. Our results encourage the development of models for protein evolution that take into account the conservation of dynamical features. PMID:15749782

Traveling wave solutions and conservation laws for nonlinear evolution equation

NASA Astrophysics Data System (ADS)

Baleanu, Dumitru; Inc, Mustafa; Yusuf, Abdullahi; Aliyu, Aliyu Isa

2018-02-01

In this work, the Riccati-Bernoulli sub-ordinary differential equation and modified tanh-coth methods are used to reach soliton solutions of the nonlinear evolution equation. We acquire new types of traveling wave solutions for the governing equation. We show that the equation is nonlinear self-adjoint by obtaining suitable substitution. Therefore, we construct conservation laws for the equation using new conservation theorem. The obtained solutions in this work may be used to explain and understand the physical nature of the wave spreads in the most dispersive medium. The constraint condition for the existence of solitons is stated. Some three dimensional figures for some of the acquired results are illustrated.

Between wilderness and the middle landscape: A rocky road

Treesearch

Lisi Krall

2007-01-01

Wilderness preservation, as one branch of conservation, demonstrates a decidedly different cultural ethos than the utilitarian branch. Thus, preservation and utilitarian conservation represent different habits of thought fermenting in the cask of l9th century economic evolution. More specifically, the utilitarian branch of conservation can easily be viewed as an...

The Fourth World Conservation Lecture: The Evolution of Conservation and Contemporary Issues.

ERIC Educational Resources Information Center

Kassas, Mohammed

1985-01-01

Traces the international movements that focused on the conservation and protection of nature within the past five decades. Explains how man-nature relationships are influenced by the interaction of the three systems of the biosphere, technosphere, and sociosphere. Issues involved with deforestation and desertification are also described. (ML)

Conservation of hot regions in protein-protein interaction in evolution.

PubMed

Hu, Jing; Li, Jiarui; Chen, Nansheng; Zhang, Xiaolong

2016-11-01

The hot regions of protein-protein interactions refer to the active area which formed by those most important residues to protein combination process. With the research development on protein interactions, lots of predicted hot regions can be discovered efficiently by intelligent computing methods, while performing biology experiments to verify each every prediction is hardly to be done due to the time-cost and the complexity of the experiment. This study based on the research of hot spot residue conservations, the proposed method is used to verify authenticity of predicted hot regions that using machine learning algorithm combined with protein's biological features and sequence conservation, though multiple sequence alignment, module substitute matrix and sequence similarity to create conservation scoring algorithm, and then using threshold module to verify the conservation tendency of hot regions in evolution. This research work gives an effective method to verify predicted hot regions in protein-protein interactions, which also provides a useful way to deeply investigate the functional activities of protein hot regions. Copyright © 2016. Published by Elsevier Inc.

Algebraic aspects of evolution partial differential equation arising in the study of constant elasticity of variance model from financial mathematics

NASA Astrophysics Data System (ADS)

Motsepa, Tanki; Aziz, Taha; Fatima, Aeeman; Khalique, Chaudry Masood

2018-03-01

The optimal investment-consumption problem under the constant elasticity of variance (CEV) model is investigated from the perspective of Lie group analysis. The Lie symmetry group of the evolution partial differential equation describing the CEV model is derived. The Lie point symmetries are then used to obtain an exact solution of the governing model satisfying a standard terminal condition. Finally, we construct conservation laws of the underlying equation using the general theorem on conservation laws.

Towards investigation of evolution of dynamical systems with independence of time accuracy: more classes of systems

NASA Astrophysics Data System (ADS)

Gurzadyan, V. G.; Kocharyan, A. A.

2015-07-01

The recently developed method (Paper 1) enabling one to investigate the evolution of dynamical systems with an accuracy not dependent on time is developed further. The classes of dynamical systems which can be studied by that method are much extended, now including systems that are: (1) non-Hamiltonian, conservative; (2) Hamiltonian with time-dependent perturbation; (3) non-conservative (with dissipation). These systems cover various types of N-body gravitating systems of astrophysical and cosmological interest, such as the orbital evolution of planets, minor planets, artificial satellites due to tidal, non-tidal perturbations and thermal thrust, evolving close binary stellar systems, and the dynamics of accretion disks.

DNA barcodes for ecology, evolution, and conservation.

PubMed

Kress, W John; García-Robledo, Carlos; Uriarte, Maria; Erickson, David L

2015-01-01

The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed. Published by Elsevier Ltd.

A Parent-Offspring Trade-Off Limits the Evolution of an Ontogenetic Niche Shift.

PubMed

Ten Brink, Hanna; de Roos, André M

2017-07-01

Many free-living animal species, including the majority of fish, insects, and amphibians, change their food and habitat during their life. Even though these ontogenetic changes in niche are common, it is not well understood which ecological conditions have favored the evolution of these shifts. Using an adaptive dynamics approach, we show that it is evolutionarily advantageous to switch to an alternative food source in the course of ontogeny when this results in a higher intake rate for the switching consumers. Individuals are, however, not able to specialize on this new food source when this negatively affects the performance early in life on the original food source. Selection on these early life stages is so strong that in species with a complete diet shift, evolution results in large juveniles and adults that are maladapted to the alternative food source while their offspring are specialized on the original food source when young. These outcomes suggest strong selection to decouple the different life stages, such that they can maximize their performance on different food sources independently from each other. Metamorphosis could be a way to decouple the different life stages and therefore evolve in species that feed on multiple food sources during their life.

Pathophysiology of language switching and mixing in an early bilingual child with subcortical aphasia.

PubMed

Mariën, Peter; Abutalebi, Jubin; Engelborghs, Sebastiaan; De Deyn, Peter P

2005-12-01

Acquired aphasia after circumscribed vascular subcortical lesions has not been reported in bilingual children. We report clinical and neuroimaging findings in an early bilingual boy who incurred equally severe transcortical sensory aphasia in his first language (L1) and second language (L2) after a posterior left thalamic hemorrhage. Following recurrent bleeding of the lesion the aphasic symptoms substantially aggravated. Spontaneous pathological language switching and mixing were found in both languages. Remission of these phenomena was reflected on brain perfusion SPECT revealing improved perfusion in the left frontal lobe and left caudate nucleus. The parallelism between the evolution of language symptoms and the SPECT findings may demonstrate that a subcortical left frontal lobe circuity is crucially involved in language switching and mixing.

Clustering and Flow Conservation Monitoring Tool for Software Defined Networks

PubMed Central

Puente Fernández, Jesús Antonio

2018-01-01

Prediction systems present some challenges on two fronts: the relation between video quality and observed session features and on the other hand, dynamics changes on the video quality. Software Defined Networks (SDN) is a new concept of network architecture that provides the separation of control plane (controller) and data plane (switches) in network devices. Due to the existence of the southbound interface, it is possible to deploy monitoring tools to obtain the network status and retrieve a statistics collection. Therefore, achieving the most accurate statistics depends on a strategy of monitoring and information requests of network devices. In this paper, we propose an enhanced algorithm for requesting statistics to measure the traffic flow in SDN networks. Such an algorithm is based on grouping network switches in clusters focusing on their number of ports to apply different monitoring techniques. Such grouping occurs by avoiding monitoring queries in network switches with common characteristics and then, by omitting redundant information. In this way, the present proposal decreases the number of monitoring queries to switches, improving the network traffic and preventing the switching overload. We have tested our optimization in a video streaming simulation using different types of videos. The experiments and comparison with traditional monitoring techniques demonstrate the feasibility of our proposal maintaining similar values decreasing the number of queries to the switches. PMID:29614049

Switch II Mutants Reveal Coupling between the Nucleotide- and Actin-Binding Regions in Myosin V

PubMed Central

Trivedi, Darshan V.; David, Charles; Jacobs, Donald J.; Yengo, Christopher M.

2012-01-01

Conserved active-site elements in myosins and other P-loop NTPases play critical roles in nucleotide binding and hydrolysis; however, the mechanisms of allosteric communication among these mechanoenzymes remain unresolved. In this work we introduced the E442A mutation, which abrogates a salt-bridge between switch I and switch II, and the G440A mutation, which abolishes a main-chain hydrogen bond associated with the interaction of switch II with the γ phosphate of ATP, into myosin V. We used fluorescence resonance energy transfer between mant-labeled nucleotides or IAEDANS-labeled actin and FlAsH-labeled myosin V to examine the conformation of the nucleotide- and actin-binding regions, respectively. We demonstrate that in the absence of actin, both the G440A and E442A mutants bind ATP with similar affinity and result in only minor alterations in the conformation of the nucleotide-binding pocket (NBP). In the presence of ADP and actin, both switch II mutants disrupt the formation of a closed NBP actomyosin.ADP state. The G440A mutant also prevents ATP-induced opening of the actin-binding cleft. Our results indicate that the switch II region is critical for stabilizing the closed NBP conformation in the presence of actin, and is essential for communication between the active site and actin-binding region. PMID:22713570

Evolutionary analysis of the jacalin-related lectin family genes in 11 fishes.

PubMed

Cao, Jun; Lv, Yueqing

2016-09-01

Jacalin-related lectins are a type of carbohydrate-binding proteins, which are distributed across a wide variety of organisms and involved in some important biological processes. The evolution of this gene family in fishes is unknown. Here, 47 putative jacalin genes in 11 fish species were identified and divided into 4 groups through phylogenetic analysis. Conserved gene organization and motif distribution existed in each group, suggesting their functional conservation. Some fishes have eleven jacalin genes, while others have only one or zero gene in their genomes, suggesting dynamic changes in the number of jacalin genes during the evolution of fishes. Intragenic recombination played a key role in the evolution of jacalin genes. Synteny analyses of jacalin genes in some fishes implied conserved and dynamic evolution characteristics of this gene family and related genome segments. Moreover, a few functional divergence sites were identified within each group pairs. Divergent expression profiles of the zebra fish jacalin genes were further investigated in different stresses. The results provided a foundation for exploring the characterization of the jacalin genes in fishes and will offer insights for additional functional studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Forelimb kinematics and motor patterns of swimming loggerhead sea turtles (Caretta caretta): are motor patterns conserved in the evolution of new locomotor strategies?

PubMed

Rivera, Angela R V; Wyneken, Jeanette; Blob, Richard W

2011-10-01

Novel functions in animals may evolve through changes in morphology, muscle activity or a combination of both. The idea that new functions or behavior can arise solely through changes in structure, without concurrent changes in the patterns of muscle activity that control movement of those structures, has been formalized as the neuromotor conservation hypothesis. In vertebrate locomotor systems, evidence for neuromotor conservation is found across evolutionary transitions in the behavior of terrestrial species, and in evolutionary transitions from terrestrial species to flying species. However, evolutionary transitions in the locomotion of aquatic species have received little comparable study to determine whether changes in morphology and muscle function were coordinated through the evolution of new locomotor behavior. To evaluate the potential for neuromotor conservation in an ancient aquatic system, we quantified forelimb kinematics and muscle activity during swimming in the loggerhead sea turtle, Caretta caretta. Loggerhead forelimbs are hypertrophied into wing-like flippers that produce thrust via dorsoventral forelimb flapping. We compared kinematic and motor patterns from loggerheads with previous data from the red-eared slider, Trachemys scripta, a generalized freshwater species exhibiting unspecialized forelimb morphology and anteroposterior rowing motions during swimming. For some forelimb muscles, comparisons between C. caretta and T. scripta support neuromotor conservation; for example, the coracobrachialis and the latissimus dorsi show similar activation patterns. However, other muscles (deltoideus, pectoralis and triceps) do not show neuromotor conservation; for example, the deltoideus changes dramatically from a limb protractor/elevator in sliders to a joint stabilizer in loggerheads. Thus, during the evolution of flapping in sea turtles, drastic restructuring of the forelimb was accompanied by both conservation and evolutionary novelty in limb motor patterns.

ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism.

PubMed

Parke, Courtney L; Wojcik, Edward J; Kim, Sunyoung; Worthylake, David K

2010-02-19

Motor proteins couple steps in ATP binding and hydrolysis to conformational switching both in and remote from the active site. In our kinesin.AMPPPNP crystal structure, closure of the active site results in structural transformations appropriate for microtubule binding and organizes an orthosteric two-water cluster. We conclude that a proton is shared between the lytic water, positioned for gamma-phosphate attack, and a second water that serves as a general base. To our knowledge, this is the first experimental detection of the catalytic base for any ATPase. Deprotonation of the second water by switch residues likely triggers subsequent large scale structural rearrangements. Therefore, the catalytic base is responsible for initiating nucleophilic attack of ATP and for relaying the positive charge over long distances to initiate mechanotransduction. Coordination of switch movements via sequential proton transfer along paired water clusters may be universal for nucleotide triphosphatases with conserved active sites, such as myosins and G-proteins.

Light induced kickoff of magnetic domain walls in Ising chains

NASA Astrophysics Data System (ADS)

Bogani, Lapo

2012-02-01

Controlling the speed at which systems evolve is a challenge shared by all disciplines, and otherwise unrelated areas use common theoretical frameworks towards this goal. A particularly widespread model is Glauber dynamics, which describes the time evolution of the Ising model and can be applied to any binary system. Here we show, using molecular nanowires under irradiation, that Glauber dynamics can be controlled by a novel domain-wall kickoff mechanism. Contrary to known processes, the kickoff has unambiguous fingerprints, slowing down the spin-flip attempt rate by several orders of magnitude, and following a scaling law. The required irradiation power is very low, a substantial improvement over present methods of magnetooptical switching: in our experimental demonstration we switched molecular nanowires with light, using powers thousands of times lower than in previous optical switching methods. This manipulation of stochastic dynamic processes is extremely clean, leading to fingerprint signatures and scaling laws. These observations can be used, in material science, to better study domain-wall displacements and solitons in discrete lattices. These results provide a new way to control and study stochastic dynamic processes. Being general for Glauber dynamics, they can be extended to different kinds of magnetic nanowires and to a myriad of fields, ranging from social evolution to neural networks and chemical reactivity. For nanoelectronics and molecular spintronics the kickoff affords external control of molecular spin-valves and a magnetic fingerprint in single molecule measurements. It can also be applied to the dynamics of mechanical switches and the related study of phasons and order-disorder transitions.

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.

PubMed

Braasch, Ingo; Gehrke, Andrew R; Smith, Jeramiah J; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M; Campbell, Michael S; Barrell, Daniel; Martin, Kyle J; Mulley, John F; Ravi, Vydianathan; Lee, Alison P; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E G; Sun, Yi; Hertel, Jana; Beam, Michael J; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H; Litman, Gary W; Litman, Ronda T; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F; Wang, Han; Taylor, John S; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M J; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T; Venkatesh, Byrappa; Holland, Peter W H; Guiguen, Yann; Bobe, Julien; Shubin, Neil H; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H

2016-04-01

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons

PubMed Central

Braasch, Ingo; Gehrke, Andrew R.; Smith, Jeramiah J.; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M.; Campbell, Michael S.; Barrell, Daniel; Martin, Kyle J.; Mulley, John F.; Ravi, Vydianathan; Lee, Alison P.; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E. G.; Sun, Yi; Hertel, Jana; Beam, Michael J.; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H.; Litman, Gary W.; Litman, Ronda T.; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F.; Wang, Han; Taylor, John S.; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M. J.; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A.; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T.; Venkatesh, Byrappa; Holland, Peter W. H.; Guiguen, Yann; Bobe, Julien; Shubin, Neil H.; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H.

2016-01-01

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before the teleost genome duplication (TGD). The slowly evolving gar genome conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization, and development (e.g., Hox, ParaHox, and miRNA genes). Numerous conserved non-coding elements (CNEs, often cis-regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles of such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses revealed that the sum of expression domains and levels from duplicated teleost genes often approximate patterns and levels of gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes, and the function of human regulatory sequences. PMID:26950095

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

Insect sex determination: it all evolves around transformer.

PubMed

Verhulst, Eveline C; van de Zande, Louis; Beukeboom, Leo W

2010-08-01

Insects exhibit a variety of sex determining mechanisms including male or female heterogamety and haplodiploidy. The primary signal that starts sex determination is processed by a cascade of genes ending with the conserved switch doublesex that controls sexual differentiation. Transformer is the doublesex splicing regulator and has been found in all examined insects, indicating its ancestral function as a sex-determining gene. Despite this conserved function, the variation in transformer nucleotide sequence, amino acid composition and protein structure can accommodate a multitude of upstream sex determining signals. Transformer regulation of doublesex and its taxonomic distribution indicate that the doublesex-transformer axis is conserved among all insects and that transformer is the key gene around which variation in sex determining mechanisms has evolved.

Structural Dynamics in Ras and Related Proteins upon Nucleotide Switching.

PubMed

Harrison, Rane A; Lu, Jia; Carrasco, Martin; Hunter, John; Manandhar, Anuj; Gondi, Sudershan; Westover, Kenneth D; Engen, John R

2016-11-20

Structural dynamics of Ras proteins contributes to their activity in signal transduction cascades. Directly targeting Ras proteins with small molecules may rely on the movement of a conserved structural motif, switch II. To understand Ras signaling and advance Ras-targeting strategies, experimental methods to measure Ras dynamics are required. Here, we demonstrate the utility of hydrogen-deuterium exchange (HDX) mass spectrometry (MS) to measure Ras dynamics by studying representatives from two branches of the Ras superfamily, Ras and Rho. A comparison of differential deuterium exchange between active (GMPPNP-bound) and inactive (GDP-bound) proteins revealed differences between the families, with the most notable differences occurring in the phosphate-binding loop and switch II. The P-loop exchange signature correlated with switch II dynamics observed in molecular dynamics simulations focused on measuring main-chain movement. HDX provides a means of evaluating Ras protein dynamics, which may be useful for understanding the mechanisms of Ras signaling, including activated signaling of pathologic mutants, and for targeting strategies that rely on protein dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases

PubMed Central

Bradshaw, Niels; Levdikov, Vladimir M; Zimanyi, Christina M; Gaudet, Rachelle; Wilkinson, Anthony J; Losick, Richard

2017-01-01

PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activity in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site. DOI: http://dx.doi.org/10.7554/eLife.26111.001 PMID:28527238

Mapping of the Lassa virus LAMP1 binding site reveals unique determinants not shared by other old world arenaviruses.

PubMed

Israeli, Hadar; Cohen-Dvashi, Hadas; Shulman, Anastasiya; Shimon, Amir; Diskin, Ron

2017-04-01

Cell entry of many enveloped viruses occurs by engagement with cellular receptors, followed by internalization into endocytic compartments and pH-induced membrane fusion. A previously unnoticed step of receptor switching was found to be critical during cell entry of two devastating human pathogens: Ebola and Lassa viruses. Our recent studies revealed the functional role of receptor switching to LAMP1 for triggering membrane fusion by Lassa virus and showed the involvement of conserved histidines in this switching, suggesting that other viruses from this family may also switch to LAMP1. However, when we investigated viruses that are genetically close to Lassa virus, we discovered that they cannot bind LAMP1. A crystal structure of the receptor-binding module from Morogoro virus revealed structural differences that allowed mapping of the LAMP1 binding site to a unique set of Lassa residues not shared by other viruses in its family, illustrating a key difference in the cell-entry mechanism of Lassa virus that may contribute to its pathogenicity.

Constrained vertebrate evolution by pleiotropic genes.

PubMed

Hu, Haiyang; Uesaka, Masahiro; Guo, Song; Shimai, Kotaro; Lu, Tsai-Ming; Li, Fang; Fujimoto, Satoko; Ishikawa, Masato; Liu, Shiping; Sasagawa, Yohei; Zhang, Guojie; Kuratani, Shigeru; Yu, Jr-Kai; Kusakabe, Takehiro G; Khaitovich, Philipp; Irie, Naoki

2017-11-01

Despite morphological diversification of chordates over 550 million years of evolution, their shared basic anatomical pattern (or 'bodyplan') remains conserved by unknown mechanisms. The developmental hourglass model attributes this to phylum-wide conserved, constrained organogenesis stages that pattern the bodyplan (the phylotype hypothesis); however, there has been no quantitative testing of this idea with a phylum-wide comparison of species. Here, based on data from early-to-late embryonic transcriptomes collected from eight chordates, we suggest that the phylotype hypothesis would be better applied to vertebrates than chordates. Furthermore, we found that vertebrates' conserved mid-embryonic developmental programmes are intensively recruited to other developmental processes, and the degree of the recruitment positively correlates with their evolutionary conservation and essentiality for normal development. Thus, we propose that the intensively recruited genetic system during vertebrates' organogenesis period imposed constraints on its diversification through pleiotropic constraints, which ultimately led to the common anatomical pattern observed in vertebrates.

Understanding Host-Switching by Ecological Fitting

PubMed Central

Araujo, Sabrina B. L.; Braga, Mariana Pires; Brooks, Daniel R.; Agosta, Salvatore J.; Hoberg, Eric P.; von Hartenthal, Francisco W.; Boeger, Walter A.

2015-01-01

Despite the fact that parasites are highly specialized with respect to their hosts, empirical evidence demonstrates that host switching rather than co-speciation is the dominant factor influencing the diversification of host-parasite associations. Ecological fitting in sloppy fitness space has been proposed as a mechanism allowing ecological specialists to host-switch readily. That proposal is tested herein using an individual-based model of host switching. The model considers a parasite species exposed to multiple host resources. Through time host range expansion can occur readily without the prior evolution of novel genetic capacities. It also produces non-linear variation in the size of the fitness space. The capacity for host colonization is strongly influenced by propagule pressure early in the process and by the size of the fitness space later. The simulations suggest that co-adaptation may be initiated by the temporary loss of less fit phenotypes. Further, parasites can persist for extended periods in sub-optimal hosts, and thus may colonize distantly related hosts by a "stepping-stone" process. PMID:26431199

Paul F-Brandwein Lecture 2006: Conservation Education for the 21st Century and beyond

ERIC Educational Resources Information Center

Roth, Charles E.

2008-01-01

This paper explores Paul Brandwein's contribution to the concept of conservation education in America. It examines the evolution of the concept to today's environmental education. It then identifies some of the weaknesses of current environmental education and presents ideas on how to move past them to a point where conservation education is…

Strategies for conserving forest genetic resources in the face of climate change

Treesearch

John Bradley St. Clair; Glenn Thomas Howe

2011-01-01

Conservation of genetic diversity is important for continued evolution of populations to new environments, as well as continued availability of traits of interest in genetic improvement programs. Rapidly changing climates present new threats to the conservation of forest genetic resources. We can no longer assume that in situ reserves will continue to preserve existing...

Anomalous Resistance Hysteresis in Oxide ReRAM: Oxygen Evolution and Reincorporation Revealed by In Situ TEM.

PubMed

Cooper, David; Baeumer, Christoph; Bernier, Nicolas; Marchewka, Astrid; La Torre, Camilla; Dunin-Borkowski, Rafal E; Menzel, Stephan; Waser, Rainer; Dittmann, Regina

2017-06-01

The control and rational design of redox-based memristive devices, which are highly attractive candidates for next-generation nonvolatile memory and logic applications, is complicated by competing and poorly understood switching mechanisms, which can result in two coexisting resistance hystereses that have opposite voltage polarity. These competing processes can be defined as regular and anomalous resistive switching. Despite significant characterization efforts, the complex nanoscale redox processes that drive anomalous resistive switching and their implications for current transport remain poorly understood. Here, lateral and vertical mapping of O vacancy concentrations is used during the operation of such devices in situ in an aberration corrected transmission electron microscope to explain the anomalous switching mechanism. It is found that an increase (decrease) in the overall O vacancy concentration within the device after positive (negative) biasing of the Schottky-type electrode is associated with the electrocatalytic release and reincorporation of oxygen at the electrode/oxide interface and is responsible for the resistance change. This fundamental insight presents a novel perspective on resistive switching processes and opens up new technological opportunities for the implementation of memristive devices, as anomalous switching can now be suppressed selectively or used deliberately to achieve the desirable so-called deep Reset. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolution and Expression of Tissue Globins in Ray-Finned Fishes

PubMed Central

Gallagher, Michael D.

2017-01-01

The globin gene family encodes oxygen-binding hemeproteins conserved across the major branches of multicellular life. The origins and evolutionary histories of complete globin repertoires have been established for many vertebrates, but there remain major knowledge gaps for ray-finned fish. Therefore, we used phylogenetic, comparative genomic and gene expression analyses to discover and characterize canonical “non-blood” globin family members (i.e., myoglobin, cytoglobin, neuroglobin, globin-X, and globin-Y) across multiple ray-finned fish lineages, revealing novel gene duplicates (paralogs) conserved from whole genome duplication (WGD) and small-scale duplication events. Our key findings were that: (1) globin-X paralogs in teleosts have been retained from the teleost-specific WGD, (2) functional paralogs of cytoglobin, neuroglobin, and globin-X, but not myoglobin, have been conserved from the salmonid-specific WGD, (3) triplicate lineage-specific myoglobin paralogs are conserved in arowanas (Osteoglossiformes), which arose by tandem duplication and diverged under positive selection, (4) globin-Y is retained in multiple early branching fish lineages that diverged before teleosts, and (5) marked variation in tissue-specific expression of globin gene repertoires exists across ray-finned fish evolution, including several previously uncharacterized sites of expression. In this respect, our data provide an interesting link between myoglobin expression and the evolution of air breathing in teleosts. Together, our findings demonstrate great-unrecognized diversity in the repertoire and expression of nonblood globins that has arisen during ray-finned fish evolution. PMID:28173090

Comparative Analysis of Immune Checkpoint Molecules and Their Potential Role in the Transmissible Tasmanian Devil Facial Tumor Disease

PubMed Central

Flies, Andrew S.; Blackburn, Nicholas B.; Lyons, Alan Bruce; Hayball, John D.; Woods, Gregory M.

2017-01-01

Immune checkpoint molecules function as a system of checks and balances that enhance or inhibit immune responses to infectious agents, foreign tissues, and cancerous cells. Immunotherapies that target immune checkpoint molecules, particularly the inhibitory molecules programmed cell death 1 and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), have revolutionized human oncology in recent years, yet little is known about these key immune signaling molecules in species other than primates and rodents. The Tasmanian devil facial tumor disease is caused by transmissible cancers that have resulted in a massive decline in the wild Tasmanian devil population. We have recently demonstrated that the inhibitory checkpoint molecule PD-L1 is upregulated on Tasmanian devil (Sarcophilus harrisii) facial tumor cells in response to the interferon-gamma cytokine. As this could play a role in immune evasion by tumor cells, we performed a thorough comparative analysis of checkpoint molecule protein sequences among Tasmanian devils and eight other species. We report that many of the key signaling motifs and ligand-binding sites in the checkpoint molecules are highly conserved across the estimated 162 million years of evolution since the last common ancestor of placental and non-placental mammals. Specifically, we discovered that the CTLA-4 (MYPPPY) ligand-binding motif and the CTLA-4 (GVYVKM) inhibitory domain are completely conserved across all nine species used in our comparative analysis, suggesting that the function of CTLA-4 is likely conserved in these species. We also found that cysteine residues for intra- and intermolecular disulfide bonds were also highly conserved. For instance, all 20 cysteine residues involved in disulfide bonds in the human 4-1BB molecule were also present in devil 4-1BB. Although many key sequences were conserved, we have also identified immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and immunoreceptor tyrosine-based switch motifs (ITSMs) in genes and protein domains that have not been previously reported in any species. This checkpoint molecule analysis and review of salient features for each of the molecules presented here can serve as road map for the development of a Tasmanian devil facial tumor disease immunotherapy. Finally, the strategies can be used as a guide for veterinarians, ecologists, and other researchers willing to venture into the nascent field of wild immunology. PMID:28515726

EmbRS a new two-component system that inhibits biofilm formation and saves Rubrivivax gelatinosus from sinking.

PubMed

Steunou, Anne Soisig; Liotenberg, Sylviane; Soler, Marie-Noêlle; Briandet, Romain; Barbe, Valérie; Astier, Chantal; Ouchane, Soufian

2013-06-01

Photosynthetic bacteria can switch from planktonic lifestyle to phototrophic biofilm in mats in response to environmental changes. The mechanisms of phototrophic biofilm formation are, however, not characterized. Herein, we report a two-component system EmbRS that controls the biofilm formation in a photosynthetic member of the Burkholderiales order, the purple bacterium Rubrivivax gelatinosus. EmbRS inactivation results in cells that form conspicuous bacterial veils and fast-sinking aggregates in liquid. Biofilm analyses indicated that EmbRS represses the production of an extracellular matrix and biofilm formation. Mapping of transposon mutants that partially or completely restore the wild-type (WT) phenotype allowed the identification of two gene clusters involved in polysaccharide synthesis, one fully conserved only in Thauera sp., a floc-forming wastewater bacterium. A second two-component system BmfRS and a putative diguanylate cyclase BdcA were also identified in this screen suggesting their involvement in biofilm formation in this bacterium. The role of polysaccharides in sinking of microorganisms and organic matter, as well as the importance and the evolution of such regulatory system in phototrophic microorganisms are discussed. © 2013 The Authors. Microbiology Open published by John Wiley & Sons Ltd.

Application of adaptive gridding to magnetohydrodynamic flows

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

Schnack, D.D.; Lotatti, I.; Satyanarayana, P.

1996-12-31

The numerical simulation of the primitive, three-dimensional, time-dependent, resistive MHD equations on an unstructured, adaptive poloidal mesh using the TRIM code has been reported previously. The toroidal coordinate is approximated pseudo-spectrally with finite Fourier series and Fast-Fourier Transforms. The finite-volume algorithm preserves the magnetic field as solenoidal to round-off error, and also conserves mass, energy, and magnetic flux exactly. A semi-implicit method is used to allow for large time steps on the unstructured mesh. This is important for tokamak calculations where the relevant time scale is determined by the poloidal Alfven time. This also allows the viscosity to be treatedmore » implicitly. A conjugate-gradient method with pre-conditioning is used for matrix inversion. Applications to the growth and saturation of ideal instabilities in several toroidal fusion systems has been demonstrated. Recently we have concentrated on the details of the mesh adaption algorithm used in TRIM. We present several two-dimensional results relating to the use of grid adaptivity to track the evolution of hydrodynamic and MHD structures. Examples of plasma guns, opening switches, and supersonic flow over a magnetized sphere are presented. Issues relating to mesh adaption criteria are discussed.« less

Evolution of disorder in Mediator complex and its functional relevance.

PubMed

Nagulapalli, Malini; Maji, Sourobh; Dwivedi, Nidhi; Dahiya, Pradeep; Thakur, Jitendra K

2016-02-29

Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of 'junction-MoRF' has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein-protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Inhibitory interneurons of the human prefrontal cortex display conserved evolution of the phenotype and related genes.

PubMed

Sherwood, Chet C; Raghanti, Mary Ann; Stimpson, Cheryl D; Spocter, Muhammad A; Uddin, Monica; Boddy, Amy M; Wildman, Derek E; Bonar, Christopher J; Lewandowski, Albert H; Phillips, Kimberley A; Erwin, Joseph M; Hof, Patrick R

2010-04-07

Inhibitory interneurons participate in local processing circuits, playing a central role in executive cognitive functions of the prefrontal cortex. Although humans differ from other primates in a number of cognitive domains, it is not currently known whether the interneuron system has changed in the course of primate evolution leading to our species. In this study, we examined the distribution of different interneuron subtypes in the prefrontal cortex of anthropoid primates as revealed by immunohistochemistry against the calcium-binding proteins calbindin, calretinin and parvalbumin. In addition, we tested whether genes involved in the specification, differentiation and migration of interneurons show evidence of positive selection in the evolution of humans. Our findings demonstrate that cellular distributions of interneuron subtypes in human prefrontal cortex are similar to other anthropoid primates and can be explained by general scaling rules. Furthermore, genes underlying interneuron development are highly conserved at the amino acid level in primate evolution. Taken together, these results suggest that the prefrontal cortex in humans retains a similar inhibitory circuitry to that in closely related primates, even though it performs functional operations that are unique to our species. Thus, it is likely that other significant modifications to the connectivity and molecular biology of the prefrontal cortex were overlaid on this conserved interneuron architecture in the course of human evolution.

Spatial evolution of quantum mechanical states

NASA Astrophysics Data System (ADS)

Christensen, N. D.; Unger, J. E.; Pinto, S.; Su, Q.; Grobe, R.

2018-02-01

The time-dependent Schrödinger equation is solved traditionally as an initial-time value problem, where its solution is obtained by the action of the unitary time-evolution propagator on the quantum state that is known at all spatial locations but only at t = 0. We generalize this approach by examining the spatial evolution from a state that is, by contrast, known at all times t, but only at one specific location. The corresponding spatial-evolution propagator turns out to be pseudo-unitary. In contrast to the real energies that govern the usual (unitary) time evolution, the spatial evolution can therefore require complex phases associated with dynamically relevant solutions that grow exponentially. By introducing a generalized scalar product, for which the spatial generator is Hermitian, one can show that the temporal integral over the probability current density is spatially conserved, in full analogy to the usual norm of the state, which is temporally conserved. As an application of the spatial propagation formalism, we introduce a spatial backtracking technique that permits us to reconstruct any quantum information about an atom from the ionization data measured at a detector outside the interaction region.

Lie symmetry analysis, explicit solutions and conservation laws for the space-time fractional nonlinear evolution equations

NASA Astrophysics Data System (ADS)

Inc, Mustafa; Yusuf, Abdullahi; Aliyu, Aliyu Isa; Baleanu, Dumitru

2018-04-01

This paper studies the symmetry analysis, explicit solutions, convergence analysis, and conservation laws (Cls) for two different space-time fractional nonlinear evolution equations with Riemann-Liouville (RL) derivative. The governing equations are reduced to nonlinear ordinary differential equation (ODE) of fractional order using their Lie point symmetries. In the reduced equations, the derivative is in Erdelyi-Kober (EK) sense, power series technique is applied to derive an explicit solutions for the reduced fractional ODEs. The convergence of the obtained power series solutions is also presented. Moreover, the new conservation theorem and the generalization of the Noether operators are developed to construct the nonlocal Cls for the equations . Some interesting figures for the obtained explicit solutions are presented.

Conservation of protein structure over four billion years.

PubMed

Ingles-Prieto, Alvaro; Ibarra-Molero, Beatriz; Delgado-Delgado, Asuncion; Perez-Jimenez, Raul; Fernandez, Julio M; Gaucher, Eric A; Sanchez-Ruiz, Jose M; Gavira, Jose A

2013-09-03

Little is known about the evolution of protein structures and the degree of protein structure conservation over planetary time scales. Here, we report the X-ray crystal structures of seven laboratory resurrections of Precambrian thioredoxins dating up to approximately four billion years ago. Despite considerable sequence differences compared with extant enzymes, the ancestral proteins display the canonical thioredoxin fold, whereas only small structural changes have occurred over four billion years. This remarkable degree of structure conservation since a time near the last common ancestor of life supports a punctuated-equilibrium model of structure evolution in which the generation of new folds occurs over comparatively short periods and is followed by long periods of structural stasis. Copyright © 2013 Elsevier Ltd. All rights reserved.

Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution.

PubMed

Havird, Justin C; Whitehill, Nicholas S; Snow, Christopher D; Sloan, Daniel B

2015-12-01

Interactions between nuclear and mitochondrial gene products are critical for eukaryotic cell function. Nuclear genes encoding mitochondrial-targeted proteins (N-mt genes) experience elevated rates of evolution, which has often been interpreted as evidence of nuclear compensation in response to elevated mitochondrial mutation rates. However, N-mt genes may be under relaxed functional constraints, which could also explain observed increases in their evolutionary rate. To disentangle these hypotheses, we examined patterns of sequence and structural evolution in nuclear- and mitochondrial-encoded oxidative phosphorylation proteins from species in the angiosperm genus Silene with vastly different mitochondrial mutation rates. We found correlated increases in N-mt gene evolution in species with fast-evolving mitochondrial DNA. Structural modeling revealed an overrepresentation of N-mt substitutions at positions that directly contact mutated residues in mitochondrial-encoded proteins, despite overall patterns of conservative structural evolution. These findings support the hypothesis that selection for compensatory changes in response to mitochondrial mutations contributes to the elevated rate of evolution in N-mt genes. We discuss these results in light of theories implicating mitochondrial mutation rates and mitonuclear coevolution as drivers of speciation and suggest comparative and experimental approaches that could take advantage of heterogeneity in rates of mtDNA evolution across eukaryotes to evaluate such theories. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Flipping the Metabolic Switch: Understanding and Applying Health Benefits of Fasting

PubMed Central

Anton, Stephen D.; Moehl, Keelin; Donahoo, William T.; Marosi, Krisztina; Lee, Stephanie; Mainous, Arch G.; Leeuwenburgh, Christiaan; Mattson, Mark P.

2017-01-01

Intermittent fasting (IF) is a term used to describe a variety of eating patterns in which no or few calories are consumed for time periods that can range from 12 hours to several days, on a recurring basis. Here we focus on the physiological responses of major organ systems, including the musculoskeletal system, to the onset of the metabolic switch – the point of negative energy balance at which liver glycogen stores are depleted and fatty acids are mobilized (typically beyond 12 hours after cessation of food intake). Emerging findings suggest the metabolic switch from glucose to fatty acid-derived ketones represents an evolutionarily conserved trigger point that shifts metabolism from lipid/cholesterol synthesis and fat storage to mobilization of fat through fatty acid oxidation and fatty-acid derived ketones, which serve to preserve muscle mass and function. Thus, IF regimens that induce the metabolic switch have the potential to improve body composition in overweight individuals. Moreover, IF regimens also induce the coordinated activation of signaling pathways that optimize physiological function, enhance performance, and slow aging and disease processes. Future randomized controlled IF trials should use biomarkers of the metabolic switch (e.g., plasma ketone levels) as a measure of compliance and the magnitude of negative energy balance during the fasting period. PMID:29086496

Flipping the Metabolic Switch: Understanding and Applying the Health Benefits of Fasting.

PubMed

Anton, Stephen D; Moehl, Keelin; Donahoo, William T; Marosi, Krisztina; Lee, Stephanie A; Mainous, Arch G; Leeuwenburgh, Christiaan; Mattson, Mark P

2018-02-01

Intermittent fasting (IF) is a term used to describe a variety of eating patterns in which no or few calories are consumed for time periods that can range from 12 hours to several days, on a recurring basis. This review is focused on the physiological responses of major organ systems, including the musculoskeletal system, to the onset of the metabolic switch: the point of negative energy balance at which liver glycogen stores are depleted and fatty acids are mobilized (typically beyond 12 hours after cessation of food intake). Emerging findings suggest that the metabolic switch from glucose to fatty acid-derived ketones represents an evolutionarily conserved trigger point that shifts metabolism from lipid/cholesterol synthesis and fat storage to mobilization of fat through fatty acid oxidation and fatty acid-derived ketones, which serve to preserve muscle mass and function. Thus, IF regimens that induce the metabolic switch have the potential to improve body composition in overweight individuals. Moreover, IF regimens also induce the coordinated activation of signaling pathways that optimize physiological function, enhance performance, and slow aging and disease processes. Future randomized controlled IF trials should use biomarkers of the metabolic switch (e.g., plasma ketone levels) as a measure of compliance and of the magnitude of negative energy balance during the fasting period. © 2017 The Obesity Society.

Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates

PubMed Central

Harrison, Peter W.; Caravas, Jason A.; Raghanti, Mary Ann; Phillips, Kimberley A.; Mundy, Nicholas I.

2017-01-01

The adaptive significance of human brain evolution has been frequently studied through comparisons with other primates. However, the evolution of increased brain size is not restricted to the human lineage but is a general characteristic of primate evolution. Whether or not these independent episodes of increased brain size share a common genetic basis is unclear. We sequenced and de novo assembled the transcriptome from the neocortical tissue of the most highly encephalized nonhuman primate, the tufted capuchin monkey (Cebus apella). Using this novel data set, we conducted a genome-wide analysis of orthologous brain-expressed protein coding genes to identify evidence of conserved gene–phenotype associations and species-specific adaptations during three independent episodes of brain size increase. We identify a greater number of genes associated with either total brain mass or relative brain size across these six species than show species-specific accelerated rates of evolution in individual large-brained lineages. We test the robustness of these associations in an expanded data set of 13 species, through permutation tests and by analyzing how genome-wide patterns of substitution co-vary with brain size. Many of the genes targeted by selection during brain expansion have glutamatergic functions or roles in cell cycle dynamics. We also identify accelerated evolution in a number of individual capuchin genes whose human orthologs are associated with human neuropsychiatric disorders. These findings demonstrate the value of phenotypically informed genome analyses, and suggest at least some aspects of human brain evolution have occurred through conserved gene–phenotype associations. Understanding these commonalities is essential for distinguishing human-specific selection events from general trends in brain evolution. PMID:28391320

Non-equilibrium time evolution of higher order cumulants of conserved charges and event-by-event analysis

NASA Astrophysics Data System (ADS)

Kitazawa, Masakiyo; Asakawa, Masayuki; Ono, Hirosato

2014-01-01

We investigate the time evolution of higher order cumulants of conserved charges in a volume with the diffusion master equation. Applying the result to the diffusion of non-Gaussian fluctuations in the hadronic stage of relativistic heavy ion collisions, we show that the fourth-order cumulant of net-electric charge at LHC energy is suppressed compared with the recently observed second-order cumulant at ALICE, if the higher order cumulants at hadronization are suppressed compared with their values in the hadron phase in equilibrium. The significance of the experimental information on the rapidity window dependence of various cumulants in investigating the history of the dynamical evolution of the hot medium created in relativistic heavy ion collisions is emphasized.

Loss of the insulator protein CTCF during nematode evolution

PubMed Central

Heger, Peter; Marin, Birger; Schierenberg, Einhard

2009-01-01

Background The zinc finger (ZF) protein CTCF (CCCTC-binding factor) is highly conserved in Drosophila and vertebrates where it has been shown to mediate chromatin insulation at a genomewide level. A mode of genetic regulation that involves insulators and insulator binding proteins to establish independent transcriptional units is currently not known in nematodes including Caenorhabditis elegans. We therefore searched in nematodes for orthologs of proteins that are involved in chromatin insulation. Results While orthologs for other insulator proteins were absent in all 35 analysed nematode species, we find orthologs of CTCF in a subset of nematodes. As an example for these we cloned the Trichinella spiralis CTCF-like gene and revealed a genomic structure very similar to the Drosophila counterpart. To investigate the pattern of CTCF occurrence in nematodes, we performed phylogenetic analysis with the ZF protein sets of completely sequenced nematodes. We show that three ZF proteins from three basal nematodes cluster together with known CTCF proteins whereas no zinc finger protein of C. elegans and other derived nematodes does so. Conclusion Our findings show that CTCF and possibly chromatin insulation are present in basal nematodes. We suggest that the insulator protein CTCF has been secondarily lost in derived nematodes like C. elegans. We propose a switch in the regulation of gene expression during nematode evolution, from the common vertebrate and insect type involving distantly acting regulatory elements and chromatin insulation to a so far poorly characterised mode present in more derived nematodes. Here, all or some of these components are missing. Instead operons, polycistronic transcriptional units common in derived nematodes, seemingly adopted their function. PMID:19712444

Streamwise Vorticity Generation in Laminar and Turbulent Jets

NASA Technical Reports Server (NTRS)

Demuren, Aodeji O.; Wilson, Robert V.

1999-01-01

Complex streamwise vorticity fields are observed in the evolution of non-circular jets. Generation mechanisms are investigated via Reynolds-averaged (RANS), large-eddy (LES) and direct numerical (DNS) simulations of laminar and turbulent rectangular jets. Complex vortex interactions are found in DNS of laminar jets, but axis-switching is observed only when a single instability mode is present in the incoming mixing layer. With several modes present, the structures are not coherent and no axis-switching occurs, RANS computations also produce no axis-switching. On the other hand, LES of high Reynolds number turbulent jets produce axis-switching even for cases with several instability modes in the mixing layer. Analysis of the source terms of the mean streamwise vorticity equation through post-processing of the instantaneous results shows that, complex interactions of gradients of the normal and shear Reynolds stresses are responsible for the generation of streamwise vorticity which leads to axis-switching. RANS computations confirm these results. k - epsilon turbulence model computations fail to reproduce the phenomenon, whereas algebraic Reynolds stress model (ASM) computations, in which the secondary normal and shear stresses are computed explicitly, succeeded in reproducing the phenomenon accurately.

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes.

PubMed

Lv, Jie; Havlak, Paul; Putnam, Nicholas H

2011-10-05

Many metazoan genomes conserve chromosome-scale gene linkage relationships ("macro-synteny") from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ) is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation. We examine a family of simple (one-parameter) extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context ("DCJ-[C]"), and is available as open source software from http://github.com/putnamlab/dcj-c. A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.

Evolution of larval competitiveness and associated life-history traits in response to host shifts in a seed beetle.

PubMed

Fox, C W; Messina, F J

2018-02-01

Resource competition is frequently strong among parasites that feed within small discrete resource patches, such as seeds or fruits. The properties of a host can influence the behavioural, morphological and life-history traits of associated parasites, including traits that mediate competition within the host. For seed parasites, host size may be an especially important determinant of competitive ability. Using the seed beetle, Callosobruchus maculatus, we performed replicated, reciprocal host shifts to examine the role of seed size in determining larval competitiveness and associated traits. Populations ancestrally associated with either a small host (mung bean) or a large one (cowpea) were switched to each other's host for 36 generations. Compared to control lines (those remaining on the ancestral host), lines switched from the small host to the large host evolved greater tolerance of co-occurring larvae within seeds (indicated by an increase in the frequency of small seeds yielding two adults), smaller egg size and higher fecundity. Each change occurred in the direction predicted by the traits of populations already adapted to cowpea. However, we did not observe the expected decline in adult mass following the shift to the larger host. Moreover, lines switched from the large host (cowpea) to the small host (mung bean) did not evolve the predicted increase in larval competitiveness or egg size, but did exhibit the predicted increase in body mass. Our results thus provide mixed support for the hypothesis that host size determines the evolution of competition-related traits of seed beetles. Evolutionary responses to the two host shifts were consistent among replicate lines, but the evolution of larval competition was asymmetric, with larval competitiveness evolving as predicted in one direction of host shift, but not the reverse. Nevertheless, our results indicate that switching hosts is sufficient to produce repeatable and rapid changes in the competition strategy and fitness-related traits of insect populations. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Access to Corporate Information Systems: Datafiles, Classified Documents, and Information Resources.

ERIC Educational Resources Information Center

Baumgartner, Kurt O.; And Others

1988-01-01

Three articles discuss aspects of corporate information systems: (1) "Packet Switching Networks: Worldwide Access to Corporate Datafiles" (Kurt O. Baumgartner); "Classified Documents in the Corporate Library" (Patricia M. Shores); and "From Library to Information Center: Case Studies in the Evolution of Corporate…

Evolution of meiotic recombination genes in maize and teosinte.

PubMed

Sidhu, Gaganpreet K; Warzecha, Tomasz; Pawlowski, Wojciech P

2017-01-25

Meiotic recombination is a major source of genetic variation in eukaryotes. The role of recombination in evolution is recognized but little is known about how evolutionary forces affect the recombination pathway itself. Although the recombination pathway is fundamentally conserved across different species, genetic variation in recombination components and outcomes has been observed. Theoretical predictions and empirical studies suggest that changes in the recombination pathway are likely to provide adaptive abilities to populations experiencing directional or strong selection pressures, such as those occurring during species domestication. We hypothesized that adaptive changes in recombination may be associated with adaptive evolution patterns of genes involved in meiotic recombination. To examine how maize evolution and domestication affected meiotic recombination genes, we studied patterns of sequence polymorphism and divergence in eleven genes controlling key steps in the meiotic recombination pathway in a diverse set of maize inbred lines and several accessions of teosinte, the wild ancestor of maize. We discovered that, even though the recombination genes generally exhibited high sequence conservation expected in a pathway controlling a key cellular process, they showed substantial levels and diverse patterns of sequence polymorphism. Among others, we found differences in sequence polymorphism patterns between tropical and temperate maize germplasms. Several recombination genes displayed patterns of polymorphism indicative of adaptive evolution. Despite their ancient origin and overall sequence conservation, meiotic recombination genes can exhibit extensive and complex patterns of molecular evolution. Changes in these genes could affect the functioning of the recombination pathway, and may have contributed to the successful domestication of maize and its expansion to new cultivation areas.

Observations of two-dimensional magnetic field evolution in a plasma opening switch

NASA Astrophysics Data System (ADS)

Shpitalnik, R.; Weingarten, A.; Gomberoff, K.; Krasik, Ya.; Maron, Y.

1998-03-01

The time dependent magnetic field distribution was studied in a coaxial 100-ns positive-polarity Plasma Opening Switch (POS) by observing the Zeeman effect in ionic line emission. Measurements local in three dimensions are obtained by doping the plasma using laser evaporation techniques. Fast magnetic field penetration with a relatively sharp magnetic field front (⩽1 cm) is observed at the early stages of the pulse (t≲25). Later in the pulse, the magnetic field is observed at the load-side edge of the plasma, leaving "islands" of low magnetic field at the plasma center that last for about 10 ns. The two-dimensional (2-D) structure of the magnetic field in the r,z plane is compared to the results of an analytical model based on electron-magneto-hydrodynamics, that utilizes the measured 2-D plasma density distribution and assumes fast magnetic field penetration along both POS electrodes. The model results provide quantitative explanation for the magnetic field evolution observed.

Probing domain switching dynamics in ferroelectric thick films by small field e31,f piezoelectric measurement

NASA Astrophysics Data System (ADS)

Cheng, Hongbo; Ouyang, Jun; Kanno, Isaku

2017-07-01

Epitaxial Pb(Zr0.53Ti0.47)O3 films were grown on (001) Pt/(001) MgO via rf-magnetron sputtering. Switching dynamics of 90° and 180° domains under bi-polar electric fields were probed by using small-field e31 ,f measurements in which the evolution of the transverse piezoelectric response with the bias voltage represents a set of fingerprints of the evolving domain structure. Furthermore, the asymmetric e31 ,f-V curves revealed a strong built-in electric field, which was verified by the standard polarization-electric field hysteresis measurement. Finally, X-ray 2θ-scan patterns under DC bias voltages were collected for the piezoelectric specimen. The domain switching sequence indicated by the XRD results is consistent with that revealed by the e31 ,f measurement.

Harmonic Bloch and dipole oscillations and their transition in elliptical optical waveguide arrays

NASA Astrophysics Data System (ADS)

Chan, Yun San; Zheng, Ming Jie; Yu, Kin Wah

2011-03-01

We have studied harmonic oscillations in an elliptical optical waveguide array in which the couplings between neighboring waveguides are varied in accord with a Kac matrix so that the propagation constant eigenvalues can take equally spaced values. As a result, the long-living optical Bloch oscillation (BO) and dipole oscillation (DO) are obtained. Moreover, when a linear gradient in the propagation constant is applied, we achieve a switching from DO to BO and vice versa by ramping up or down the gradient profile]. The various optical oscillations as well as their switching are investigated by field evolution analysis and confirmed by Hamiltonian optics. The equally spaced eigenvalues in the propagation constant allow viable applications in transmitting images, switching and routing of optical signals. Work supported by the General Research Fund of the Hong Kong SAR Government.

Generation and the role of dislocations in single-crystalline phase-change In 2 Se 3 nanowires under electrical pulses

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

Mafi, Elham; Tao, Xin; Zhu, Wenguang

2016-07-08

Using single crystalline In2Se3 nanowires as a platform, we have studied the RESET switching (from low to high electrical resistance) in this phase-change material under electric pulses. Particularly, we correlated the atomic-scale structural evolutions with local electrical resistance variations, by performing transmission electron microscopy and scanning Kelvin probe microscopy on the same nanowires. By coupling the experimental results with density functional theory calculations, we show that the immobile dislocations generated via vacancy condensations are responsible for the RESET switching and that the material maintains the single crystallinity during the process. This new mechanism is fundamentally different from the crystalline-amorphous transition,more » which is commonly understood as the underlying process for the RESET switching in similar phase-change materials.« less

Cognitive and Affective Changes in Mild to Moderate Alzheimer’s Disease Patients Undergoing Switch of Cholinesterase Inhibitors: A 6-Month Observational Study

PubMed Central

Spalletta, Gianfranco; Caltagirone, Carlo; Padovani, Alessandro; Sorbi, Sandro; Attar, Mahmood; Colombo, Delia; Cravello, Luca

2014-01-01

Patients with Alzheimer’s disease after an initial response to cholinesterase inhibitors may complain a later lack of efficacy. This, in association with incident neuropsychiatric symptoms, may worsen patient quality of life. Thus, the switch to another cholinesterase inhibitor could represent a valid therapeutic strategy. The aim of this study was to investigate the effectiveness of the switch from one to another cholinesterase inhibitor on cognitive and affective symptoms in mild to moderate Alzheimer disease patients. Four hundred twenty-three subjects were included from the EVOLUTION study, an observational, longitudinal, multicentre study conducted on Alzheimer disease patients who switched to different cholinesterase inhibitor due either to lack/loss of efficacy or response, reduced tolerability or poor compliance. All patients underwent cognitive and neuropsychiatric assessments, carried out before the switch (baseline), and at 3 and 6-month follow-up. A significant effect of the different switch types was found on Mini-Mental State Examination score during time, with best effectiveness on mild Alzheimer’s disease patients switching from oral cholinesterase inhibitors to rivastigmine patch. Depressive symptoms, when measured using continuous Neuropsychiatric Inventory values, decreased significantly, while apathy symptoms remained stable over the 6 months after the switch. However, frequency of both depression and apathy, when measured categorically using Neuropsychiatric Inventory cut-off scores, did not change significantly during time. In mild to moderate Alzheimer disease patients with loss of efficacy and tolerability during cholinesterase inhibitor treatment, the switch to another cholinesterase inhibitor may represent an important option for slowing cognitive deterioration. The evidence of apathy stabilization and the positive tendency of depressive symptom improvement should definitively be confirmed in double-blind controlled studies. PMID:24586603

MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

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

Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.

2004-10-28

We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

Reactive molecular dynamics simulations of switching processes of azobenzene-based monolayer on surface

NASA Astrophysics Data System (ADS)

Tian, Ziqi; Wen, Jin; Ma, Jing

2013-07-01

It is a challenge to simulate the switching process of functional self-assembled monolayers (SAMs) on metal surfaces, since the systems consist of thousands of atoms and the switching is triggered by quantum-mechanical events. Herein a molecular dynamics simulation with a reactive rotation potential of N=N bond is implemented to investigate the dynamic conformational changes and packing effects on the stimuli-responsive isomerization of the terminally thiol functionalized azobiphenyls (AZOs), which are bound on the Au(111) surface. To, respectively, distinguish the time evolutions that start from cis and trans initial configurations, two different functions are established to model the potential energy curves for cis-to-trans and trans-to-cis transitions, instead of the only one cosine function used in the conventional non-reactive force fields. In order to simulate the conformation transitions of the AZO film on surface, a random switching function, depending on the N=N twisting angle, is constructed to consider both forward and backward cis/trans isomerization events and to trigger the reaction by changing the N atom types automatically. The factors that will influence the isomerization process, including the choice of ensembles and thermostat algorithms, the time intervals separating each switching, and the forms of the switching function, are systematically tested. Most AZO molecules switch from the cis to trans configuration with a coverage of 5.76 × 10-6 mol/m2 on a picosecond time scale, and a low coverage might make the switching irreversible, which is in agreement with the experiments.

Ecological interactions are evolutionarily conserved across the entire tree of life.

PubMed

Gómez, José M; Verdú, Miguel; Perfectti, Francisco

2010-06-17

Ecological interactions are crucial to understanding both the ecology and the evolution of organisms. Because the phenotypic traits regulating species interactions are largely a legacy of their ancestors, it is widely assumed that ecological interactions are phylogenetically conserved, with closely related species interacting with similar partners. However, the existing empirical evidence is inadequate to appropriately evaluate the hypothesis of phylogenetic conservatism in ecological interactions, because it is both ecologically and taxonomically biased. In fact, most studies on the evolution of ecological interactions have focused on specialized organisms, such as some parasites or insect herbivores, belonging to a limited subset of the overall tree of life. Here we study the evolution of host use in a large and diverse group of interactions comprising both specialist and generalist acellular, unicellular and multicellular organisms. We show that, as previously found for specialized interactions, generalized interactions can be evolutionarily conserved. Significant phylogenetic conservatism of interaction patterns was equally likely to occur in symbiotic and non-symbiotic interactions, as well as in mutualistic and antagonistic interactions. Host-use differentiation among species was higher in phylogenetically conserved clades, irrespective of their generalization degree and taxonomic position within the tree of life. Our findings strongly suggest a shared pattern in the organization of biological systems through evolutionary time, mediated by marked conservatism of ecological interactions among taxa.

Characterisation of the current switch mechanism in two-stage wire array Z-pinches

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

Burdiak, G. C.; Lebedev, S. V.; Harvey-Thompson, A. J.

2015-11-15

In this paper, we describe the operation of a two-stage wire array z-pinch driven by the 1.4 MA, 240 ns rise-time Magpie pulsed-power device at Imperial College London. In this setup, an inverse wire array acts as a fast current switch, delivering a current pre-pulse into a cylindrical load wire array, before rapidly switching the majority of the generator current into the load after a 100–150 ns dwell time. A detailed analysis of the evolution of the load array during the pre-pulse is presented. Measurements of the load resistivity and energy deposition suggest significant bulk heating of the array mass occurs. Themore » ∼5 kA pre-pulse delivers ∼0.8 J of energy to the load, leaving it in a mixed, predominantly liquid-vapour state. The main current switch occurs as the inverse array begins to explode and plasma expands into the load region. Electrical and imaging diagnostics indicate that the main current switch may evolve in part as a plasma flow switch, driven by the expansion of a magnetic cavity and plasma bubble along the length of the load array. Analysis of implosion trajectories suggests that approximately 1 MA switches into the load in 100 ns, corresponding to a doubling of the generator dI/dt. Potential scaling of the device to higher current machines is discussed.« less

Tempo and Mode of Gene Duplication in Mammalian Ribosomal Protein Evolution

PubMed Central

Gajdosik, Matthew D.; Simon, Amanda; Nelson, Craig E.

2014-01-01

Gene duplication has been widely recognized as a major driver of evolutionary change and organismal complexity through the generation of multi-gene families. Therefore, understanding the forces that govern the evolution of gene families through the retention or loss of duplicated genes is fundamentally important in our efforts to study genome evolution. Previous work from our lab has shown that ribosomal protein (RP) genes constitute one of the largest classes of conserved duplicated genes in mammals. This result was surprising due to the fact that ribosomal protein genes evolve slowly and transcript levels are very tightly regulated. In our present study, we identified and characterized all RP duplicates in eight mammalian genomes in order to investigate the tempo and mode of ribosomal protein family evolution. We show that a sizable number of duplicates are transcriptionally active and are very highly conserved. Furthermore, we conclude that existing gene duplication models do not readily account for the preservation of a very large number of intact retroduplicated ribosomal protein (RT-RP) genes observed in mammalian genomes. We suggest that selection against dominant-negative mutations may underlie the unexpected retention and conservation of duplicated RP genes, and may shape the fate of newly duplicated genes, regardless of duplication mechanism. PMID:25369106

Experimental tests of coherence and entanglement conservation under unitary evolutions

NASA Astrophysics Data System (ADS)

Černoch, Antonín; Bartkiewicz, Karol; Lemr, Karel; Soubusta, Jan

2018-04-01

We experimentally demonstrate the migration of coherence between composite quantum systems and their subsystems. The quantum systems are implemented using polarization states of photons in two experimental setups. The first setup is based on a linear optical controlled-phase quantum gate and the second scheme utilizes effects of nonlinear optics. Our experiment allows one to verify the relation between correlations of the subsystems and the coherence of the composite system, which was given in terms of a conservation law for maximal accessible coherence by Svozilík et al. [J. Svozilík et al., Phys. Rev. Lett. 115, 220501 (2015), 10.1103/PhysRevLett.115.220501]. We observe that the maximal accessible coherence is conserved for the implemented class of global evolutions of the composite system.

Myosin MyTH4-FERM structures highlight important principles of convergent evolution.

PubMed

Planelles-Herrero, Vicente José; Blanc, Florian; Sirigu, Serena; Sirkia, Helena; Clause, Jeffrey; Sourigues, Yannick; Johnsrud, Daniel O; Amigues, Beatrice; Cecchini, Marco; Gilbert, Susan P; Houdusse, Anne; Titus, Margaret A

2016-05-24

Myosins containing MyTH4-FERM (myosin tail homology 4-band 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found in a wide range of phylogenetically divergent organisms, such as humans and the social amoeba Dictyostelium (Dd). Interestingly, evolutionarily distant MF myosins have similar roles in the extension of actin-filled membrane protrusions such as filopodia and bind to microtubules (MT), suggesting that the core functions of these MF myosins have been highly conserved over evolution. The structures of two DdMyo7 signature MF domains have been determined and comparison with mammalian MF structures reveals that characteristic features of MF domains are conserved. However, across millions of years of evolution conserved class-specific insertions are seen to alter the surfaces and the orientation of subdomains with respect to each other, likely resulting in new sites for binding partners. The MyTH4 domains of Myo10 and DdMyo7 bind to MT with micromolar affinity but, surprisingly, their MT binding sites are on opposite surfaces of the MyTH4 domain. The structural analysis in combination with comparison of diverse MF myosin sequences provides evidence that myosin tail domain features can be maintained without strict conservation of motifs. The results illustrate how tuning of existing features can give rise to new structures while preserving the general properties necessary for myosin tails. Thus, tinkering with the MF domain enables it to serve as a multifunctional platform for cooperative recruitment of various partners, allowing common properties such as autoinhibition of the motor and microtubule binding to arise through convergent evolution.

Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders

PubMed Central

Haney, Robert A.; Clarke, Thomas H.; Gadgil, Rujuta; Fitzpatrick, Ryan; Hayashi, Cheryl Y.; Ayoub, Nadia A.; Garb, Jessica E.

2016-01-01

Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. By assembling and analyzing multitissue transcriptomes from the Western black widow spider and two closely related species with distinct venom toxicity phenotypes, we do not find that gene duplication and duplicate retention is greater in gene families with venom gland biased expression in comparison with broadly expressed families. Positive selection has acted on some venom toxin families, but does not appear to be in excess for families with venom gland biased expression. Moreover, we find 309 distinct gene families that have single transcripts with venom gland biased expression, suggesting that the switching of genes to venom gland expression in numerous unrelated gene families has been a dominant mode of evolution. We also find ample variation in protein sequences of venom gland–specific transcripts, lineage-specific family sizes, and ortholog expression among species. This variation might contribute to the variable venom toxicity of these species. PMID:26733576

The Wor1-like protein Fgp1 regulates pathogenicity, toxin synthesis and reproduction in the phytopathogenic fungus Fusarium graminearum

USDA-ARS?s Scientific Manuscript database

WOR1 is a gene for a conserved fungal regulatory protein controlling the dimorphic switch and pathogenicity in Candida albicans and its ortholog in the plant pathogen Fusarium oxysporum, called SGE1, is also required for pathogenicity and expression of plant effector proteins. F. graminearum, an imp...

An Evaluation of Magazines Suitable for Public Libraries for the Presence of Alkaline Paper.

ERIC Educational Resources Information Center

Gambrill, Linda

Conservation of library materials is becoming an increasing concern, and there has been some effort by publishers to avert the problems created by acidic paper by switching to acid-free alkaline paper. University publishers, responded to this concern by committing themselves to using acid-free paper; however, most commercial publishers, who…

Designing marine reserves to reflect local socioeconomic conditions: lessons from long-enduring customary management systems

NASA Astrophysics Data System (ADS)

Cinner, J. E.

2007-12-01

Coral reef conservation strategies such as marine protected areas have met limited success in many developing countries. Some researchers attribute part of these shortcomings to inadequate attention to the social context of conserving marine resources. To gain insights into applying Western conservation theory more successfully in the socioeconomic context of developing countries, this study examines how long-enduring, customary reef closures appear to reflect local socioeconomic conditions in two Papua New Guinean communities. Attributes of the customary management (including size, shape, permanence, and gear restrictions) are examined in relation to prevailing socioeconomic conditions (including resource users’ ability to switch gears, fishing grounds, and occupations). Customary closures in the two communities appear to reflect local socioeconomic circumstances in three ways. First, in situations where people can readily switch between occupations, full closures are acceptable with periodic harvests to benefit from the closure. In comparison, communities with high dependence on the marine resources are more conducive to employing strategies that restrict certain gear types while still allowing others. Second, where there is multiple clan and family spatial ownership of resources, the communities have one closure per clan/family; one large no-take area would have disproportionate affect on those compared to the rest of the community. In contrast, communities that have joint ownership can establish one large closure as long as there are other areas available to harvest. Third, historical and trade relationships with neighboring communities can influence regulations by creating the need for occasional harvests to provide fish for feasts. This study further demonstrates the importance of understanding the socioeconomic context of factors such as community governance and levels of dependence for the conservation of marine resources.

Chromosome size in diploid eukaryotic species centers on the average length with a conserved boundary

USDA-ARS?s Scientific Manuscript database

Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation...

Substantial Loss of Conserved and Gain of Novel MicroRNA Families in Flatworms

PubMed Central

Fromm, Bastian; Worren, Merete Molton; Hahn, Christoph; Hovig, Eivind; Bachmann, Lutz

2013-01-01

Recent studies on microRNA (miRNA) evolution focused mainly on the comparison of miRNA complements between animal clades. However, evolution of miRNAs within such groups is poorly explored despite the availability of comparable data that in some cases lack only a few key taxa. For flatworms (Platyhelminthes), miRNA complements are available for some free-living flatworms and all major parasitic lineages, except for the Monogenea. We present the miRNA complement of the monogenean flatworm Gyrodactylus salaris that facilitates a comprehensive analysis of miRNA evolution in Platyhelminthes. Using the newly designed bioinformatics pipeline miRCandRef, the miRNA complement was disentangled from next-generation sequencing of small RNAs and genomic DNA without a priori genome assembly. It consists of 39 miRNA hairpin loci of conserved miRNA families, and 22 novel miRNAs. A comparison with the miRNA complements of Schmidtea mediterranea (Turbellaria), Schistosoma japonicum (Trematoda), and Echinococcus granulosus (Cestoda) reveals a substantial loss of conserved bilaterian, protostomian, and lophotrochozoan miRNAs. Eight of the 46 expected conserved miRNAs were lost in all flatworms, 16 in Neodermata and 24 conserved miRNAs could not be detected in the cestode and the trematode. Such a gradual loss of miRNAs has not been reported before for other animal phyla. Currently, little is known about miRNAs in Platyhelminthes, and for the majority of the lost miRNAs there is no prediction of function. As suggested earlier they might be related to morphological simplifications. The presence and absence of 153 conserved miRNAs was compared for platyhelminths and 32 other metazoan taxa. Phylogenetic analyses support the monophyly of Platyhelminthes (Turbellaria + Neodermata [Monogenea {Trematoda + Cestoda}]). PMID:24025793

Convergent evolution of hemoglobin switching in jawed and jawless vertebrates.

PubMed

Rohlfing, Kim; Stuhlmann, Friederike; Docker, Margaret F; Burmester, Thorsten

2016-02-01

During development, humans and other jawed vertebrates (Gnathostomata) express distinct hemoglobin genes, resulting in different hemoglobin tetramers. Embryonic and fetal hemoglobin have higher oxygen affinities than the adult hemoglobin, sustaining the oxygen demand of the developing organism. Little is known about the expression of hemoglobins during development of jawless vertebrates (Agnatha). We identified three hemoglobin switches in the life cycle of the sea lamprey. Three hemoglobin genes are specifically expressed in the embryo, four genes in the filter feeding larva (ammocoete), and nine genes correspond to the adult hemoglobin chains. During the development from the parasitic to the reproductive adult, the composition of hemoglobin changes again, with a massive increase of chain aHb1. A single hemoglobin chain is expressed constitutively in all stages. We further showed the differential expression of other globin genes: Myoglobin 1 is most highly expressed in the reproductive adult, myoglobin 2 expression peaks in the larva. Globin X1 is restricted to the embryo; globin X2 was only found in the reproductive adult. Cytoglobin is expressed at low levels throughout the life cycle. Because the hemoglobins of jawed and jawless vertebrates evolved independently from a common globin ancestor, hemoglobin switching must also have evolved convergently in these taxa. Notably, the ontogeny of sea lamprey hemoglobins essentially recapitulates their phylogeny, with the embryonic hemoglobins emerging first, followed by the evolution of larval and adult hemoglobins.

Sedimentary sequence evolution in a Foredeep basin: Eastern Venezuela

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

Bejarano, C.; Funes, D.; Sarzalho, S.

1996-08-01

Well log-seismic sequence stratigraphy analysis in the Eastern Venezuela Foreland Basin leads to study of the evolution of sedimentary sequences onto the Cretaceous-Paleocene passive margin. This basin comprises two different foredeep sub-basins: The Guarico subbasin to the west, older, and the Maturin sub-basin to the east, younger. A foredeep switching between these two sub-basins is observed at 12.5 m.y. Seismic interpretation and well log sections across the study area show sedimentary sequences with transgressive sands and coastal onlaps to the east-southeast for the Guarico sub-basin, as well as truncations below the switching sequence (12.5 m.y.), and the Maturin sub-basin showsmore » apparent coastal onlaps to the west-northwest, as well as a marine onlap (deeper water) in the west, where it starts to establish. Sequence stratigraphy analysis of these sequences with well logs allowed the study of the evolution of stratigraphic section from Paleocene to middle Miocene (68.0-12.0 m.y.). On the basis of well log patterns, the sequences were divided in regressive-transgressive-regressive sedimentary cycles caused by changes in relative sea level. Facies distributions were analyzed and the sequences were divided into simple sequences or sub- sequences of a greater frequencies than third order depositional sequences.« less

Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives

PubMed Central

Burggren, Warren

2016-01-01

Epigenetics increasingly occupies a pivotal position in our understanding of inheritance, natural selection and, perhaps, even evolution. A survey of the PubMed database, however, reveals that the great majority (>93%) of epigenetic papers have an intra-, rather than an inter-generational focus, primarily on mechanisms and disease. Approximately ~1% of epigenetic papers even mention the nexus of epigenetics, natural selection and evolution. Yet, when environments are dynamic (e.g., climate change effects), there may be an “epigenetic advantage” to phenotypic switching by epigenetic inheritance, rather than by gene mutation. An epigenetically-inherited trait can arise simultaneously in many individuals, as opposed to a single individual with a gene mutation. Moreover, a transient epigenetically-modified phenotype can be quickly “sunsetted”, with individuals reverting to the original phenotype. Thus, epigenetic phenotype switching is dynamic and temporary and can help bridge periods of environmental stress. Epigenetic inheritance likely contributes to evolution both directly and indirectly. While there is as yet incomplete evidence of direct permanent incorporation of a complex epigenetic phenotype into the genome, doubtlessly, the presence of epigenetic markers and the phenotypes they create (which may sort quite separately from the genotype within a population) will influence natural selection and, so, drive the collective genotype of a population. PMID:27231949

Tectonic mode switches and the nature of orogenesis

NASA Astrophysics Data System (ADS)

Lister, Gordon; Forster, Marnie

2009-12-01

The birth and death of many mountain belts occurs in lithosphere that over-rides major subduction zones. Here the tectonic mode (shortening versus extension) can abruptly switch, even during continuous and otherwise smooth convergence. If the hinge line of the foundering slab rapidly retreats (i.e. rolls back), the foundering slab creates a gravitational potential well into which the orogen collapses. This motion, coupled with stress guides, can "pull" the orogen apart. A slowing of roll-back (or of hinge retreat) means that the subduction flexure may subsequently begin to be "pushed back" or be "pushed over" by the advancing orogen. The consequence of such changes in relative motion is that orogenic belts are affected by abrupt tectonic mode switches. The change from "push" to "pull" leads to a sudden change from horizontal extension to horizontal shortening, potentially throughout the entire mass of the orogenic lithosphere that over-rides the subducting slab. The sequencing of these tectonic mode switches affects the thermal evolution of the orogen, and thus fundamentally determines the nature of orogenesis. This insight led to us to our quite different views as to how orogens work. It is evident that orogens affected by abrupt "push-pull" mode switches are characterized by high-pressure metamorphism, whereas orogens affected by abrupt "pull-push" mode switches are characterized by high-temperature metamorphism, magmatism and anatexis.

Principles of time evolution in classical physics

NASA Astrophysics Data System (ADS)

Güémez, J.; Fiolhais, M.

2018-07-01

We address principles of time evolution in classical mechanical/thermodynamical systems in translational and rotational motion, in three cases: when there is conservation of mechanical energy, when there is energy dissipation and when there is mechanical energy production. In the first case, the time derivative of the Hamiltonian vanishes. In the second one, when dissipative forces are present, the time evolution is governed by the minimum potential energy principle, or, equivalently, maximum increase of the entropy of the universe. Finally, in the third situation, when internal sources of work are available to the system, it evolves in time according to the principle of minimum Gibbs function. We apply the Lagrangian formulation to the systems, dealing with the non-conservative forces using restriction functions such as the Rayleigh dissipative function.

Contemporary cultural evolution of a conspecific recognition signal following serial translocations.

PubMed

Parker, Kevin A; Hauber, Mark E; Brunton, Dianne H

2010-08-01

The divergence of conspecific recognition signals (CRS) among isolated populations facilitates the evolution of behavioral barriers to gene flow. The influence of CRS evolution on signal effectiveness in isolated populations can be assessed by testing the salience of changes in CRS from surviving ancestral populations but founder events are rarely detected. The population history of the North Island (NI) saddleback Philesturnus rufusater is absolutely known following conservation translocations which increased the number of populations from 1 to 15. With one exception there is no gene flow between these populations. The translocations have generated interisland divergence of male rhythmical song (MRS), a culturally transmitted CRS. We conducted an experimental test of behavioral discrimination in NI saddlebacks exposed to familiar and unfamiliar MRS and found that responses were significantly stronger for familiar MRS, consistent with a model of contemporary cultural evolution leading to discrimination between geographic song variants. Significantly, this result demonstrates the rapid tempo with which discrimination of CRS might evolve within isolated populations and supports both bottleneck and cultural mutation hypotheses in CRS evolution. The evolutionary implications of contemporary cultural evolution in the production and perception of CRS merit debate on the time frames over which conservation management is evaluated.

Long-term phenotypic evolution of bacteria.

PubMed

Plata, Germán; Henry, Christopher S; Vitkup, Dennis

2015-01-15

For many decades comparative analyses of protein sequences and structures have been used to investigate fundamental principles of molecular evolution. In contrast, relatively little is known about the long-term evolution of species' phenotypic and genetic properties. This represents an important gap in our understanding of evolution, as exactly these proprieties play key roles in natural selection and adaptation to diverse environments. Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. Overall, bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow long-term exponential divergence. The observed average divergence trend, with approximately similar fractions of phenotypic properties changing per unit time, continues for billions of years. We experimentally confirm the predicted divergence trend using the phenotypic profiles of 40 diverse bacterial species across more than 60 growth conditions. Our analysis suggests that, at long evolutionary distances, gene essentiality is significantly more conserved than the ability to utilize different nutrients, while synthetic lethality is significantly less conserved. We also find that although a rapid phenotypic evolution is sometimes observed within the same species, a transition from high to low phenotypic similarity occurs primarily at the genus level.

The Calcineurin Signaling Network Evolves Via Conserved Kinase–Phosphatase Modules That Transcend Substrate Identity

PubMed Central

Bodenmiller, Bernd; Wanka, Stefanie; Landry, Christian R.; Aebersold, Ruedi; Cyert, Martha S.

2014-01-01

Summary To define the first functional network for calcineurin, the conserved Ca2+/calmodulin-regulated phosphatase, we systematically identified its substrates in S. cerevisiae using phosphoproteomics and bioinformatics, followed by co-purification and dephosphorylation assays. This study establishes new calcineurin functions and reveals mechanisms that shape calcineurin network evolution. Analyses of closely related yeasts show that many proteins were recently recruited to the network by acquiring a calcineurin-recognition motif. Calcineurin substrates in yeast and mammals are distinct due to network rewiring but surprisingly are phosphorylated by similar kinases. We postulate that co-recognition of conserved substrate features, including phosphorylation and docking motifs, preserves calcineurin-kinase opposition during evolution. One example we document is a composite docking site that confers substrate recognition by both calcineurin and MAPK. We propose that conserved kinase-phosphatase pairs define the architecture of signaling networks and allow other connections between kinases and phosphatases to develop and establish common regulatory motifs in signaling networks. PMID:24930733

Entanglement conservation, ER=EPR, and a new classical area theorem for wormholes

DOE PAGES

Remmen, Grant N.; Bao, Ning; Pollack, Jason

2016-07-11

We consider the question of entanglement conservation in the context of the ER=EPR correspondence equating quantum entanglement with wormholes. In quantum mechanics, the entanglement between a system and its complement is conserved under unitary operations that act independently on each; ER=EPR suggests that an analogous statement should hold for wormholes. We accordingly prove a new area theorem in general relativity: for a collection of dynamical wormholes and black holes in a spacetime satisfying the null curvature condition, the maximin area for a subset of the horizons (giving the largest area attained by the minimal cross section of the multi-wormhole throatmore » separating the subset from its complement) is invariant under classical time evolution along the outermost apparent horizons. The evolution can be completely general, including horizon mergers and the addition of classical matter satisfying the null energy condition. In conclusion, this theorem is the gravitational dual of entanglement conservation and thus constitutes an explicit characterization of the ER=EPR duality in the classical limit.« less

Entanglement conservation, ER=EPR, and a new classical area theorem for wormholes

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

Remmen, Grant N.; Bao, Ning; Pollack, Jason

We consider the question of entanglement conservation in the context of the ER=EPR correspondence equating quantum entanglement with wormholes. In quantum mechanics, the entanglement between a system and its complement is conserved under unitary operations that act independently on each; ER=EPR suggests that an analogous statement should hold for wormholes. We accordingly prove a new area theorem in general relativity: for a collection of dynamical wormholes and black holes in a spacetime satisfying the null curvature condition, the maximin area for a subset of the horizons (giving the largest area attained by the minimal cross section of the multi-wormhole throatmore » separating the subset from its complement) is invariant under classical time evolution along the outermost apparent horizons. The evolution can be completely general, including horizon mergers and the addition of classical matter satisfying the null energy condition. In conclusion, this theorem is the gravitational dual of entanglement conservation and thus constitutes an explicit characterization of the ER=EPR duality in the classical limit.« less

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing

PubMed Central

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-01-01

ABSTRACT Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure. PMID:28277933

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

PubMed

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-10-03

Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.

Mapping Flexibility and the Assembly Switch of Cell Division Protein FtsZ by Computational and Mutational Approaches*♦

PubMed Central

Martín-Galiano, Antonio J.; Buey, Rubén M.; Cabezas, Marta; Andreu, José M.

2010-01-01

The molecular switch for nucleotide-regulated assembly and disassembly of the main prokaryotic cell division protein FtsZ is unknown despite the numerous crystal structures that are available. We have characterized the functional motions in FtsZ with a computational consensus of essential dynamics, structural comparisons, sequence conservation, and networks of co-evolving residues. Employing this information, we have constructed 17 mutants, which alter the FtsZ functional cycle at different stages, to modify FtsZ flexibility. The mutant phenotypes ranged from benign to total inactivation and included increased GTPase, reduced assembly, and stabilized assembly. Six mutations clustering at the long cleft between the C-terminal β-sheet and core helix H7 deviated FtsZ assembly into curved filaments with inhibited GTPase, which still polymerize cooperatively. These mutations may perturb the predicted closure of the C-terminal domain onto H7 required for switching between curved and straight association modes and for GTPase activation. By mapping the FtsZ assembly switch, this work also gives insight into FtsZ druggability because the curved mutations delineate the putative binding site of the promising antibacterial FtsZ inhibitor PC190723. PMID:20472561

Mapping flexibility and the assembly switch of cell division protein FtsZ by computational and mutational approaches.

PubMed

Martín-Galiano, Antonio J; Buey, Rubén M; Cabezas, Marta; Andreu, José M

2010-07-16

The molecular switch for nucleotide-regulated assembly and disassembly of the main prokaryotic cell division protein FtsZ is unknown despite the numerous crystal structures that are available. We have characterized the functional motions in FtsZ with a computational consensus of essential dynamics, structural comparisons, sequence conservation, and networks of co-evolving residues. Employing this information, we have constructed 17 mutants, which alter the FtsZ functional cycle at different stages, to modify FtsZ flexibility. The mutant phenotypes ranged from benign to total inactivation and included increased GTPase, reduced assembly, and stabilized assembly. Six mutations clustering at the long cleft between the C-terminal beta-sheet and core helix H7 deviated FtsZ assembly into curved filaments with inhibited GTPase, which still polymerize cooperatively. These mutations may perturb the predicted closure of the C-terminal domain onto H7 required for switching between curved and straight association modes and for GTPase activation. By mapping the FtsZ assembly switch, this work also gives insight into FtsZ druggability because the curved mutations delineate the putative binding site of the promising antibacterial FtsZ inhibitor PC190723.

Conservation and diversification of Msx protein in metazoan evolution.

PubMed

Takahashi, Hirokazu; Kamiya, Akiko; Ishiguro, Akira; Suzuki, Atsushi C; Saitou, Naruya; Toyoda, Atsushi; Aruga, Jun

2008-01-01

Msx (/msh) family genes encode homeodomain (HD) proteins that control ontogeny in many animal species. We compared the structures of Msx genes from a wide range of Metazoa (Porifera, Cnidaria, Nematoda, Arthropoda, Tardigrada, Platyhelminthes, Mollusca, Brachiopoda, Annelida, Echiura, Echinodermata, Hemichordata, and Chordata) to gain an understanding of the role of these genes in phylogeny. Exon-intron boundary analysis suggested that the position of the intron located N-terminally to the HDs was widely conserved in all the genes examined, including those of cnidarians. Amino acid (aa) sequence comparison revealed 3 new evolutionarily conserved domains, as well as very strong conservation of the HDs. Two of the three domains were associated with Groucho-like protein binding in both a vertebrate and a cnidarian Msx homolog, suggesting that the interaction between Groucho-like proteins and Msx proteins was established in eumetazoan ancestors. Pairwise comparison among the collected HDs and their C-flanking aa sequences revealed that the degree of sequence conservation varied depending on the animal taxa from which the sequences were derived. Highly conserved Msx genes were identified in the Vertebrata, Cephalochordata, Hemichordata, Echinodermata, Mollusca, Brachiopoda, and Anthozoa. The wide distribution of the conserved sequences in the animal phylogenetic tree suggested that metazoan ancestors had already acquired a set of conserved domains of the current Msx family genes. Interestingly, although strongly conserved sequences were recovered from the Vertebrata, Cephalochordata, and Anthozoa, the sequences from the Urochordata and Hydrozoa showed weak conservation. Because the Vertebrata-Cephalochordata-Urochordata and Anthozoa-Hydrozoa represent sister groups in the Chordata and Cnidaria, respectively, Msx sequence diversification may have occurred differentially in the course of evolution. We speculate that selective loss of the conserved domains in Msx family proteins contributed to the diversification of animal body organization.

Electrical Characterization of Critical Phase Change Conditions in Nanoscale Ge2Sb2Te5 Pillars

NASA Astrophysics Data System (ADS)

Ozatay, Ozhan; Stipe, Barry; Katine, Jordan; Terris, Bruce

2008-03-01

Following the original work of Ovshinsky on disordered semiconductors that exhibit ovonic threshold switching (OTS) there has been substantial interest in the electronic reversible switching properties of chalcogenides^1. The current induced phase transitions between polycrystalline and amorphous states in these materials offer orders of magnitude changes in the conductance which makes them an ideal candidate for non-volatile data storage applications. In this work we investigate the scaling of critical programming conditions required to observe such transitions between highly resistive (disordered) and highly conductive (ordered) states by constructing a resistance map with various pulse widths and amplitudes under different cooling conditions (as a function of pulse trailing edge). We study the evolution of critical phase change conditions as a function of contact size (50nm-1μm) and shape (circle-square-rectangle). We compare the resulting switching behaviour with the predictions of a finite-element model of the electro-thermal physics to analyze the nature of the switching dynamics at the nanoscale. ^1 S-H. Lee, Y. Jung, R. Agarwal, Nature Nanotechnology; doi:10:1038/nnano.2007.291

Noise-driven switching and chaotic itinerancy among dynamic states in a three-mode intracavity second-harmonic generation laser operating on a Λ transition

NASA Astrophysics Data System (ADS)

Otsuka, Kenju; Ohtomo, Takayuki; Maniwa, Tsuyoshi; Kawasaki, Hazumi; Ko, Jing-Yuan

2003-09-01

We studied the antiphase self-pulsation in a globally coupled three-mode laser operating in different optical spectrum configurations. We observed locking of modal pulsation frequencies, quasiperiodicity, clustering behaviors, and chaos, resulting from the nonlinear interaction among modes. The robustness of [p:q:r] three-frequency locking states and quasiperiodic oscillations against residual noise has been examined by using joint time-frequency analysis of long-term experimental time series. Two sharply antithetical types of switching behaviors among different dynamic states were observed during temporal evolutions; noise-driven switching and self-induced switching, which manifests itself in chaotic itinerancy. The modal interplay behind observed behaviors was studied by using the statistical dynamic quantity of the information circulation. Well-organized information flows among modes, which correspond to the number of degeneracies of modal pulsation frequencies, were found to be established in accordance with the inherent antiphase dynamics. Observed locking behaviors, quasiperiodic motions, and chaotic itinerancy were reproduced by numerical simulation of the model equations.

EVIDENCE OF MAGNETIC FIELD SWITCH-OFF IN COLLISIONLESS MAGNETIC RECONNECTION

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

Innocenti, M. E.; Lapenta, G.; Goldman, M.

2015-09-10

The long-term evolution of large domain particle-in-cell simulations of collisionless magnetic reconnection is investigated following observations that show two possible outcomes for collisionless reconnection: toward a Petschek-like configuration or toward multiple X points. In the present simulation, a mixed scenario develops. At earlier time, plasmoids are emitted, disrupting the formation of Petschek-like structures. Later, an almost stationary monster plasmoid forms, preventing the emission of other plasmoids. A situation reminiscent of Petschek’s switch-off then ensues. Switch-off is obtained through a slow shock/rotational discontinuity compound structure. Two external slow shocks (SS) located at the separatrices reduce the in-plane tangential component of themore » magnetic field, but not to zero. Two transitions reminiscent of rotational discontinuities (RD) in the internal part of the exhaust then perform the final switch-off. Both the SS and the RD are characterized through analysis of their Rankine–Hugoniot jump conditions. A moderate guide field is used to suppress the development of the firehose instability in the exhaust.« less

Role of allosteric switch residue histidine 195 in maintaining active-site asymmetry in presynaptic filaments of bacteriophage T4 UvsX recombinase.

PubMed

Farb, Joshua N; Morrical, Scott W

2009-01-16

Recombinases of the highly conserved RecA/Rad51 family play central roles in homologous recombination and DNA double-stranded break repair. RecA/Rad51 enzymes form presynaptic filaments on single-stranded DNA (ssDNA) that are allosterically activated to catalyze ATPase and DNA strand-exchange reactions. Information is conveyed between DNA- and ATP-binding sites, in part, by a highly conserved glutamine residue (Gln194 in Escherichia coli RecA) that acts as an allosteric switch. The T4 UvsX protein is a divergent RecA ortholog and contains histidine (His195) in place of glutamine at the allosteric switch position. UvsX and RecA catalyze similar strand-exchange reactions, but differ in other properties. UvsX produces both ADP and AMP as products of its ssDNA-dependent ATPase activity--a property that is unique among characterized recombinases. Details of the kinetics of ssDNA-dependent ATP hydrolysis reactions indicate that UvsX-ssDNA presynaptic filaments are asymmetric and contain two classes of ATPase active sites: one that generates ADP, and another that generates AMP. Active-site asymmetry is reduced by mutations at the His195 position, since UvsX-H195Q and UvsX-H195A mutants both exhibit stronger ssDNA-dependent ATPase activity, with lower cooperativity and markedly higher ADP/AMP product ratios, than wild-type UvsX. Reduced active-site asymmetry correlates strongly with reduced ssDNA-binding affinity and DNA strand-exchange activity in both H195Q and H195A mutants. These and other results support a model in which allosteric switch residue His195 controls the formation of an asymmetric conformation of UvsX-ssDNA filaments that is active in DNA strand exchange. The implications of our findings for UvsX recombination functions, and for RecA functions in general, are discussed.

Opto-microwave Butler matrixes based front-end for a multi-beam large direct radiating array antenna

NASA Astrophysics Data System (ADS)

Piqueras, M. A.; Mengual, T.; Navasquillo, O.; Sotom, M.; Caille, G.

2017-09-01

The evolution of broadband communication satellites shows a clear trend towards beam forming and beam-switching systems with efficient multiple access schemes with wide bandwidths, for which to be economically viable, the communication price shall be as low as possible.

The ARPANET and DARPA Internet.

ERIC Educational Resources Information Center

Perry, Dennis G.; And Others

1988-01-01

Reviews the development and growth of the ARPANET, a wide-area packet switching network initiated by the U.S. Department of Defense in 1969. Evolution of the ARPANET into the DARPA (Advanced Research Projects Agency) Internet in the 1970s and current uses of the internet are discussed. (16 references) (MES)

Taking climate change seriously: An analysis of op-ed articles in Spanish press.

PubMed

Domínguez, Martí; Lafita, Íngrid; Mateu, Anna

2017-10-01

In this article, we study the evolution of opinion genres regarding climate change in three Spanish newspapers ( El País, El Mundo, and ABC). Analyzing the op-ed articles in these newspapers, we observe a significant change in the evolution of opinion. While denialism was very present in conservative press in 2007, 7 years later it is almost absent from El Mundo, and its presence in ABC is much lower and inactive: this shows that scientific consensus has prevailed over time and Spanish denialism has weakened, exclusively supported by political arguments by the most conservative parties.

GLOBECOM '89 - IEEE Global Telecommunications Conference and Exhibition, Dallas, TX, Nov. 27-30, 1989, Conference Record. Volumes 1, 2, & 3

NASA Astrophysics Data System (ADS)

The present conference discusses topics in multiwavelength network technology and its applications, advanced digital radio systems in their propagation environment, mobile radio communications, switching programmability, advancements in computer communications, integrated-network management and security, HDTV and image processing in communications, basic exchange communications radio advancements in digital switching, intelligent network evolution, speech coding for telecommunications, and multiple access communications. Also discussed are network designs for quality assurance, recent progress in coherent optical systems, digital radio applications, advanced communications technologies for mobile users, communication software for switching systems, AI and expert systems in network management, intelligent multiplexing nodes, video and image coding, network protocols and performance, system methods in quality and reliability, the design and simulation of lightwave systems, local radio networks, mobile satellite communications systems, fiber networks restoration, packet video networks, human interfaces for future networks, and lightwave networking.

[Storing succinylcholine in prehospital settings following the recommendations of the French National Agency for the safety of medicines].

PubMed

Lefort, H; Mendibil, A; Margerin, S; Cuquel, A-C; Jost, D; Tazarourte, K; Domanski, L; Tourtier, J-P

2014-06-01

The French National Pharmaceuticals Agency (ANSM) has recommanded in July 2012 not to break the cold chain before using succinylcholine (Celocurine®). to understand the pre-clinical evolution of the conservation modes of this curare. Descriptive study before (year 2011) and after (year 2012). Online survey to French Samu/Smur. SMUR location, conservation method at clinical base, in the mobile unit (UMH) and at the patient. Principal decision criteria: evolution of the conservation modes before and after the recommendation (qualitatives variables compared with a Fisher test). Out of 101 SAMU/SMUR, 62 answered. Conservation modes of succinylcholine vials were significantly different (P<0.001). Proper conservation was observed in 26 % of the cases before and 43 % after. Mobile units (UMH) equipped with a fridge increased from one out of two to 77 %. The lack of conservation modes passive or active on UMH went from 31 % to 3.4 % with isotherms bags with ice when a fridge was not available. The destruction of capsules at current temperature in a 24-hour period increased: 22 % before, 47 % after (P=0.04). After recommendations from ANSM, conservation modes and destruction of succinylcholine in a prehospital environment were significantly impacted. Copyright © 2014 Société française d’anesthésie et de réanimation (Sfar). Published by Elsevier SAS. All rights reserved.

Solvation and Evolution Dynamics of an Excess Electron in Supercritical CO2

NASA Astrophysics Data System (ADS)

Wang, Zhiping; Liu, Jinxiang; Zhang, Meng; Cukier, Robert I.; Bu, Yuxiang

2012-05-01

We present an ab initio molecular dynamics simulation of the dynamics of an excess electron solvated in supercritical CO2. The excess electron can exist in three types of states: CO2-core localized, dual-core localized, and diffuse states. All these states undergo continuous state conversions via a combination of long lasting breathing oscillations and core switching, as also characterized by highly cooperative oscillations of the excess electron volume and vertical detachment energy. All of these oscillations exhibit a strong correlation with the electron-impacted bending vibration of the core CO2, and the core-switching is controlled by thermal fluctuations.

Advances in methods to characterize ligand-induced ionic lock and rotamer toggle molecular switch in G protein-coupled receptors.

PubMed

Xie, Xiang-Qun; Chowdhury, Ananda

2013-01-01

Structural biology of GPCRs has made significant progress upon recently developed technologies for GPCRs expression/purification and elucidation of GPCRs crystal structures. The crystal structures provide a snapshot of the receptor structural disposition of GPCRs itself or with cocrystallized ligands, and the results are congruent with biophysical and computer modeling studies reported about GPCRs conformational and dynamics flexibility, regulated activation, and the various stabilizing interactions, such as "molecular switches." The molecular switches generally constitute the most conserved domains within a particular GPCR superfamily. Often agonist-induced receptor activation proceeds by the disruption of majority of these interactions, while antagonist and inverse agonist act as blockers and structural stabilizers, respectively. Several elegant studies, particularly for the β2AR, have demonstrated the relationship between ligand structure, receptor conformational changes, and corresponding pharmacological outcomes. Thus, it is of great importance to understand GPCRs activation related to cell signaling pathways. Herein, we summarize the steps to produce functional GPCRs, generate suitably fluorescent labeled GPCRs and the procedure to use that to understand if ligand-induced activation can proceed by activation of the GPCRs via ionic lock switch and/or rotamer toggle switch mechanisms. Such understanding of ligand structure and mechanism of receptor activation will provide great insight toward uncovering newer pathways of GPCR activation and aid in structure-based drug design. Copyright © 2013 Elsevier Inc. All rights reserved.

The Switch from Low-Pressure Sodium to Light Emitting Diodes Does Not Affect Bat Activity at Street Lights

PubMed Central

Rowse, Elizabeth G.; Harris, Stephen; Jones, Gareth

2016-01-01

We used a before-after-control-impact paired design to examine the effects of a switch from low-pressure sodium (LPS) to light emitting diode (LED) street lights on bat activity at twelve sites across southern England. LED lights produce broad spectrum ‘white’ light compared to LPS street lights that emit narrow spectrum, orange light. These spectral differences could influence the abundance of insects at street lights and thereby the activity of the bats that prey on them. Most of the bats flying around the LPS lights were aerial-hawking species, and the species composition of bats remained the same after the switch-over to LED. We found that the switch-over from LPS to LED street lights did not affect the activity (number of bat passes), or the proportion of passes containing feeding buzzes, of those bat species typically found in close proximity to street lights in suburban environments in Britain. This is encouraging from a conservation perspective as many existing street lights are being, or have been, switched to LED before the ecological consequences have been assessed. However, lighting of all spectra studied to date generally has a negative impact on several slow-flying bat species, and LED lights are rarely frequented by these ‘light-intolerant’ bat species. PMID:27008274

Hindrance of conservation biology by delays in the submission of manuscripts.

PubMed

O'Donnell, Ryan P; Supp, Sarah R; Cobbold, Stephanie M

2010-04-01

Timely dissemination of scientific findings depends not only on rapid publication of submitted manuscripts, a topic which has received much discussion, but also on rapid submission of research after the research is completed. We measured submission delay (time from the last date of data collection to the submission of a manuscript) for every paper from 14 journals in 2007 and compared these submission delays among four fields of biology (conservation, taxonomy, behavior, and evolution). Manuscripts published in leading journals in the field of conservation biology have the longest delays in publication of accepted manuscripts and the longest intervals between completion of research and submission of the manuscript. Delay in manuscript submission accounts for more than half of the total time from last date of data collection to publication. Across fields, the number of authors was significantly negatively correlated with submission delay, but conservation journals had the second highest number of authors and the greatest submission delay, so submission of conservation manuscripts was not hindered by a shortage of collaboration relative to other fields. Rejection rates were greater in conservation journals than in behavior and evolution, but rejection times were faster; thus, there were no obvious net differences among fields in the time papers spent waiting to be rejected. Publication delay has been reduced significantly in the last 7 years, but was still greater in conservation journals than in any of the other three fields we studied. Thus, the urgent field of conservation biology is hindered in both preparation and publication of manuscripts.

Evolution of the SCS curve number method and its applications to continuous runoff simulation

USDA-ARS?s Scientific Manuscript database

The Natural Resources Conservation Service (NRCS) [previously Soil Conservation Service (SCS)] developed the SCS runoff curve-number (CN) method for estimating direct runoff from storm rainfall. The NRCS uses the CN method for designing structures and for evaluating their effectiveness. Structural...

[Conservative treatment of a chronic rupture of Achilles tendon: case report].

PubMed

González-Murillo, M; Rodrigo-Alonso, A; Figueiredo-González, H; Salgado-Rodrigo, A M; Mota-Blanco, S M

2016-01-01

We report a case of a 64 years-old-female patient with ruptured left Achilles tendon within two months of evolution that has gone unnoticed. By the application of a conservative treatment recovered complete and symmetrical functionality in five months time after the injury.

A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.

PubMed

Gustafson, Chelsea L; Parsley, Nicole C; Asimgil, Hande; Lee, Hsiau-Wei; Ahlbach, Christopher; Michael, Alicia K; Xu, Haiyan; Williams, Owen L; Davis, Tara L; Liu, Andrew C; Partch, Carrie L

2017-05-18

The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination. Copyright © 2017 Elsevier Inc. All rights reserved.

Stability analysis of switched cellular neural networks: A mode-dependent average dwell time approach.

PubMed

Huang, Chuangxia; Cao, Jie; Cao, Jinde

2016-10-01

This paper addresses the exponential stability of switched cellular neural networks by using the mode-dependent average dwell time (MDADT) approach. This method is quite different from the traditional average dwell time (ADT) method in permitting each subsystem to have its own average dwell time. Detailed investigations have been carried out for two cases. One is that all subsystems are stable and the other is that stable subsystems coexist with unstable subsystems. By employing Lyapunov functionals, linear matrix inequalities (LMIs), Jessen-type inequality, Wirtinger-based inequality, reciprocally convex approach, we derived some novel and less conservative conditions on exponential stability of the networks. Comparing to ADT, the proposed MDADT show that the minimal dwell time of each subsystem is smaller and the switched system stabilizes faster. The obtained results extend and improve some existing ones. Moreover, the validness and effectiveness of these results are demonstrated through numerical simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.

A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors

NASA Astrophysics Data System (ADS)

Ortega, Davi R.; Yang, Chen; Ames, Peter; Baudry, Jerome; Parkinson, John S.; Zhulin, Igor B.

2013-12-01

Bacterial chemoreceptors are widely used as a model system for elucidating the molecular mechanisms of transmembrane signalling and have provided a detailed understanding of how ligand binding by the receptor modulates the activity of its associated kinase CheA. However, the mechanisms by which conformational signals move between signalling elements within a receptor dimer and how they control kinase activity remain unknown. Here, using long molecular dynamics simulations, we show that the kinase-activating cytoplasmic tip of the chemoreceptor fluctuates between two stable conformations in a signal-dependent manner. A highly conserved residue, Phe396, appears to serve as the conformational switch, because flipping of the stacked aromatic rings of an interacting F396-F396‧ pair in the receptor homodimer takes place concomitantly with the signal-related conformational changes. We suggest that interacting aromatic residues, which are common stabilizers of protein tertiary structure, might serve as rotameric molecular switches in other biological processes as well.

Conformational switching in the coiled-coil domains of a proteasomal ATPase regulates substrate processing.

PubMed

Snoberger, Aaron; Brettrager, Evan J; Smith, David M

2018-06-18

Protein degradation in all domains of life requires ATPases that unfold and inject proteins into compartmentalized proteolytic chambers. Proteasomal ATPases in eukaryotes and archaea contain poorly understood N-terminally conserved coiled-coil domains. In this study, we engineer disulfide crosslinks in the coiled-coils of the archaeal proteasomal ATPase (PAN) and report that its three identical coiled-coil domains can adopt three different conformations: (1) in-register and zipped, (2) in-register and partially unzipped, and (3) out-of-register. This conformational heterogeneity conflicts with PAN's symmetrical OB-coiled-coil crystal structure but resembles the conformational heterogeneity of the 26S proteasomal ATPases' coiled-coils. Furthermore, we find that one coiled-coil can be conformationally constrained even while unfolding substrates, and conformational changes in two of the coiled-coils regulate PAN switching between resting and active states. This switching functionally mimics similar states proposed for the 26S proteasome from cryo-EM. These findings thus build a mechanistic framework to understand regulation of proteasome activity.

Functionally conserved enhancers with divergent sequences in distant vertebrates

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

Yang, Song; Oksenberg, Nir; Takayama, Sachiko

To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. In conclusion, our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.

Functionally conserved enhancers with divergent sequences in distant vertebrates

DOE PAGES

Yang, Song; Oksenberg, Nir; Takayama, Sachiko; ...

2015-10-30

To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. In conclusion, our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.

Accelerated Evolution of the Pituitary Adenylate Cyclase-Activating Polypeptide Precursor Gene During Human Origin

PubMed Central

Wang, Yin-qiu; Qian, Ya-ping; Yang, Su; Shi, Hong; Liao, Cheng-hong; Zheng, Hong-Kun; Wang, Jun; Lin, Alice A.; Cavalli-Sforza, L. Luca; Underhill, Peter A.; Chakraborty, Ranajit; Jin, Li; Su, Bing

2005-01-01

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide abundantly expressed in the central nervous system and involved in regulating neurogenesis and neuronal signal transduction. The amino acid sequence of PACAP is extremely conserved across vertebrate species, indicating a strong functional constraint during the course of evolution. However, through comparative sequence analysis, we demonstrated that the PACAP precursor gene underwent an accelerated evolution in the human lineage since the divergence from chimpanzees, and the amino acid substitution rate in humans is at least seven times faster than that in other mammal species resulting from strong Darwinian positive selection. Eleven human-specific amino acid changes were identified in the PACAP precursors, which are conserved from murine to African apes. Protein structural analysis suggested that a putative novel neuropeptide might have originated during human evolution and functioned in the human brain. Our data suggested that the PACAP precursor gene underwent adaptive changes during human origin and may have contributed to the formation of human cognition. PMID:15834139

Aspect-ratio dependence of magnetization reversal in cylindrical ferromagnetic nanowires

NASA Astrophysics Data System (ADS)

Sultan, Musaab S.; Atkinson, Del

2016-05-01

The magnetization reversal behavior in isolated cylindrical and square cross-section Ni81Fe19 nanowires was systematically studied as a function of nanowire cross-section dimensions from 10 up to 200 nm using micromagnetic simulations. This approach provides access to the switching field, remanence ratio and most significantly the magnetization structures during reversal, which allows the evolution of magnetization processes to be studied with scaling of the cross-sectional dimensions. The dimensional trends in reversal behavior for both square and circular cross-section were comparable throughout the range of dimensions studied. The thinnest nanowires showed simple square switching and 100% remanence. With increasing diameter the switching field reduces and above 40 nm the reversal behavior shows an increasing rotational component prior to sharp switching of the magnetization. The magnitude of the reversible component increases with increasing dimensions up to 150 nm, above which the magnetization reversal process is more complicated and the hysteresis loops are no longer bistable. The micromagnetic structures evolve from simple uniform parallel single domain states in the thinnest wires through the formation of vortex-like end states in thicker wires to complex multidomain structures during the reversal of the thickest wires. In the later cases the reversal is not simple curling-like behavior, although the angular switching field dependence was comparable with curling.

How MAP kinase modules function as robust, yet adaptable, circuits.

PubMed

Tian, Tianhai; Harding, Angus

2014-01-01

Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution.

How MAP kinase modules function as robust, yet adaptable, circuits

PubMed Central

Tian, Tianhai; Harding, Angus

2014-01-01

Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution. PMID:25483189

The Switch to Private Pension Plans for Teachers, 1982-2002: A Case of Freedom of Choice or Financial Scandal?

ERIC Educational Resources Information Center

Griggs, Clive

2009-01-01

In the early 1980s the Conservative Administration introduced legislation to promote private personal pension plans for public sector workers. An army of commission-driven sales staff from the financial services industry sought to persuade teachers and others to abandon their inflation-proof pension schemes for those offered by private companies.…

Extant fold-switching proteins are widespread.

PubMed

Porter, Lauren L; Looger, Loren L

2018-06-05

A central tenet of biology is that globular proteins have a unique 3D structure under physiological conditions. Recent work has challenged this notion by demonstrating that some proteins switch folds, a process that involves remodeling of secondary structure in response to a few mutations (evolved fold switchers) or cellular stimuli (extant fold switchers). To date, extant fold switchers have been viewed as rare byproducts of evolution, but their frequency has been neither quantified nor estimated. By systematically and exhaustively searching the Protein Data Bank (PDB), we found ∼100 extant fold-switching proteins. Furthermore, we gathered multiple lines of evidence suggesting that these proteins are widespread in nature. Based on these lines of evidence, we hypothesized that the frequency of extant fold-switching proteins may be underrepresented by the structures in the PDB. Thus, we sought to identify other putative extant fold switchers with only one solved conformation. To do this, we identified two characteristic features of our ∼100 extant fold-switching proteins, incorrect secondary structure predictions and likely independent folding cooperativity, and searched the PDB for other proteins with similar features. Reassuringly, this method identified dozens of other proteins in the literature with indication of a structural change but only one solved conformation in the PDB. Thus, we used it to estimate that 0.5-4% of PDB proteins switch folds. These results demonstrate that extant fold-switching proteins are likely more common than the PDB reflects, which has implications for cell biology, genomics, and human health. Copyright © 2018 the Author(s). Published by PNAS.

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

PubMed Central

Sanges, Remo; Hadzhiev, Yavor; Gueroult-Bellone, Marion; Roure, Agnes; Ferg, Marco; Meola, Nicola; Amore, Gabriele; Basu, Swaraj; Brown, Euan R.; De Simone, Marco; Petrera, Francesca; Licastro, Danilo; Strähle, Uwe; Banfi, Sandro; Lemaire, Patrick; Birney, Ewan; Müller, Ferenc; Stupka, Elia

2013-01-01

Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’. PMID:23393190

Spin-polarized charge transport in HgTe/CdTe quantum well topological insulator under a ferromagnetic metal strip

NASA Astrophysics Data System (ADS)

Wu, Zhenhua; Luo, Kun; Yu, Jiahan; Wu, Xiaobo; Lin, Liangzhong

2018-02-01

Electron tunneling through a single magnetic barrier in a HgTe topological insulator has been theoretically investigated. We find that the perpendicular magnetic field would not lead to spin-flip of the edge states due to the conservation of the angular moment. By tuning the magnetic field and the Fermi energy, the edge channels can be transited from switch-on states to switch-off states and the current from unpolarized states can be filtered to fully spin polarized states. These features offer us an efficient way to control charge/spin transport in a HgTe/CdTe quantum well, and pave a way to construct the nanoelectronic devices utilizing the topological edge states.

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

Ortiz, Gerardo, E-mail: ortizg@indiana.edu; Cobanera, Emilio

We investigate Majorana modes of number-conserving fermionic superfluids from both basic physics principles, and concrete models perspectives. After reviewing a criterion for establishing topological superfluidity in interacting systems, based on many-body fermionic parity switches, we reveal the emergence of zero-energy modes anticommuting with fermionic parity. Those many-body Majorana modes are constructed as coherent superpositions of states with different number of fermions. While realization of Majorana modes beyond mean field is plausible, we show that the challenge to quantum-control them is compounded by particle-conservation, and more realistic protocols will have to balance engineering needs with astringent constraints coming from superselection rules.more » Majorana modes in number-conserving systems are the result of a peculiar interplay between quantum statistics, fermionic parity, and an unusual form of spontaneous symmetry breaking. We test these ideas on the Richardson–Gaudin–Kitaev chain, a number-conserving model solvable by way of the algebraic Bethe ansatz, and equivalent in mean field to a long-range Kitaev chain.« less

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system.

PubMed

Hanson, Sara J; Byrne, Kevin P; Wolfe, Kenneth H

2014-11-11

Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)-like loci and a mechanism for silencing two of them. How this system originated is unknown, because the three-locus system is present throughout the family Saccharomycetaceae, whereas species in the sister Candida clade have only one locus and do not switch. Here we show that yeasts in a third clade, the methylotrophs, have a simpler two-locus switching system based on reversible inversion of a section of chromosome with MATa genes at one end and MATalpha genes at the other end. In Hansenula polymorpha the 19-kb invertible region lies beside a centromere so that, depending on the orientation, either MATa or MATalpha is silenced by centromeric chromatin. In Pichia pastoris, the orientation of a 138-kb invertible region puts either MATa or MATalpha beside a telomere and represses transcription of MATa2 or MATalpha2. Both species are homothallic, and inversion of their MAT regions can be induced by crossing two strains of the same mating type. The three-locus system of S. cerevisiae, which uses a nonconservative mechanism to replace DNA at MAT, likely evolved from a conservative two-locus system that swapped genes between expression and nonexpression sites by inversion. The increasing complexity of the switching apparatus, with three loci, donor bias, and cell lineage tracking, can be explained by continuous selection to increase sporulation ability in young colonies. Our results provide an evolutionary context for the diversity of switching and silencing mechanisms.

Molecular evolution of the vertebrate mechanosensory cell and ear.

PubMed

Fritzsch, Bernd; Beisel, Kirk W; Pauley, Sarah; Soukup, Garrett

2007-01-01

The molecular basis of mechanosensation, mechanosensory cell development and mechanosensory organ development is reviewed with an emphasis on its evolution. In contrast to eye evolution and development, which apparently modified a genetic program through intercalation of genes between the master control genes on the top (Pax6, Eya1, Six1) of the hierarchy and the structural genes (rhodopsin) at the bottom, the as yet molecularly unknown mechanosensory channel precludes such a firm conclusion for mechanosensors. However, recent years have seen the identification of several structural genes which are involved in mechanosensory tethering and several transcription factors controlling mechanosensory cell and organ development; these warrant the interpretation of available data in very much the same fashion as for eye evolution: molecular homology combined with potential morphological parallelism. This assertion of molecular homology is strongly supported by recent findings of a highly conserved set of microRNAs that appear to be associated with mechanosensory cell development across phyla. The conservation of transcription factors and their regulators fits very well to the known or presumed mechanosensory specializations which can be mostly grouped as variations of a common cellular theme. Given the widespread distribution of the molecular ability to form mechanosensory cells, it comes as no surprise that structurally different mechanosensory organs evolved in different phyla, presenting a variation of a common theme specified by a conserved set of transcription factors in their cellular development. Within vertebrates and arthropods, some mechanosensory organs evolved into auditory organs, greatly increasing sensitivity to sound through modifications of accessory structures to direct sound to the specific sensory epithelia. However, while great attention has been paid to the evolution of these accessory structures in vertebrate fossils, comparatively less attention has been spent on the evolution of the inner ear and the central auditory system. Recent advances in our molecular understanding of ear and brain development provide novel avenues to this neglected aspect of auditory neurosensory evolution.

Sequence Comparisons of Odorant Receptors among Tortricid Moths Reveal Different Rates of Molecular Evolution among Family Members

PubMed Central

Carraher, Colm; Authier, Astrid; Steinwender, Bernd; Newcomb, Richard D.

2012-01-01

In insects, odorant receptors detect volatile cues involved in behaviours such as mate recognition, food location and oviposition. We have investigated the evolution of three odorant receptors from five species within the moth genera Ctenopseustis and Planotrotrix, family Tortricidae, which fall into distinct clades within the odorant receptor multigene family. One receptor is the orthologue of the co-receptor Or83b, now known as Orco (OR2), and encodes the obligate ion channel subunit of the receptor complex. In comparison, the other two receptors, OR1 and OR3, are ligand-binding receptor subunits, activated by volatile compounds produced by plants - methyl salicylate and citral, respectively. Rates of sequence evolution at non-synonymous sites were significantly higher in OR1 compared with OR2 and OR3. Within the dataset OR1 contains 109 variable amino acid positions that are distributed evenly across the entire protein including transmembrane helices, loop regions and termini, while OR2 and OR3 contain 18 and 16 variable sites, respectively. OR2 shows a high level of amino acid conservation as expected due to its essential role in odour detection; however we found unexpected differences in the rate of evolution between two ligand-binding odorant receptors, OR1 and OR3. OR3 shows high sequence conservation suggestive of a conserved role in odour reception, whereas the higher rate of evolution observed in OR1, particularly at non-synonymous sites, may be suggestive of relaxed constraint, perhaps associated with the loss of an ancestral role in sex pheromone reception. PMID:22701634

Host Switching in Lyssavirus History from the Chiroptera to the Carnivora Orders

PubMed Central

Badrane, Hassan; Tordo, Noël

2001-01-01

Lyssaviruses are unsegmented RNA viruses causing rabies. Their vectors belong to the Carnivora and Chiroptera orders. We studied 36 carnivoran and 17 chiropteran lyssaviruses representing the main genotypes and variants. We compared their genes encoding the surface glycoprotein, which is responsible for receptor recognition and membrane fusion. The glycoprotein is the main protecting antigen and bears virulence determinants. Point mutation is the main force in lyssavirus evolution, as Sawyer's test and phylogenetic analysis showed no evidence of recombination. Tests of neutrality indicated a neutral model of evolution, also supported by globally high ratios of synonymous substitutions (dS) to nonsynonymous substitutions (dN) (>7). Relative-rate tests suggested similar rates of evolution for all lyssavirus lineages. Therefore, the absence of recombination and similar evolutionary rates make phylogeny-based conclusions reliable. Phylogenetic reconstruction strongly supported the hypothesis that host switching occurred in the history of lyssaviruses. Indeed, lyssaviruses evolved in chiropters long before the emergence of carnivoran rabies, very likely following spillovers from bats. Using dated isolates, the average rate of evolution was estimated to be roughly 4.3 × 10−4 dS/site/year. Consequently, the emergence of carnivoran rabies from chiropteran lyssaviruses was determined to have occurred 888 to 1,459 years ago. Glycoprotein segments accumulating more dN than dS were distinctly detected in carnivoran and chiropteran lyssaviruses. They may have contributed to the adaptation of the virus to the two distinct mammal orders. In carnivoran lyssaviruses they overlapped the main antigenic sites, II and III, whereas in chiropteran lyssaviruses they were located in regions of unknown functions. PMID:11483755

Adaptive Evolution of Eel Fluorescent Proteins from Fatty Acid Binding Proteins Produces Bright Fluorescence in the Marine Environment.

PubMed

Gruber, David F; Gaffney, Jean P; Mehr, Shaadi; DeSalle, Rob; Sparks, John S; Platisa, Jelena; Pieribone, Vincent A

2015-01-01

We report the identification and characterization of two new members of a family of bilirubin-inducible fluorescent proteins (FPs) from marine chlopsid eels and demonstrate a key region of the sequence that serves as an evolutionary switch from non-fluorescent to fluorescent fatty acid-binding proteins (FABPs). Using transcriptomic analysis of two species of brightly fluorescent Kaupichthys eels (Kaupichthys hyoproroides and Kaupichthys n. sp.), two new FPs were identified, cloned and characterized (Chlopsid FP I and Chlopsid FP II). We then performed phylogenetic analysis on 210 FABPs, spanning 16 vertebrate orders, and including 163 vertebrate taxa. We show that the fluorescent FPs diverged as a protein family and are the sister group to brain FABPs. Our results indicate that the evolution of this family involved at least three gene duplication events. We show that fluorescent FABPs possess a unique, conserved tripeptide Gly-Pro-Pro sequence motif, which is not found in non-fluorescent fatty acid binding proteins. This motif arose from a duplication event of the FABP brain isoforms and was under strong purifying selection, leading to the classification of this new FP family. Residues adjacent to the motif are under strong positive selection, suggesting a further refinement of the eel protein's fluorescent properties. We present a phylogenetic reconstruction of this emerging FP family and describe additional fluorescent FABP members from groups of distantly related eels. The elucidation of this class of fish FPs with diverse properties provides new templates for the development of protein-based fluorescent tools. The evolutionary adaptation from fatty acid-binding proteins to fluorescent fatty acid-binding proteins raises intrigue as to the functional role of bright green fluorescence in this cryptic genus of reclusive eels that inhabit a blue, nearly monochromatic, marine environment.

The porous borders of the protein world.

PubMed

Cordes, Matthew H J; Stewart, Katie L

2012-02-08

Fold switching may play a role in the evolution of new protein folds and functions. He et al., in this issue of Structure, use protein design to illustrate that the same drastic change in a protein fold can occur via multiple different mutational pathways. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evidence of birth-and-death evolution of 5S rRNA gene in Channa species (Teleostei, Perciformes).

PubMed

Barman, Anindya Sundar; Singh, Mamta; Singh, Rajeev Kumar; Lal, Kuldeep Kumar

2016-12-01

In higher eukaryotes, minor rDNA family codes for 5S rRNA that is arranged in tandem arrays and comprises of a highly conserved 120 bp long coding sequence with a variable non-transcribed spacer (NTS). Initially the 5S rDNA repeats are considered to be evolved by the process of concerted evolution. But some recent reports, including teleost fishes suggested that evolution of 5S rDNA repeat does not fit into the concerted evolution model and evolution of 5S rDNA family may be explained by a birth-and-death evolution model. In order to study the mode of evolution of 5S rDNA repeats in Perciformes fish species, nucleotide sequence and molecular organization of five species of genus Channa were analyzed in the present study. Molecular analyses revealed several variants of 5S rDNA repeats (four types of NTS) and networks created by a neighbor net algorithm for each type of sequences (I, II, III and IV) did not show a clear clustering in species specific manner. The stable secondary structure is predicted and upstream and downstream conserved regulatory elements were characterized. Sequence analyses also shown the presence of two putative pseudogenes in Channa marulius. Present study supported that 5S rDNA repeats in genus Channa were evolved under the process of birth-and-death.

Structure, Receptor Binding, and Antigenicity of Influenza Virus Hemagglutinins from the 1957 H2N2 Pandemic

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

Xu, Rui; McBride, Ryan; Paulson, James C.

2010-03-04

The hemagglutinin (HA) envelope protein of influenza viruses mediates essential viral functions, including receptor binding and membrane fusion, and is the major viral antigen for antibody neutralization. The 1957 H2N2 subtype (Asian flu) was one of the three great influenza pandemics of the last century and caused 1 million deaths globally from 1957 to 1968. Three crystal structures of 1957 H2 HAs have been determined at 1.60 to 1.75 {angstrom} resolutions to investigate the structural basis for their antigenicity and evolution from avian to human binding specificity that contributed to its introduction into the human population. These structures, which representmore » the highest resolutions yet recorded for a complete ectodomain of a glycosylated viral surface antigen, along with the results of glycan microarray binding analysis, suggest that a hydrophobicity switch at residue 226 and elongation of receptor-binding sites were both critical for avian H2 HA to acquire human receptor specificity. H2 influenza viruses continue to circulate in birds and pigs and, therefore, remain a substantial threat for transmission to humans. The H2 HA structure also reveals a highly conserved epitope that could be harnessed in the design of a broader and more universal influenza A virus vaccine.« less

Cloning of noggin gene from hydra and analysis of its functional conservation using Xenopus laevis embryos.

PubMed

Chandramore, Kalpana; Ito, Yuzuro; Takahashi, Shuji; Asashima, Makoto; Ghaskadbi, Surendra

2010-01-01

Hydra, a member of phylum Cnidaria that arose early in evolution, is endowed with a defined axis, organized nervous system, and active behavior. It is a powerful model system for the elucidation of evolution of developmental mechanisms in animals. Here, we describe the identification and cloning of noggin-like gene from hydra. Noggin is a secreted protein involved at multiple stages of vertebrate embryonic development including neural induction and is known to exert its effects by inhibiting the bone morphogenetic protein (BMP)-signaling pathway. Sequence analysis revealed that hydra Noggin shows considerable similarity with its orthologs at the amino acid level. When microinjected in the early Xenopus embryos, hydra noggin mRNA induced a secondary axis in 100% of the injected embryos, demonstrating functional conservation of hydra noggin in vertebrates. This was further confirmed by the partial rescue of Xenopus embryos by hydra noggin mRNA from UV-induced ventralization. By using animal cap assay in Xenopus embryos, we demonstrate that these effects of hydra noggin in Xenopus embryos are because of inhibition of BMP signaling by Noggin. Our data indicate that BMP/Noggin antagonism predates the bilaterian divergence and is conserved during the evolution.

Hydrogen, metals, bifurcating electrons, and proton gradients: the early evolution of biological energy conservation.

PubMed

Martin, William F

2012-03-09

Life is a persistent, self-specified set of far from equilibrium chemical reactions. In modern microbes, core carbon and energy metabolism are what keep cells alive. In very early chemical evolution, the forerunners of carbon and energy metabolism were the processes of generating reduced carbon compounds from CO(2) and the mechanisms of harnessing energy as compounds capable of doing some chemical work. The process of serpentinization at alkaline hydrothermal vents holds promise as a model for the origin of early reducing power, because Fe(2+) in the Earth's crust reduces water to H(2) and inorganic carbon to methane. The overall geochemical process of serpentinization is similar to the biochemical process of methanogenesis, and methanogenesis is similar to acetogenesis in that both physiologies allow energy conservation from the reduction of CO(2) with electrons from H(2). Electron bifurcation is a newly recognized cytosolic process that anaerobes use generate low potential electrons, it plays an important role in some forms of methanogenesis and, via speculation, possibly in acetogenesis. Electron bifurcation likely figures into the early evolution of biological energy conservation. Copyright © 2011. Published by Elsevier B.V.

Transient Evolutional Dynamics of Quantum-Dot Molecular Phase Coherence for Sensitive Optical Switching

NASA Astrophysics Data System (ADS)

Shen, Jian Qi; Gu, Jing

2018-04-01

Atomic phase coherence (quantum interference) in a multilevel atomic gas exhibits a number of interesting phenomena. Such an atomic quantum coherence effect can be generalized to a quantum-dot molecular dielectric. Two quantum dots form a quantum-dot molecule, which can be described by a three-level Λ-configuration model { |0> ,|1> ,|2> } , i.e., the ground state of the molecule is the lower level |0> and the highly degenerate electronic states in the two quantum dots are the two upper levels |1> ,|2> . The electromagnetic characteristics due to the |0>-|1> transition can be controllably manipulated by a tunable gate voltage (control field) that drives the |2>-|1> transition. When the gate voltage is switched on, the quantum-dot molecular state can evolve from one steady state (i.e., |0>-|1> two-level dressed state) to another steady state (i.e., three-level coherent-population-trapping state). In this process, the electromagnetic characteristics of a quantum-dot molecular dielectric, which is modified by the gate voltage, will also evolve. In this study, the transient evolutional behavior of the susceptibility of a quantum-dot molecular thin film and its reflection spectrum are treated by using the density matrix formulation of the multilevel systems. The present field-tunable and frequency-sensitive electromagnetic characteristics of a quantum-dot molecular thin film, which are sensitive to the applied gate voltage, can be utilized to design optical switching devices.

Recombination and the evolution of coordinated phenotypic expression in a frequency-dependent game

PubMed Central

Arbilly, Michal; Motro, Uzi; Feldman, Marcus W.; Lotem, Arnon

2011-01-01

A long standing question in evolutionary biology concerns the maintenance of adaptive combinations of traits in the presence of recombination. This problem may be solved if positive epistasis selects for reducing the rate of recombination between such traits, but this requires sufficiently strong epistasis. Here we use a model that we developed previously to analyze a frequency-dependent strategy game in asexual populations, to study how adaptive combinations of traits may be maintained in the presence of recombination when epistasis is too weak to select for genetic linkage. Previously, in the asexual case, our model demonstrated the evolution of adaptive associations between social foraging strategies and learning rules. We verify that these adaptive associations, which are represented by different two-locus haplotypes, can easily be broken by genetic recombination. We also confirm that a modifier allele that reduces the rate of recombination fails to evolve (due to weak epistasis). However, we find that under the same conditions of weak epistasis, there is an alternative mechanism that allows association between traits to evolve. This is based on a genetic switch that responds to the presence of one social foraging allele by activating one of two alternative learning alleles that are carried by all individuals. We suggest that such coordinated phenotypic expression by genetic switches offers a general and robust mechanism for the evolution of adaptive combinations of traits in the presence of recombination. PMID:21945887

Compensatory Evolution of Intrinsic Transcription Terminators in Bacillus Cereus

PubMed Central

Safina, Ksenia R.; Mironov, Andrey A.

2017-01-01

Many RNA molecules possess complicated secondary structure critical to their function. Mutations in double-helical regions of RNA may disrupt Watson–Crick (WC) interactions causing structure destabilization or even complete loss of function. Such disruption can be compensated by another mutation restoring base pairing, as has been shown for mRNA, rRNA and tRNA. Here, we investigate the evolution of intrinsic transcription terminators between closely related strains of Bacillus cereus. While the terminator structure is maintained by strong natural selection, as evidenced by the low frequency of disrupting mutations, we observe multiple instances of pairs of disrupting-compensating mutations in RNA structure stems. Such two-step switches between different WC pairs occur very fast, consistent with the low fitness conferred by the intermediate non-WC variant. Still, they are not instantaneous, and probably involve transient fixation of the intermediate variant. The GU wobble pair is the most frequent intermediate, and remains fixed longer than other intermediates, consistent with its less disruptive effect on the RNA structure. Double switches involving non-GU intermediates are more frequent at the ends of RNA stems, probably because they are associated with smaller fitness loss. Together, these results show that the fitness landscape of bacterial transcription terminators is rather rugged, but that the fitness valleys associated with unpaired stem nucleotides are rather shallow, facilitating evolution. PMID:28201729

The evolution of fungus-growing termites and their mutualistic fungal symbionts

PubMed Central

Aanen, Duur K.; Eggleton, Paul; Rouland-Lefèvre, Corinne; Guldberg-Frøslev, Tobias; Rosendahl, Søren; Boomsma, Jacobus J.

2002-01-01

We have estimated phylogenies of fungus-growing termites and their associated mutualistic fungi of the genus Termitomyces using Bayesian analyses of DNA sequences. Our study shows that the symbiosis has a single African origin and that secondary domestication of other fungi or reversal of mutualistic fungi to a free-living state has not occurred. Host switching has been frequent, especially at the lower taxonomic levels, and nests of single termite species can have different symbionts. Data are consistent with horizontal transmission of fungal symbionts in both the ancestral state of the mutualism and most of the extant taxa. Clonal vertical transmission of fungi, previously shown to be common in the genus Microtermes (via females) and in the species Macrotermes bellicosus (via males) [Johnson, R. A., Thomas, R. J., Wood, T. G. & Swift, M. J. (1981) J. Nat. Hist. 15, 751–756], is derived with two independent origins. Despite repeated host switching, statistical tests taking phylogenetic uncertainty into account show a significant congruence between the termite and fungal phylogenies, because mutualistic interactions at higher taxonomic levels show considerable specificity. We identify common characteristics of fungus-farming evolution in termites and ants, which apply despite the major differences between these two insect agricultural systems. We hypothesize that biparental colony founding may have constrained the evolution of vertical symbiont transmission in termites but not in ants where males die after mating. PMID:12386341

The puzzling orbital period evolution of the LMXB AX J1745.6-2901

NASA Astrophysics Data System (ADS)

Ponti, G.; De, K.; Munoz-Darias, T.; Stella, L.; Nandra, K.

2017-10-01

The discovery of gravitational waves through mergers of binary black holes raises the question of how such compact systems form, renewing issues related to the orbital evolution of binary systems. Eclipsing X-ray binaries are excellent tools to constrain the orbital period evolution and how the system loses angular momentum. I will present an X-ray eclipse timing analysis (spanning an interval of more than 20 yr) of one of such objects, AX J1745.6-2901. Its orbital period is decreasing at a rate Pdotorb=-4.03+-0.32 e-11 s s-1, at least one order of magnitude larger than expected from conservative mass transfer and angular momentum losses due to gravitational waves and magnetic braking, and it might result from either non-conservative mass transfer or magnetic activity changing the quadrupole moment of the companion star. I will also show that imprinted on the long-term evolution of the orbit, there are highly significant eclipse leads delays of 10-30 s, characterized by a clear state dependence in which, on average, eclipses occur earlier during the hard state. Finally, I will discuss whether accretion disc winds might have an impact onto the orbital evolution.

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells

PubMed Central

Camp, J. Gray; Weiser, Matthew; Cocchiaro, Jordan L.; Kingsley, David M.; Furey, Terrence S.; Sheikh, Shehzad Z.; Rawls, John F.

2017-01-01

The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs) in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS) found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development and physiology. PMID:28850571

Controlled exciton transfer between quantum dots with acoustic phonons taken into account

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

Golovinski, P. A., E-mail: golovinski@bk.ru

2015-09-15

A system of excitons in two quantum dots coupled by the dipole–dipole interaction is investigated. The excitation transfer process controlled by the optical Stark effect at nonresonant frequencies is considered and the effect of the interaction between excitons and acoustic phonons in a medium on this process is taken into account. The system evolution is described using quantum Heisenberg equations. A truncated set of equations is obtained and the transfer dynamics is numerically simulated. High-efficiency picosecond switching of the excitation transfer by a laser pulse with a rectangular envelope is demonstrated. The dependence of picosecond switching on the quantum-dot parametersmore » and optical-pulse length is presented.« less

Coupling continuous damage and debris fragmentation for energy absorption prediction by cfrp structures during crushing

NASA Astrophysics Data System (ADS)

Espinosa, Christine; Lachaud, Frédéric; Limido, Jérome; Lacome, Jean-Luc; Bisson, Antoine; Charlotte, Miguel

2015-05-01

Energy absorption during crushing is evaluated using a thermodynamic based continuum damage model inspired from the Matzenmiller-Lubliner-Taylors model. It was found that for crash-worthiness applications, it is necessary to couple the progressive ruin of the material to a representation of the matter openings and debris generation. Element kill technique (erosion) and/or cohesive elements are efficient but not predictive. A technique switching finite elements into discrete particles at rupture is used to create debris and accumulated mater during the crushing of the structure. Switching criteria are evaluated using the contribution of the different ruin modes in the damage evolution, energy absorption, and reaction force generation.

Conserved Quantities in General Relativity: From the Quasi-Local Level to Spatial Infinity

NASA Astrophysics Data System (ADS)

Chen, Po-Ning; Wang, Mu-Tao; Yau, Shing-Tung

2015-08-01

We define quasi-local conserved quantities in general relativity by using the optimal isometric embedding in Wang and Yau (Commun Math Phys 288(3):919-942, 2009) to transplant Killing fields in the Minkowski spacetime back to the 2-surface of interest in a physical spacetime. To each optimal isometric embedding, a dual element of the Lie algebra of the Lorentz group is assigned. Quasi-local angular momentum and quasi-local center of mass correspond to pairing this element with rotation Killing fields and boost Killing fields, respectively. They obey classical transformation laws under the action of the Poincaré group. We further justify these definitions by considering their limits as the total angular momentum and the total center of mass of an isolated system. These expressions were derived from the Hamilton-Jacobi analysis of the gravitational action and thus satisfy conservation laws. As a result, we obtained an invariant total angular momentum theorem in the Kerr spacetime. For a vacuum asymptotically flat initial data set of order 1, it is shown that the limits are always finite without any extra assumptions. We also study these total conserved quantities on a family of asymptotically flat initial data sets evolving by the vacuum Einstein evolution equation. It is shown that the total angular momentum is conserved under the evolution. For the total center of mass, the classical dynamical formula relating the center of mass, energy, and linear momentum is recovered, in the nonlinear context of initial data sets evolving by the vacuum Einstein evolution equation. The definition of quasi-local angular momentum provides an answer to the second problem in classical general relativity on Penrose's list (Proc R Soc Lond Ser A 381(1780):53-63, 1982).

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

PubMed Central

Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-01

Background Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Results Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Conclusion Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies. PMID:19154605

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers.

PubMed

Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-20

Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

Static and Turn-on Switching Characteristics of 4H-Silicon Carbide SITs to 200 deg C

NASA Technical Reports Server (NTRS)

Niedra, Janis M.; Schwarze, Gene E.

2005-01-01

Test results are presented for normally-off 4H-SiC Static Induction Transistors (SITs) intended for power switching and are among the first normally-off such devices realized in SiC. At zero gate bias, the gate p-n junction depletion layers extend far enough into the conduction channel to cut off the channel. Application of forward gate bias narrows the depletion regions, opening up the channel to conduction by majority carriers. In the present devices, narrow vertical channels get pinched by depletion regions from opposite sides. Since the material is SiC, the devices are usable at temperatures above 150 C. Static curve and pulse mode switching observations were done at selected temperatures up to 200 C on a device with average static characteristics from a batch of similar devices. Gate and drain currents were limited to about 400 mA and 3.5 A, respectively. The drain voltage was limited to roughly 300 V, which is conservative for this 600 V rated device. At 23 C, 1 kW, or even more, could be pulse mode switched in 65 ns (10 to 90 percent) into a 100 load. But at 200 C, the switching capability is greatly reduced in large part by the excessive gate current required. Severe collapse of the saturated drain-to-source current was observed at 200 C. The relation of this property to channel mobility is reviewed.

Evolution of magnetism of Cr nanoclusters on a Au(111) surface

NASA Astrophysics Data System (ADS)

Gotsis, Harry; Kioussis, Nicholas; Papaconstantopoulos, Dimitri

2004-03-01

Advances in low-temperature scanning tunneling microscopy under ultrahigh vacuum have provided new opportunities for investigating the magnetic structures of nanoclusters adsorbed on surfaces. Recent STM studies of Cr trimers on the Au(111) surface suggest a switching between two distinct electronic states. We have carried out ab initio electronic structure calculations to investigate the structural, electronic and magnetic properties of isolated Cr atoms, Cr dimers and trimers in different geometry. We will present results for the evolution of magnetic behavior including noncollinear magnetism and provide insight in the connection between magnetism and geometry.

Interworking evolution of mobile satellite and terrestrial networks

NASA Technical Reports Server (NTRS)

Matyas, R.; Kelleher, P.; Moller, P.; Jones, T.

1993-01-01

There is considerable interest among mobile satellite service providers in interworking with terrestrial networks to provide a universal global network. With such interworking, subscribers may be provided a common set of services such as those planned for the Public Switched Telephone Network (PSTN), the Integrated Services Digital Network (ISDN), and future Intelligent Networks (IN's). This paper first reviews issues in satellite interworking. Next the status and interworking plans of terrestrial mobile communications service providers are examined with early examples of mobile satellite interworking including a discussion of the anticipated evolution towards full interworking between mobile satellite and both fixed and mobile terrestrial networks.

Plasma density evolution in plasma opening switch obtained by a time-resolved sensitive He-Ne interferometer

NASA Astrophysics Data System (ADS)

Chen, Lin; Ren, Jing; Guo, Fan; Zhou, LiangJi; Li, Ye; He, An; Jiang, Wei

2014-03-01

To understand the formation process of vacuum gap in coaxial microsecond conduction time plasma opening switch (POS), we have made measurements of the line-integrated plasma density during switch operation using a time-resolved sensitive He-Ne interferometer. The conduction current and conduction time in experiments are about 120 kA and 1 μs, respectively. As a result, more than 85% of conduction current has been transferred to an inductive load with rise time of 130 ns. The radial dependence of the density is measured by changing the radial location of the line-of-sight for shots with the same nominal POS parameters. During the conduction phase, the line-integrated plasma density in POS increases at all radial locations over the gun-only case by further ionization of material injected from the guns. The current conduction is observed to cause a radial redistribution of the switch plasma. A vacuum gap forms rapidly in the plasma at 5.5 mm from the center conductor, which is consistent with the location where magnetic pressure is the largest, allowing current to be transferred from the POS to the load.

Characterization of switching field distributions in Ising-like magnetic arrays

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

Fraleigh, Robert D.; Kempinger, Susan; Lammert, Paul E.

The switching field distribution within arrays of single-domain ferromagnetic islands incorporates both island-island interactions and quenched disorder in island geometry. Separating these two contributions is important for disentangling the effects of disorder and interactions in themagnetization dynamics of island arrays. Using submicron, spatially resolved Kerr imaging in an external magnetic field for islands with perpendicular magnetic anisotropy, we map out the evolution of island arrays during hysteresis loops. Resolving and tracking individual islands across four different lattice types and a range of interisland spacings, we can extract the individual switching fields of every island and thereby quantitatively determine the contributionsmore » of interactions and quenched disorder in the arrays. The width of the switching field distribution is found to be well fitted by a simple model comprising the sum of an array-independent contribution (interpreted as disorder induced) and a term proportional to the maximum field the entire rest of the array could exert on a single island, i.e., in a fully polarized state. This supports the claim that disorder in these arrays is primarily a single-island property and provides a methodology by which to quantify such disorder.« less

Characterization of switching field distributions in Ising-like magnetic arrays

NASA Astrophysics Data System (ADS)

Fraleigh, Robert D.; Kempinger, Susan; Lammert, Paul E.; Zhang, Sheng; Crespi, Vincent H.; Schiffer, Peter; Samarth, Nitin

2017-04-01

The switching field distribution within arrays of single-domain ferromagnetic islands incorporates both island-island interactions and quenched disorder in island geometry. Separating these two contributions is important for disentangling the effects of disorder and interactions in the magnetization dynamics of island arrays. Using submicron, spatially resolved Kerr imaging in an external magnetic field for islands with perpendicular magnetic anisotropy, we map out the evolution of island arrays during hysteresis loops. Resolving and tracking individual islands across four different lattice types and a range of interisland spacings, we can extract the individual switching fields of every island and thereby quantitatively determine the contributions of interactions and quenched disorder in the arrays. The width of the switching field distribution is found to be well fitted by a simple model comprising the sum of an array-independent contribution (interpreted as disorder induced) and a term proportional to the maximum field the entire rest of the array could exert on a single island, i.e., in a fully polarized state. This supports the claim that disorder in these arrays is primarily a single-island property and provides a methodology by which to quantify such disorder.

Conservation laws of wave action and potential enstrophy for Rossby waves in a stratified atmosphere

NASA Technical Reports Server (NTRS)

Straus, D. M.

1983-01-01

The evolution of wave energy, enstrophy, and wave motion for atmospheric Rossby waves in a variable mean flow are discussed from a theoretical and pedagogic standpoint. In the absence of mean flow gradients, the wave energy density satisfies a local conservation law, with the appropriate flow velocity being the group velocity. In the presence of mean flow variations, wave energy is not conserved, but wave action is, provided the mean flow is independent of longitude. Wave enstrophy is conserved for arbitrary variations of the mean flow. Connections with Eiiassen-Palm flux are also discussed.

Conservation laws of wave action and potential enstrophy for Rossby waves in a stratified atmosphere

NASA Technical Reports Server (NTRS)

Straus, D. M.

1983-01-01

The evolution of wave energy, enstrophy, and wave motion for atmospheric Rossby waves in a variable mean flow are discussed from a theoretical and pedagogic standpoint. In the absence of mean flow gradients, the wave energy density satisfies a local conservation law, with the appropriate flow velocity being the group velocity. In the presence of mean flow variations, wave energy is not conserved, but wave action is, provided the mean flow is independent of longitude. Wave enstrophy is conserved for arbitrary variations of the mean flow. Connections with Eliassen-Palm flux are also discussed.

The bankfull hydraulic geometry of evolving meander bends

NASA Astrophysics Data System (ADS)

Monegaglia, F.; Tubino, M.; Zolezzi, G.

2017-12-01

Changes in the bankfull hydraulic geometry of meandering rivers associated with meander growth from incipient meandering to cutoffs have seldom been analysed in detail. Such information is also needed by meander morphodynamic models, most of which simulate the evolution of bankfull channel geometry by simply accounting for channel slope reduction inversely proportional to elongation, while changes in bankfull channel width are often neglected or, when they are considered, they are not consistent with the few available observations. To address these gaps we first perform an extensive, systematic, bend-scale evolutionary analysis of bankfull channel widths in several large meandering rivers in the Amazon basin, over a three decades time period, from remotely sensed field data. The analysis consistently show a slight decreasing trend of the bankfull channel width during the planform evolution towards cutoff. Furthermore, we develop a physically based model for the evolution of bankfull channel geometry during the planform development of meandering rivers. The model is based on the conservation of sediment discharge. An integrated one-dimensional Exner equation that accounts for meander elongation, sediment supply conservation and sediment income from the channel banks, allows us to predict the evolution of the channel slope. The evolution of the channel width is modeled through a threshold equation. The model correctly predicts the slight variability of channel width during meander development and a gentler reduction of the channel slope, which is mitigated by the conservation of sediment supply. The bankfull geometry of highly dynamic meandering rivers is predicted to be elongation-dominated, while the one related to slowly evolving meandering rivers is sediment supply-dominated. Finally, we discuss the implications of the proposed modeling framework in terms of planform structure, meander shape and morphodynamic influence.

Evolution of the vertebrate insulin receptor substrate (Irs) gene family.

PubMed

Al-Salam, Ahmad; Irwin, David M

2017-06-23

Insulin receptor substrate (Irs) proteins are essential for insulin signaling as they allow downstream effectors to dock with, and be activated by, the insulin receptor. A family of four Irs proteins have been identified in mice, however the gene for one of these, IRS3, has been pseudogenized in humans. While it is known that the Irs gene family originated in vertebrates, it is not known when it originated and which members are most closely related to each other. A better understanding of the evolution of Irs genes and proteins should provide insight into the regulation of metabolism by insulin. Multiple genes for Irs proteins were identified in a wide variety of vertebrate species. Phylogenetic and genomic neighborhood analyses indicate that this gene family originated very early in vertebrae evolution. Most Irs genes were duplicated and retained in fish after the fish-specific genome duplication. Irs genes have been lost of various lineages, including Irs3 in primates and birds and Irs1 in most fish. Irs3 and Irs4 experienced an episode of more rapid protein sequence evolution on the ancestral mammalian lineage. Comparisons of the conservation of the proteins sequences among Irs paralogs show that domains involved in binding to the plasma membrane and insulin receptors are most strongly conserved, while divergence has occurred in sequences involved in interacting with downstream effector proteins. The Irs gene family originated very early in vertebrate evolution, likely through genome duplications, and in parallel with duplications of other components of the insulin signaling pathway, including insulin and the insulin receptor. While the N-terminal sequences of these proteins are conserved among the paralogs, changes in the C-terminal sequences likely allowed changes in biological function.

THE INTERACTION BETWEEN L1-TYPE PROTEINS AND ANKYRINS - A MASTER SWITCH FOR L1-TYPE CAM FUNCTION #

PubMed Central

HORTSCH, MICHAEL; NAGARAJ, KAKANAHALLI; GODENSCHWEGE, TANJA A.

2008-01-01

L1-type cell adhesion molecules (CAMs) are important mediators of neural differentiation, including axonal outgrowth and pathfinding and also of synapse formation and maintenance. In addition, their interactions with cytoskeletal components are highly conserved and regulated. How these different aspects of CAM functionality relate to each other is not well understood. Based on results from our and other laboratories we propose that Ankyrin-binding to L1-type CAMs provides a master switch. The interaction with Ankyrins directs L1-type adhesive proteins into different functional contexts, either Ankyrin-independent functions, such as neurite outgrowth and axonal pathfinding or into Ankyrin-dependent functions, such as L1’s role at axon initial segments (AIS), paranodal regions, synapses and in dendrites. PMID:18839070

Friction Force: From Mechanics to Thermodynamics

ERIC Educational Resources Information Center

Ferrari, Christian; Gruber, Christian

2010-01-01

We study some mechanical problems in which a friction force is acting on a system. Using the fundamental concepts of state, time evolution and energy conservation, we explain how to extend Newtonian mechanics to thermodynamics. We arrive at the two laws of thermodynamics and then apply them to investigate the time evolution and heat transfer of…

Evolutionary Creation: Moving beyond the Evolution versus Creation Debate

ERIC Educational Resources Information Center

Lamoureux, Denis O.

2010-01-01

Evolutionary creation offers a conservative Christian approach to evolution. It explores biblical faith and evolutionary science through a Two Divine Books model and proposes a complementary relationship between Scripture and science. The Book of God's Words discloses the spiritual character of the world, while the Book of God's Works reveals the…

Comparative population genetics of a mimicry locus among hybridizing Heliconius butterfly species.

PubMed

Chamberlain, N L; Hill, R I; Baxter, S W; Jiggins, C D; Kronforst, M R

2011-09-01

The comimetic Heliconius butterfly species pair, H. erato and H. melpomene, appear to use a conserved Mendelian switch locus to generate their matching red wing patterns. Here we investigate whether H. cydno and H. pachinus, species closely related to H. melpomene, use this same switch locus to generate their highly divergent red and brown color pattern elements. Using an F2 intercross between H. cydno and H. pachinus, we first map the genomic positions of two novel red/brown wing pattern elements; the G locus, which controls the presence of red vs brown at the base of the ventral wings, and the Br locus, which controls the presence vs absence of a brown oval pattern on the ventral hind wing. The results reveal that the G locus is tightly linked to markers in the genomic interval that controls red wing pattern elements of H. erato and H. melpomene. Br is on the same linkage group but approximately 26 cM away. Next, we analyze fine-scale patterns of genetic differentiation and linkage disequilibrium throughout the G locus candidate interval in H. cydno, H. pachinus and H. melpomene, and find evidence for elevated differentiation between H. cydno and H. pachinus, but no localized signature of association. Overall, these results indicate that the G locus maps to the same interval as the locus controlling red patterning in H. melpomene and H. erato. This, in turn, suggests that the genes controlling red pattern elements may be homologous across Heliconius, supporting the hypothesis that Heliconius butterflies use a limited suite of conserved genetic switch loci to generate both convergent and divergent wing patterns.

Evolution of wealth in a non-conservative economy driven by local Nash equilibria.

PubMed

Degond, Pierre; Liu, Jian-Guo; Ringhofer, Christian

2014-11-13

We develop a model for the evolution of wealth in a non-conservative economic environment, extending a theory developed in Degond et al. (2014 J. Stat. Phys. 154, 751-780 (doi:10.1007/s10955-013-0888-4)). The model considers a system of rational agents interacting in a game-theoretical framework. This evolution drives the dynamics of the agents in both wealth and economic configuration variables. The cost function is chosen to represent a risk-averse strategy of each agent. That is, the agent is more likely to interact with the market, the more predictable the market, and therefore the smaller its individual risk. This yields a kinetic equation for an effective single particle agent density with a Nash equilibrium serving as the local thermodynamic equilibrium. We consider a regime of scale separation where the large-scale dynamics is given by a hydrodynamic closure with this local equilibrium. A class of generalized collision invariants is developed to overcome the difficulty of the non-conservative property in the hydrodynamic closure derivation of the large-scale dynamics for the evolution of wealth distribution. The result is a system of gas dynamics-type equations for the density and average wealth of the agents on large scales. We recover the inverse Gamma distribution, which has been previously considered in the literature, as a local equilibrium for particular choices of the cost function. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

X Chromosome Evolution in Cetartiodactyla

PubMed Central

Proskuryakova, Anastasia A.; Kulemzina, Anastasia I.; Makunin, Alexey I.; Kukekova, Anna V.; Lynn Johnson, Jennifer; Lemskaya, Natalya A.; Beklemisheva, Violetta R.; Roelke-Parker, Melody E.; Bellizzi, June; Ryder, Oliver A.; O’Brien, Stephen J.; Graphodatsky, Alexander S.

2017-01-01

The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern between species. It is hypothesized that this sex chromosome has undergone multiple rearrangements that changed the centromere position and the order of syntenic segments over the last 80 million years of Cetartiodactyla speciation. To investigate its evolution we have selected 26 evolutionarily conserved bacterial artificial chromosome (BAC) clones from the cattle CHORI-240 library evenly distributed along the cattle X chromosome. High-resolution BAC maps of the X chromosome on a representative range of cetartiodactyl species from different branches: pig (Suidae), alpaca (Camelidae), gray whale (Cetacea), hippopotamus (Hippopotamidae), Java mouse-deer (Tragulidae), pronghorn (Antilocapridae), Siberian musk deer (Moschidae), and giraffe (Giraffidae) were obtained by fluorescent in situ hybridization. To trace the X chromosome evolution during fast radiation in specious families, we performed mapping in several cervids (moose, Siberian roe deer, fallow deer, and Pere David’s deer) and bovid (muskox, goat, sheep, sable antelope, and cattle) species. We have identified three major conserved synteny blocks and rearrangements in different cetartiodactyl lineages and found that the recently described phenomenon of the evolutionary new centromere emergence has taken place in the X chromosome evolution of Cetartiodactyla at least five times. We propose the structure of the putative ancestral cetartiodactyl X chromosome by reconstructing the order of syntenic segments and centromere position for key groups. PMID:28858207

Divergence and evolution of cotton bHLH proteins from diploid to allotetraploid.

PubMed

Liu, Bingliang; Guan, Xueying; Liang, Wenhua; Chen, Jiedan; Fang, Lei; Hu, Yan; Guo, Wangzhen; Rong, Junkang; Xu, Guohua; Zhang, Tianzhen

2018-02-23

Polyploidy is considered a major driving force in genome expansion, yielding duplicated genes whose expression may be conserved or divergence as a consequence of polyploidization. We compared the genome sequences of tetraploid cotton (Gossypium hirsutum) and its two diploid progenitors, G. arboreum and G. raimondii, and found that the bHLH genes were conserved over the polyploidization. Oppositely, the expression of the homeolgous gene pairs was diversified. The biased homeologous proportion for bHLH family is significantly higher (64.6%) than the genome wide homeologous expression bias (40%). Compared with cacao (T. cacao), orthologous genes only accounted for a small proportion (41.7%) of whole cotton bHLHs family. The further Ks analysis indicated that bHLH genes underwent at least two distinct episodes of whole genome duplication: a recent duplication (1.0-60.0 million years ago, MYA, 0.005 < Ks < 0.312) and an old duplication (> 60.0 MYA, 0.312 < Ks < 3.0). The old duplication event might have played a key role in the expansion of the bHLH family. Both recent and old duplicated pairs (68.8%) showed a divergent expression profile, indicating specialized functions. The expression diversification of the duplicated genes suggested it might be a universal feature of the long-term evolution of cotton. Overview of cotton bHLH proteins indicated a conserved and divergent evolution from diploids to allotetraploid. Our results provided an excellent example for studying the long-term evolution of polyploidy.

Stepwise Evolution of Coral Biomineralization Revealed with Genome-Wide Proteomics and Transcriptomics

PubMed Central

Sawada, Hitoshi; Satoh, Noriyuki

2016-01-01

Despite the importance of stony corals in many research fields related to global issues, such as marine ecology, climate change, paleoclimatogy, and metazoan evolution, very little is known about the evolutionary origin of coral skeleton formation. In order to investigate the evolution of coral biomineralization, we have identified skeletal organic matrix proteins (SOMPs) in the skeletal proteome of the scleractinian coral, Acropora digitifera, for which large genomic and transcriptomic datasets are available. Scrupulous gene annotation was conducted based on comparisons of functional domain structures among metazoans. We found that SOMPs include not only coral-specific proteins, but also protein families that are widely conserved among cnidarians and other metazoans. We also identified several conserved transmembrane proteins in the skeletal proteome. Gene expression analysis revealed that expression of these conserved genes continues throughout development. Therefore, these genes are involved not only skeleton formation, but also in basic cellular functions, such as cell-cell interaction and signaling. On the other hand, genes encoding coral-specific proteins, including extracellular matrix domain-containing proteins, galaxins, and acidic proteins, were prominently expressed in post-settlement stages, indicating their role in skeleton formation. Taken together, the process of coral skeleton formation is hypothesized as: 1) formation of initial extracellular matrix between epithelial cells and substrate, employing pre-existing transmembrane proteins; 2) additional extracellular matrix formation using novel proteins that have emerged by domain shuffling and rapid molecular evolution and; 3) calcification controlled by coral-specific SOMPs. PMID:27253604

Thermodynamic stability of biomolecules and evolution.

PubMed

Chakravarty, Ashim K

2017-08-01

The thermodynamic stability of biomolecules in the perspective of evolution is a complex issue and needs discussion. Intra molecular bonds maintain the structure and the state of internal energy (E) of a biomolecule at "local minima". In this communication, possibility of loss in internal energy level of a biomolecule through the changes in the bonds has been discussed, that might earn more thermodynamic stability for the molecule. In the process variations in structure and functions of the molecule could occur. Thus, E of a biomolecule is likely to have energy stature for minimization. Such change in energy status is an intrinsic factor for evolving biomolecules buying more stability and generating variations in the structure and function of DNA molecules undergoing natural selection. Thus, the variations might very well contribute towards the process of evolution. A brief discussion on conserved sequence in the light of proposition in this communication has been made at the end. Extension of the idea may resolve certain standing problems in evolution, such as maintenance of conserved sequences in genome of diverse species, pre- versus post adaptive mutations, 'orthogenesis', etc. Copyright © 2017 Elsevier Ltd. All rights reserved.

Niche conservatism as an emerging principle in ecology and conservation biology.

PubMed

Wiens, John J; Ackerly, David D; Allen, Andrew P; Anacker, Brian L; Buckley, Lauren B; Cornell, Howard V; Damschen, Ellen I; Jonathan Davies, T; Grytnes, John-Arvid; Harrison, Susan P; Hawkins, Bradford A; Holt, Robert D; McCain, Christy M; Stephens, Patrick R

2010-10-01

The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within-species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?). 2010 Blackwell Publishing Ltd/CNRS.

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system

PubMed Central

Hanson, Sara J.; Byrne, Kevin P.; Wolfe, Kenneth H.

2014-01-01

Saccharomyces cerevisiae has a complex system for switching the mating type of haploid cells, requiring the genome to have three mating-type (MAT)–like loci and a mechanism for silencing two of them. How this system originated is unknown, because the three-locus system is present throughout the family Saccharomycetaceae, whereas species in the sister Candida clade have only one locus and do not switch. Here we show that yeasts in a third clade, the methylotrophs, have a simpler two-locus switching system based on reversible inversion of a section of chromosome with MATa genes at one end and MATalpha genes at the other end. In Hansenula polymorpha the 19-kb invertible region lies beside a centromere so that, depending on the orientation, either MATa or MATalpha is silenced by centromeric chromatin. In Pichia pastoris, the orientation of a 138-kb invertible region puts either MATa or MATalpha beside a telomere and represses transcription of MATa2 or MATalpha2. Both species are homothallic, and inversion of their MAT regions can be induced by crossing two strains of the same mating type. The three-locus system of S. cerevisiae, which uses a nonconservative mechanism to replace DNA at MAT, likely evolved from a conservative two-locus system that swapped genes between expression and nonexpression sites by inversion. The increasing complexity of the switching apparatus, with three loci, donor bias, and cell lineage tracking, can be explained by continuous selection to increase sporulation ability in young colonies. Our results provide an evolutionary context for the diversity of switching and silencing mechanisms. PMID:25349420

Vector solitons in harmonic mode-locked erbium-doped fiber lasers

NASA Astrophysics Data System (ADS)

Habruseva, Tatiana; Mkhitaryan, Mkhitar; Mou, Chengbo; Rozhin, Aleksey; Turitsyn, Sergei K.; Sergeyev, Sergey V.

2014-05-01

We report experimental study of vector solitons for the fundamental and harmonic mode-locked operation in erbiumdoper fiber lasers with carbon nanotubes based saturable absorbers and anomalous dispersion cavities. We measure evolution of the output pulses polarization and demonstrate vector solitons with various polarization attractors, including locked polarization, periodic polarization switching, and polarization precession.

Incorporating evolution of transcription factor binding sites into annotated alignments.

PubMed

Bais, Abha S; Grossmann, Stefen; Vingron, Martin

2007-08-01

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits)are generated. Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification methods do not explicitly consider this.Additionally, prediction of conserved binding sites is carried out in a multi-step approach that segregates alignment from TFBS annotation. In this paper, we demonstrate how the simultaneous alignment and annotation approach of SimAnn can be further extended to incorporate TFBS evolutionary relationships. We study how alignments and binding site predictions interplay at varying evolutionary distances and for various profile qualities.

Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function.

PubMed

Di, Chao; Xu, Wenying; Su, Zhen; Yuan, Joshua S

2010-10-07

PHB (Prohibitin) gene family is involved in a variety of functions important for different biological processes. PHB genes are ubiquitously present in divergent species from prokaryotes to eukaryotes. Human PHB genes have been found to be associated with various diseases. Recent studies by our group and others have shown diverse function of PHB genes in plants for development, senescence, defence, and others. Despite the importance of the PHB gene family, no comprehensive gene family analysis has been carried to evaluate the relatedness of PHB genes across different species. In order to better guide the gene function analysis and understand the evolution of the PHB gene family, we therefore carried out the comparative genome analysis of the PHB genes across different kingdoms. The relatedness, motif distribution, and intron/exon distribution all indicated that PHB genes is a relatively conserved gene family. The PHB genes can be classified into 5 classes and each class have a very deep evolutionary origin. The PHB genes within the class maintained the same motif patterns during the evolution. With Arabidopsis as the model species, we found that PHB gene intron/exon structure and domains are also conserved during the evolution. Despite being a conserved gene family, various gene duplication events led to the expansion of the PHB genes. Both segmental and tandem gene duplication were involved in Arabidopsis PHB gene family expansion. However, segmental duplication is predominant in Arabidopsis. Moreover, most of the duplicated genes experienced neofunctionalization. The results highlighted that PHB genes might be involved in important functions so that the duplicated genes are under the evolutionary pressure to derive new function. PHB gene family is a conserved gene family and accounts for diverse but important biological functions based on the similar molecular mechanisms. The highly diverse biological function indicated that more research needs to be carried out to dissect the PHB gene function. The conserved gene evolution indicated that the study in the model species can be translated to human and mammalian studies.

G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch.

PubMed

Kaplan, Oktay I; Berber, Burak; Hekim, Nezih; Doluca, Osman

2016-11-02

Many studies show that short non-coding sequences are widely conserved among regulatory elements. More and more conserved sequences are being discovered since the development of next generation sequencing technology. A common approach to identify conserved sequences with regulatory roles relies on topological changes such as hairpin formation at the DNA or RNA level. G-quadruplexes, non-canonical nucleic acid topologies with little established biological roles, are increasingly considered for conserved regulatory element discovery. Since the tertiary structure of G-quadruplexes is strongly dependent on the loop sequence which is disregarded by the generally accepted algorithm, we hypothesized that G-quadruplexes with similar topology and, indirectly, similar interaction patterns, can be determined using phylogenetic clustering based on differences in the loop sequences. Phylogenetic analysis of 52 G-quadruplex forming sequences in the Escherichia coli genome revealed two conserved G-quadruplex motifs with a potential regulatory role. Further analysis revealed that both motifs tend to form hairpins and G quadruplexes, as supported by circular dichroism studies. The phylogenetic analysis as described in this work can greatly improve the discovery of functional G-quadruplex structures and may explain unknown regulatory patterns. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch

PubMed Central

Lou, Chunbo; Liu, Xili; Ni, Ming; Huang, Yiqi; Huang, Qiushi; Huang, Longwen; Jiang, Lingli; Lu, Dan; Wang, Mingcong; Liu, Chang; Chen, Daizhuo; Chen, Chongyi; Chen, Xiaoyue; Yang, Le; Ma, Haisu; Chen, Jianguo; Ouyang, Qi

2010-01-01

Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of the genetic information-processing systems. In this study, we report the design and construction of a genetic sequential logic circuit in Escherichia coli. It can generate different outputs in response to the same input signal on the basis of its internal state, and ‘memorize' the output. The circuit is composed of two parts: (1) a bistable switch memory module and (2) a double-repressed promoter NOR gate module. The two modules were individually rationally designed, and they were coupled together by fine-tuning the interconnecting parts through directed evolution. After fine-tuning, the circuit could be repeatedly, alternatively triggered by the same input signal; it functions as a push-on push-off switch. PMID:20212522

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch.

PubMed

Lou, Chunbo; Liu, Xili; Ni, Ming; Huang, Yiqi; Huang, Qiushi; Huang, Longwen; Jiang, Lingli; Lu, Dan; Wang, Mingcong; Liu, Chang; Chen, Daizhuo; Chen, Chongyi; Chen, Xiaoyue; Yang, Le; Ma, Haisu; Chen, Jianguo; Ouyang, Qi

2010-01-01

Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of the genetic information-processing systems. In this study, we report the design and construction of a genetic sequential logic circuit in Escherichia coli. It can generate different outputs in response to the same input signal on the basis of its internal state, and 'memorize' the output. The circuit is composed of two parts: (1) a bistable switch memory module and (2) a double-repressed promoter NOR gate module. The two modules were individually rationally designed, and they were coupled together by fine-tuning the interconnecting parts through directed evolution. After fine-tuning, the circuit could be repeatedly, alternatively triggered by the same input signal; it functions as a push-on push-off switch.

The mitochondrial genome of Globodera ellingtonae is composed of two circles with segregated gene content and differential copy numbers

USDA-ARS?s Scientific Manuscript database

The evolution of animal mitochondrial (mt) genomes has yielded a highly conserved structure: a single circular chromosome approximately 14 to 20 kb long. Within the last two decades, exceptions to this conserved structure have been reported in a diverse set of organisms. One such exception is the di...

Into the Forest: The Evolution of a Conservation Education Program at Kalinzu Forest Reserve, Uganda

ERIC Educational Resources Information Center

Kuhar, Christopher W.; Bettinger, Tammie L.; Lehnhardt, Kathy; Townsend, Stephanie; Cox, Debbie

2007-01-01

While there are many conservation programs in east Africa, relatively little is invested in environmental education or capacity building within the community. With this in mind, the National Forest Authority of Uganda, the Ugandan Ministry of Education and Sports, Disney's Animal Kingdom[R], and the Jane Goodall Institute--Uganda entered into a…

Analysis and interpretation of diffraction data from complex, anisotropic materials

NASA Astrophysics Data System (ADS)

Tutuncu, Goknur

Most materials are elastically anisotropic and exhibit additional anisotropy beyond elastic deformation. For instance, in ferroelectric materials the main inelastic deformation mode is via domains, which are highly anisotropic crystallographic features. To quantify this anisotropy of ferroelectrics, advanced X-ray and neutron diffraction methods were employed. Extensive sets of data were collected from tetragonal BaTiO3, PZT and other ferroelectric ceramics. Data analysis was challenging due to the complex constitutive behavior of these materials. To quantify the elastic strain and texture evolution in ferroelectrics under loading, a number of data analysis techniques such as the single peak and Rietveld methods were used and their advantages and disadvantages compared. It was observed that the single peak analysis fails at low peak intensities especially after domain switching while the Rietveld method does not account for lattice strain anisotropy although it overcomes the low intensity problem via whole pattern analysis. To better account for strain anisotropy the constant stress (Reuss) approximation was employed within the Rietveld method and new formulations to estimate lattice strain were proposed. Along the way, new approaches for handling highly anisotropic lattice strain data were also developed and applied. All of the ceramics studied exhibited significant changes in their crystallographic texture after loading indicating non-180° domain switching. For a full interpretation of domain switching the spherical harmonics method was employed in Rietveld. A procedure for simultaneous refinement of multiple data sets was established for a complete texture analysis. To further interpret diffraction data, a solid mechanics model based on the self-consistent approach was used in calculating lattice strain and texture evolution during the loading of a polycrystalline ferroelectric. The model estimates both the macroscopic average response of a specimen and its hkl-dependent lattice strains for different reflections. It also tracks the number of grains (or domains) contributing to each reflection and allows for domain switching. The agreement between the model and experimental data was found to be satisfactory.

adrift, a novel bnl-induced Drosophila gene, required for tracheal pathfinding into the CNS.

PubMed

Englund, C; Uv, A E; Cantera, R; Mathies, L D; Krasnow, M A; Samakovlis, C

1999-04-01

Neurons and glial cells provide guidance cues for migrating neurons. We show here that migrating epithelial cells also contact specific neurons and glia during their pathfinding, and we describe the first gene required in the process. In wild-type Drosophila embryos, the ganglionic tracheal branch navigates a remarkably complex path along specific neural and glial substrata, switching substrata five times before reaching its ultimate target in the CNS. In adrift mutants, ganglionic branches migrate normally along the intersegmental nerve, but sporadically fail to switch to the segmental nerve and enter the CNS; they wind up meandering along the ventral epidermis instead. adrift encodes a novel nuclear protein with an evolutionarily conserved motif. The gene is required in the trachea and is expressed in the leading cells of migrating ganglionic branches where it is induced by the branchless FGF pathway. We propose that Adrift regulates expression of tracheal genes required for pathfinding on the segmental nerve, and FGF induction of adrift expression in migrating tracheal cells promotes the switch from the intersegmental to the segmental nerve.

A lysosomal switch triggers proteostasis renewal in the immortal C. elegans germ lineage.

PubMed

Bohnert, K Adam; Kenyon, Cynthia

2017-11-30

Although individuals age and die with time, an animal species can continue indefinitely, because of its immortal germ-cell lineage. How the germline avoids transmitting damage from one generation to the next remains a fundamental question in biology. Here we identify a lysosomal switch that enhances germline proteostasis before fertilization. We find that Caenorhabditis elegans oocytes whose maturation is arrested by the absence of sperm exhibit hallmarks of proteostasis collapse, including protein aggregation. Remarkably, sperm-secreted hormones re-establish oocyte proteostasis once fertilization becomes imminent. Key to this restoration is activation of the vacuolar H + -ATPase (V-ATPase), a proton pump that acidifies lysosomes. Sperm stimulate V-ATPase activity in oocytes by signalling the degradation of GLD-1, a translational repressor that blocks V-ATPase synthesis. Activated lysosomes, in turn, promote a metabolic shift that mobilizes protein aggregates for degradation, and reset proteostasis by enveloping and clearing the aggregates. Lysosome acidification also occurs during Xenopus oocyte maturation; thus, a lysosomal switch that enhances oocyte proteostasis in anticipation of fertilization may be conserved in other species.

Enforcing dust mass conservation in 3D simulations of tightly coupled grains with the PHANTOM SPH code

NASA Astrophysics Data System (ADS)

Ballabio, G.; Dipierro, G.; Veronesi, B.; Lodato, G.; Hutchison, M.; Laibe, G.; Price, D. J.

2018-06-01

We describe a new implementation of the one-fluid method in the SPH code PHANTOM to simulate the dynamics of dust grains in gas protoplanetary discs. We revise and extend previously developed algorithms by computing the evolution of a new fluid quantity that produces a more accurate and numerically controlled evolution of the dust dynamics. Moreover, by limiting the stopping time of uncoupled grains that violate the assumptions of the terminal velocity approximation, we avoid fatal numerical errors in mass conservation. We test and validate our new algorithm by running 3D SPH simulations of a large range of disc models with tightly and marginally coupled grains.

A novel marsupial hepatitis A virus corroborates complex evolutionary patterns shaping the genus Hepatovirus.

PubMed

de Oliveira Carneiro, Ianei; Sander, Anna-Lena; Silva, Namá; Moreira-Soto, Andres; Normann, Andrea; Flehmig, Bertram; Lukashev, Alexander N; Dotzauer, Andreas; Wieseke, Nicolas; Franke, Carlos Roberto; Drexler, Jan Felix

2018-04-25

The discovery of nonprimate hepatoviruses illuminated the evolutionary origins of hepatitis A virus (HAV) in small mammals. Marsupials are ancient mammals that diverged during the Jurassic from other Eutheria. Viruses from marsupials may thus provide important insight into virus evolution. To investigate Hepatovirus macroevolutionary patterns, we sampled 112 opossums in northeastern Brazil. A novel marsupial HAV (MHAV) was detected in a Brazilian Common Opossum ( Didelphis aurita ) by nested RT-PCR. MHAV concentration in liver was high at 2.5x10 9 RNA copies/gram and about 1000-fold higher than in other solid organs, suggesting hepatotropism. Hepatovirus seroprevalence in D. aurita was 26.6% using an ELISA. End-point titers in confirmatory immunofluorescence assays were high and marsupial antibodies co-localized with anti-HAV control sera, suggesting specificity of serological detection. MHAV showed all genomic hallmarks defining hepatoviruses, including late domain motifs likely involved in quasi-envelope acquisition, a predicted C-terminal pX extension of VP1, strong avoidance of CpG dinucleotides and a type 3 internal ribosomal entry site. Translated polyprotein gene sequence distances of at least 23.7% to other hepatoviruses suggested MHAV represents a novel Hepatovirus species. Conserved predicted cleavage sites suggested similarities in polyprotein processing between HAV and MHAV. MHAV was nested within rodent hepatoviruses in phylogenetic reconstructions, suggesting an ancestral hepatovirus host switch from rodents into marsupials. Co-phylogenetic reconciliations of host and hepatovirus phylogenies confirmed that host-independent macroevolutionary patterns shaped the phylogenetic relationships of extant hepatoviruses. Although Marsupials are synanthropic and consumed as wild game in Brazil, HAV community protective immunity may limit the zoonotic potential of MHAV. IMPORTANCE The hepatitis A virus (HAV) is an ubiquitous cause of acute hepatitis in humans. Recent findings revealed the evolutionary origins of HAV and the genus Hepatovirus defined by HAV in small mammals. The factors shaping the genealogy of extant hepatoviruses are unclear. We sampled marsupials, one of the most ancient mammalian lineages and identified a novel marsupial HAV (MHAV). The novel MHAV shared specific features with HAV, including hepatotropism, genome structure and a common ancestor in phylogenetic reconstructions. Co-evolutionary analyses revealed that host-independent evolutionary patterns contributed most to the current phylogeny of hepatoviruses and that MHAV was the most drastic example of a cross-order host switch of any hepatovirus observed so far. The divergence of marsupials from other mammals offers unique opportunities to investigate HAV species barriers and whether mechanisms of HAV immune control are evolutionarily conserved. Copyright © 2018 Carneiro et al.

Molecular pathways to parallel evolution: I. Gene nexuses and their morphological correlates.

PubMed

Zuckerkandl, E

1994-12-01

Aspects of the regulatory interactions among genes are probably as old as most genes are themselves. Correspondingly, similar predispositions to changes in such interactions must have existed for long evolutionary periods. Features of the structure and the evolution of the system of gene regulation furnish the background necessary for a molecular understanding of parallel evolution. Patently "unrelated" organs, such as the fat body of a fly and the liver of a mammal, can exhibit fractional homology, a fraction expected to become subject to quantitation. This also seems to hold for different organs in the same organism, such as wings and legs of a fly. In informational macromolecules, on the other hand, homology is indeed all or none. In the quite different case of organs, analogy is expected usually to represent attenuated homology. Many instances of putative convergence are likely to turn out to be predominantly parallel evolution, presumably including the case of the vertebrate and cephalopod eyes. Homology in morphological features reflects a similarity in networks of active genes. Similar nexuses of active genes can be established in cells of different embryological origins. Thus, parallel development can be considered a counterpart to parallel evolution. Specific macromolecular interactions leading to the regulation of the c-fos gene are given as an example of a "controller node" defined as a regulatory unit. Quantitative changes in gene control are distinguished from relational changes, and frequent parallelism in quantitative changes is noted in Drosophila enzymes. Evolutionary reversions in quantitative gene expression are also expected. The evolution of relational patterns is attributed to several distinct mechanisms, notably the shuffling of protein domains. The growth of such patterns may in part be brought about by a particular process of compensation for "controller gene diseases," a process that would spontaneously tend to lead to increased regulatory and organismal complexity. Despite the inferred increase in gene interaction complexity, whose course over evolutionary time is unknown, the number of homology groups for the functional and structural protein units designated as domains has probably remained rather constant, even as, in some of its branches, evolution moved toward "higher" organisms. In connection with this process, the question is raised of parallel evolution within the purview of activating and repressing master switches and in regard to the number of levels into which the hierarchies of genic master switches will eventually be resolved.

The evolution of mollusc shells.

PubMed

McDougall, Carmel; Degnan, Bernard M

2018-05-01

Molluscan shells are externally fabricated by specialized epithelial cells on the dorsal mantle. Although a conserved set of regulatory genes appears to underlie specification of mantle progenitor cells, the genes that contribute to the formation of the mature shell are incredibly diverse. Recent comparative analyses of mantle transcriptomes and shell proteomes of gastropods and bivalves are consistent with shell diversity being underpinned by a rapidly evolving mantle secretome (suite of genes expressed in the mantle that encode secreted proteins) that is the product of (a) high rates of gene co-option into and loss from the mantle gene regulatory network, and (b) the rapid evolution of coding sequences, particular those encoding repetitive low complexity domains. Outside a few conserved genes, such as carbonic anhydrase, a so-called "biomineralization toolkit" has yet to be discovered. Despite this, a common suite of protein domains, which are often associated with the extracellular matrix and immunity, appear to have been independently and often uniquely co-opted into the mantle secretomes of different species. The evolvability of the mantle secretome provides a molecular explanation for the evolution and diversity of molluscan shells. These genomic processes are likely to underlie the evolution of other animal biominerals, including coral and echinoderm skeletons. This article is categorized under: Comparative Development and Evolution > Regulation of Organ Diversity Comparative Development and Evolution > Evolutionary Novelties. © 2018 Wiley Periodicals, Inc.

Evolution of HIV-1 coreceptor usage and coreceptor switching during pregnancy.

PubMed

Ransy, Doris G; Motorina, Alena; Merindol, Natacha; Akouamba, Bertine S; Samson, Johanne; Lie, Yolanda; Napolitano, Laura A; Lapointe, Normand; Boucher, Marc; Soudeyns, Hugo

2014-03-01

Coreceptor switch from CCR5 to CXCR4 is associated with HIV disease progression. To document the evolution of coreceptor tropism during pregnancy, a longitudinal study of envelope gene sequences was performed in a group of pregnant women infected with HIV-1 of clade B (n=10) or non-B (n=9). Polymerase chain reaction (PCR) amplification of the V1-V3 region was performed on plasma viral RNA, followed by cloning and sequencing. Using geno2pheno and PSSMX4R5, the presence of X4 variants was predicted in nine of 19 subjects (X4 subjects) independent of HIV-1 clade. Six of nine X4 subjects exhibited CD4(+) T cell counts <200 cells/mm(3), and the presence of X4-capable virus was confirmed using a recombinant phenotypic assay in four of seven cases where testing was successful. In five of nine X4 subjects, a statistically significant decline in the geno2pheno false-positive rate was observed during the course of pregnancy, invariably accompanied by progressive increases in the PSSMX4R5 score, the net charge of V3, and the relative representation of X4 sequences. Evolution toward X4 tropism was also echoed in the primary structure of V2, as an accumulation of substitutions associated with CXCR4 tropism was seen in X4 subjects. Results from these experiments provide the first evidence of the ongoing evolution of coreceptor utilization from CCR5 to CXCR4 during pregnancy in a significant fraction of HIV-infected women. These results inform changes in host-pathogen interactions that lead to a directional shaping of viral populations and viral tropism during pregnancy, and provide insights into the biology of HIV transmission from mother to child.

Rate of Amino Acid Substitution Is Influenced by the Degree and Conservation of Male-Biased Transcription Over 50 Myr of Drosophila Evolution

PubMed Central

Grath, Sonja; Parsch, John

2012-01-01

Sex-biased gene expression (i.e., the differential expression of genes between males and females) is common among sexually reproducing species. However, genes often differ in their sex-bias classification or degree of sex bias between species. There is also an unequal distribution of sex-biased genes (especially male-biased genes) between the X chromosome and the autosomes. We used whole-genome expression data and evolutionary rate estimates for two different Drosophilid lineages, melanogaster and obscura, spanning an evolutionary time scale of around 50 Myr to investigate the influence of sex-biased gene expression and chromosomal location on the rate of molecular evolution. In both lineages, the rate of protein evolution correlated positively with the male/female expression ratio. Genes with highly male-biased expression, genes expressed specifically in male reproductive tissues, and genes with conserved male-biased expression over long evolutionary time scales showed the fastest rates of evolution. An analysis of sex-biased gene evolution in both lineages revealed evidence for a “fast-X” effect in which the rate of evolution was greater for X-linked than for autosomal genes. This pattern was particularly pronounced for male-biased genes. Genes located on the obscura “neo-X” chromosome, which originated from a recent X-autosome fusion, showed rates of evolution that were intermediate between genes located on the ancestral X-chromosome and the autosomes. This suggests that the shift to X-linkage led to an increase in the rate of molecular evolution. PMID:22321769

Evaluating prey switching in wolf-ungulate systems.

PubMed

Garrott, Robert A; Bruggeman, Jason E; Becker, Matthew S; Kalinowski, Steven T; White, P J

2007-09-01

Wolf restoration has become a widely accepted conservation and management practice throughout North America and Europe, though the ecosystem effects of returning top carnivores remain both scientific and societal controversies. Mathematical models predicting and describing wolf-ungulate interactions are typically limited to the wolves' primary prey, with the potential for prey switching in wolf-multiple-ungulate systems only suggested or assumed by a number of investigators. We used insights gained from experiments on small taxa and field data from ongoing wolf-ungulate studies to construct a model of predator diet composition for a wolf-elk-bison system in Yellowstone National Park, Wyoming, USA. The model explicitly incorporates differential vulnerability of the ungulate prey types to predation, predator preference, differences in prey biomass, and the possibility of prey switching. Our model demonstrates wolf diet shifts with changes in relative abundance of the two prey, with the dynamics of this shift dependent on the combined influences of preference, differential vulnerability, relative abundances of prey, and whether or not switching occurs. Differences in vulnerability between elk and bison, and strong wolf preference for elk, result in an abrupt dietary shift occurring only when elk are very rare relative to bison, whereas incorporating switching initiates the dietary shift more gradually and at higher bison-elk ratios. We demonstrate how researchers can apply these equations in newly restored wolf-two-prey systems to empirically evaluate whether prey switching is occurring. Each coefficient in the model has a biological interpretation, and most can be directly estimated from empirical data collected from field studies. Given the potential for switching to dramatically influence predator-prey dynamics and the wide range of expected prey types and abundances in some systems where wolves are present and/or being restored, we suggest that this is an important and productive line of research that should be pursued by ecologists working in wolf-ungulate systems.

Four phases of the Flint Water Crisis: Evidence from blood lead levels in children.

PubMed

Zahran, Sammy; McElmurry, Shawn P; Sadler, Richard C

2017-08-01

The Flint Water Crisis (FWC) is divisible into four phases of child water-lead exposure risk: Phase A) before the switch in water source to the Flint River (our baseline); Phase B) after the switch in water source, but before boil water advisories; Phase C) after boil water advisories, but before the switch back to the baseline water source of the Detroit Water and Sewerage Department (DWSD); and Phase D) after the switch back to DWSD. The objective of this work is to estimate water-lead attributable movements in child blood lead levels (BLLs) that correspond with the four phases in the FWC. With over 21,000 geo-referenced and time-stamped blood lead samples from children in Genesee County drawn from January 01, 2013 to July 19, 2016, we develop a series of quasi-experimental models to identify the causal effect of water-lead exposure on child BLLs in Flint. We find that the switch in water source (transitioning from phase A to B) caused mean BLLs to increase by about 0.5μg/dL, and increased the likelihood of a child presenting with a BLL ≥ 5μg/dL by a factor of 1.91-3.50, implying an additional 561 children exceeding 5μg/dL. We conservatively estimate cohort social costs (through lost earnings alone) of this increase in water-lead exposed children at $65 million, contrasted with expected annual savings of $2 million from switching water source. On the switch from Phase B to C, we find BLLs decreased about 50% from their initial rise following boil water advisories and subsequent water avoidance behaviors by households. Finally, the return to the baseline source water (Phase D) returned child BLLs to pre-FWC levels further implicating water-lead exposure as a causal source of child BLLs throughout the FWC. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

4D porosity evolution during solid-solid replacement reaction in mineral system (KBr, KCl)

NASA Astrophysics Data System (ADS)

Beaudoin, Nicolas; Hamilton, Andrea; Koehn, Daniel; Shipton, Zoe

2017-04-01

An extensive understanding of the controlling mechanisms of phase transformation is key in geosciences to better predicting the evolution of the physical parameters of rocks (porosity, permeability, and rheology) from centimetre-scale (e.g. fingering in siltstones) to kilometer-scale (e.g. Dolostone geobodies), in both the diagenetic and metamorphic domains. This contribution reports the 4D monitoring of a KBr crystal at different time steps during an experimental, fluid-mediated replacement reaction with KCl. Volumes are reconstructed based on density contrast using non-destructive X-ray Computed Tomography (XCT) at a resolution of 3 microns. A sample of KBr was immersed in a static bath of saturated KCl at room temperature and pressure. 5 scans were performed during the reaction at 5, 10, 20, 35 and 55 minutes, until 50% of the original crystal was replaced. As a control experiment, two samples reacted continuously for 15 and 55 minutes, respectively. Each 3D dataset was reconstructed to visualize and quantify the different mineral phases, the porosity distribution and connectivity, along with the reaction front morphology. In the case of successive baths, results show that the front morphology evolves from rough with small fingers to flat and thick during the reaction, suggesting a switch between advection and diffusion controlled reactant distribution through time. This switch is also reflected in the mass evolution and the rate of propagation of the replaced zone, being rapid in the first 20 minutes before reaching steady state. The porosity develops perpendicular to the crystal wall, suggesting a self-organization process governed by advection, before connecting laterally. While the reaction changes from advection controlled to diffusion controlled, the direction of the connected pores becomes parallel to the crystal walls. This phenomenon is not observed when the crystal is reacting discontinuously for 55 minutes. In the latter case, self-organization similar to extended fingering is observed, suggesting the advection to diffusion switch is related to the successive stop of reaction progress for scanning. In both cases, when considering only the reacting zone of the crystal, we can estimate the porosity created by Br-Cl substitution at 30%. The evolution of connected porosity distribution helps to understand how fluid flow can migrate in a transforming rock, for example during dolomitisation, a phenomenon extensively observed in sedimentary basins.

Molecular analysis of immunoglobulin variable genes supports a germinal center experienced normal counterpart in primary cutaneous diffuse large B-cell lymphoma, leg-type.

PubMed

Pham-Ledard, Anne; Prochazkova-Carlotti, Martina; Deveza, Mélanie; Laforet, Marie-Pierre; Beylot-Barry, Marie; Vergier, Béatrice; Parrens, Marie; Feuillard, Jean; Merlio, Jean-Philippe; Gachard, Nathalie

2017-11-01

Immunophenotype of primary cutaneous diffuse large B-cell lymphoma, leg-type (PCLBCL-LT) suggests a germinal center-experienced B lymphocyte (BCL2+ MUM1+ BCL6+/-). As maturation history of B-cell is "imprinted" during B-cell development on the immunoglobulin gene sequence, we studied the structure and sequence of the variable part of the genes (IGHV, IGLV, IGKV), immunoglobulin surface expression and features of class switching in order to determine the PCLBCL-LT cell of origin. Clonality analysis with BIOMED2 protocol and VH leader primers was done on DNA extracted from frozen skin biopsies on retrospective samples from 14 patients. The clonal DNA IGHV sequence of the tumor was aligned and compared with the closest germline sequence and homology percentage was calculated. Superantigen binding sites were studied. Features of selection pressure were evaluated with the multinomial Lossos model. A functional monoclonal sequence was observed in 14 cases as determined for IGHV (10), IGLV (2) or IGKV (3). IGV mutation rates were high (>5%) in all cases but one (median:15.5%), with superantigen binding sites conservation. Features of selection pressure were identified in 11/12 interpretable cases, more frequently negative (75%) than positive (25%). Intraclonal variation was detected in 3 of 8 tumor specimens with a low rate of mutations. Surface immunoglobulin was an IgM in 12/12 cases. FISH analysis of IGHM locus, deleted during class switching, showed heterozygous IGHM gene deletion in half of cases. The genomic PCR analysis confirmed the deletions within the switch μ region. IGV sequences were highly mutated but functional, with negative features of selection pressure suggesting one or more germinal center passage(s) with somatic hypermutation, but superantigen (SpA) binding sites conservation. Genetic features of class switch were observed, but on the non functional allele and co-existing with primary isotype IgM expression. These data suggest that cell-of origin is germinal center experienced and superantigen driven selected B-cell, in a stage between germinal center B-cell and plasma cell. Copyright © 2017 Japanese Society for Investigative Dermatology. Published by Elsevier B.V. All rights reserved.

Coevolved Mutations Reveal Distinct Architectures for Two Core Proteins in the Bacterial Flagellar Motor

PubMed Central

Pandini, Alessandro; Kleinjung, Jens; Rasool, Shafqat; Khan, Shahid

2015-01-01

Switching of bacterial flagellar rotation is caused by large domain movements of the FliG protein triggered by binding of the signal protein CheY to FliM. FliG and FliM form adjacent multi-subunit arrays within the basal body C-ring. The movements alter the interaction of the FliG C-terminal (FliGC) “torque” helix with the stator complexes. Atomic models based on the Salmonella entrovar C-ring electron microscopy reconstruction have implications for switching, but lack consensus on the relative locations of the FliG armadillo (ARM) domains (amino-terminal (FliGN), middle (FliGM) and FliGC) as well as changes during chemotaxis. The generality of the Salmonella model is challenged by the variation in motor morphology and response between species. We studied coevolved residue mutations to determine the unifying elements of switch architecture. Residue interactions, measured by their coevolution, were formalized as a network, guided by structural data. Our measurements reveal a common design with dedicated switch and motor modules. The FliM middle domain (FliMM) has extensive connectivity most simply explained by conserved intra and inter-subunit contacts. In contrast, FliG has patchy, complex architecture. Conserved structural motifs form interacting nodes in the coevolution network that wire FliMM to the FliGC C-terminal, four-helix motor module (C3-6). FliG C3-6 coevolution is organized around the torque helix, differently from other ARM domains. The nodes form separated, surface-proximal patches that are targeted by deleterious mutations as in other allosteric systems. The dominant node is formed by the EHPQ motif at the FliMMFliGM contact interface and adjacent helix residues at a central location within FliGM. The node interacts with nodes in the N-terminal FliGc α-helix triad (ARM-C) and FliGN. ARM-C, separated from C3-6 by the MFVF motif, has poor intra-network connectivity consistent with its variable orientation revealed by structural data. ARM-C could be the convertor element that provides mechanistic and species diversity. PMID:26561852

Insights into bilaterian evolution from three spiralian genomes

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

Simakov, Oleg; Marletaz, Ferdinand; Cho, Sung-Jin

2012-01-07

Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those ofmore » some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.« less

Of mice and genes: evolution of vertebrate brain development

NASA Technical Reports Server (NTRS)

Fritzsch, B.

1998-01-01

In this review the current understanding of genetic and molecular evolution of development, in particular the formation of the major axis of bilateral animals, is critically evaluated, and the early pattern formation in the hindbrain is related as much as possible to these processes. On the genetic level it is proposed that the exuberant multiplication of regulatory genes compared to that of structural genes relates to the increased flexibility of early vertebrate development. In comparisons to fruit flies, many conserved genes are found to be expressed very differently, while many others seem to reflect a comparable pattern and thus suggest a conservation of function. Even genes with a largely conserved pattern of expression may change the level at which they are expressed and the mechanisms by which they are regulated in their expression. Evolution and development of hindbrain motoneurons is reviewed, and it is concluded that both comparative data as well as more recent experimental data suggest a limited importance for the rhombomeres. Clearly, many cell fate-specifying processes work below the level of rhombomeres or in the absence of rhombomeres. It is suggested that more comparative developmental data are needed to establish firmly the relationship between homeobox genes and rhombomere specification in vertebrates other than a few model species.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

PubMed

Wolf, Yuri I; Makarova, Kira S; Yutin, Natalya; Koonin, Eugene V

2012-12-14

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer. The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).

Natural selection in chemical evolution.

PubMed

Fernando, Chrisantha; Rowe, Jonathan

2007-07-07

We propose that chemical evolution can take place by natural selection if a geophysical process is capable of heterotrophic formation of liposomes that grow at some base rate, divide by external agitation, and are subject to stochastic chemical avalanches, in the absence of nucleotides or any monomers capable of modular heredity. We model this process using a simple hill-climbing algorithm, and an artificial chemistry that is unique in exhibiting conservation of mass and energy in an open thermodynamic system. Selection at the liposome level results in the stabilization of rarely occurring molecular autocatalysts that either catalyse or are consumed in reactions that confer liposome level fitness; typically they contribute in parallel to an increasingly conserved intermediary metabolism. Loss of competing autocatalysts can sometimes be adaptive. Steady-state energy flux by the individual increases due to the energetic demands of growth, but also of memory, i.e. maintaining variations in the chemical network. Self-organizing principles such as those proposed by Kauffman, Fontana, and Morowitz have been hypothesized as an ordering principle in chemical evolution, rather than chemical evolution by natural selection. We reject those notions as either logically flawed or at best insufficient in the absence of natural selection. Finally, a finite population model without elitism shows the practical evolutionary constraints for achieving chemical evolution by natural selection in the lab.

Alternancia entre el estado de emisión de Rayos-X y Pulsar en Sistemas Binarios Interactuantes

NASA Astrophysics Data System (ADS)

De Vito, M. A.; Benvenuto, O. G.; Horvath, J. E.

2015-08-01

Redbacks belong to the family of binary systems in which one of the components is a pulsar. Recent observations show redbacks that have switched their state from pulsar - low mass companion (where the accretion of material over the pulsar has ceased) to low mass X-ray binary system (where emission is produced by the mass accretion on the pulsar), or inversely. The irradiation effect included in our models leads to cyclic mass transfer episodes, which allow close binary systems to switch between one state to other. We apply our results to the case of PSR J1723-2837, and discuss the need to include new ingredients in our code of binary evolution to describe the observed state transitions.

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

Singleton, John; Kim, Jae Wook; Topping, Craig V.

Here, we report extraordinarily large magnetic hysteresis loops in the iridates Sr 3NiIrO 5 and Sr 3CoIrO 6. We find coercive magnetic fields of up to 55 T with switched magnetic moments ≈1μ B per formula unit in Sr 3NiIrO 6 and coercive fields of up to 52 T with switched moments ≈3μ B per formula unit in Sr 3CoIrO 6. We propose that the magnetic hysteresis involves the field-induced evolution of quasi-one-dimensional chains in a frustrated triangular configuration. In conclusion, the striking magnetic behavior is likely to be linked to the unusual spin-orbit-entangled local state of the Ir 4+more » ion and its potential for anisotropic exchange interactions.« less

Protein structure and evolution: are they constrained globally by a principle derived from information theory?

PubMed

Hatton, Leslie; Warr, Gregory

2015-01-01

That the physicochemical properties of amino acids constrain the structure, function and evolution of proteins is not in doubt. However, principles derived from information theory may also set bounds on the structure (and thus also the evolution) of proteins. Here we analyze the global properties of the full set of proteins in release 13-11 of the SwissProt database, showing by experimental test of predictions from information theory that their collective structure exhibits properties that are consistent with their being guided by a conservation principle. This principle (Conservation of Information) defines the global properties of systems composed of discrete components each of which is in turn assembled from discrete smaller pieces. In the system of proteins, each protein is a component, and each protein is assembled from amino acids. Central to this principle is the inter-relationship of the unique amino acid count and total length of a protein and its implications for both average protein length and occurrence of proteins with specific unique amino acid counts. The unique amino acid count is simply the number of distinct amino acids (including those that are post-translationally modified) that occur in a protein, and is independent of the number of times that the particular amino acid occurs in the sequence. Conservation of Information does not operate at the local level (it is independent of the physicochemical properties of the amino acids) where the influences of natural selection are manifest in the variety of protein structure and function that is well understood. Rather, this analysis implies that Conservation of Information would define the global bounds within which the whole system of proteins is constrained; thus it appears to be acting to constrain evolution at a level different from natural selection, a conclusion that appears counter-intuitive but is supported by the studies described herein.

Conservation genetics and geographic patterns of genetic variation of the vulnerable officinal herb Fritillaria walujewii (Liliaceae)

Treesearch

Zhihao Su; Borong Pan; Stewart C. Sanderson; Xiaojun Shi; Xiaolong Jiang

2015-01-01

The Chinese herb Fritillaria walujewii Regel is an important officinal species that is vulnerable because of over-harvesting. Here, we examined the geographic pattern of genetic variation across the species entire range, to study its evolution process and give implication needed for the conservation. Nine haplotypes were detected on the basis of three chloroplast...

Conservation genetics and evolution in an endangered species: research in Sonoran topminnows*

PubMed Central

Hedrick, Philip W; Hurt, Carla R

2012-01-01

Conservation genetics of endangered species has primarily focused on using neutral markers to determine units of conservation and estimating evolutionary parameters. Because the endangered Sonoran topminnow can be bred in the laboratory and has a relatively short generation length, experiments to examine both detrimental and adaptive variations are also possible. Here, we discuss over two decades of empirical and experimental observations in the Sonoran topminnow. Results from this research have been used to determine species and evolutionary significant units using neutral markers, document inbreeding and outbreeding depression and genetic load using experimental crosses, and measure adaptive differences in fitness-related traits and variation in pathogen resistance among populations and major histocompatibility complex genotypes. In addition, both premating and postmating reproductive isolation between Gila and Yaqui topminnows have been experimentally determined, and the predicted and observed ancestry of these two species in experimental crosses has been examined over time. Although some have suggested that endangered species are unsuitable for experimentation because of both practical and ethical considerations, these results demonstrate that in this case an endangered species can be employed to examine fundamental questions in conservation and evolution. PMID:23346226

Evolutionary genetics of insect innate immunity.

PubMed

Viljakainen, Lumi

2015-11-01

Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on gene family evolution and evolution at the sequence level; both population genetics and molecular evolution frameworks are considered. © The Author 2015. Published by Oxford University Press.

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution.

PubMed

Mostowy, Rafal; Croucher, Nicholas J; Hanage, William P; Harris, Simon R; Bentley, Stephen; Fraser, Christophe

2014-05-01

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes.

Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution

PubMed Central

Hanage, William P.; Harris, Simon R.; Bentley, Stephen; Fraser, Christophe

2014-01-01

The bacterium Streptococcus pneumoniae (pneumococcus) is one of the most important human bacterial pathogens, and a leading cause of morbidity and mortality worldwide. The pneumococcus is also known for undergoing extensive homologous recombination via transformation with exogenous DNA. It has been shown that recombination has a major impact on the evolution of the pathogen, including acquisition of antibiotic resistance and serotype-switching. Nevertheless, the mechanism and the rates of recombination in an epidemiological context remain poorly understood. Here, we proposed several mathematical models to describe the rate and size of recombination in the evolutionary history of two very distinct pneumococcal lineages, PMEN1 and CC180. We found that, in both lineages, the process of homologous recombination was best described by a heterogeneous model of recombination with single, short, frequent replacements, which we call micro-recombinations, and rarer, multi-fragment, saltational replacements, which we call macro-recombinations. Macro-recombination was associated with major phenotypic changes, including serotype-switching events, and thus was a major driver of the diversification of the pathogen. We critically evaluate biological and epidemiological processes that could give rise to the micro-recombination and macro-recombination processes. PMID:24786281

AID induces intraclonal diversity and genomic damage in CD86+ chronic lymphocytic leukemia cells

PubMed Central

Huemer, Michael; Rebhandl, Stefan; Zaborsky, Nadja; Gassner, Franz J; Hainzl, Stefan; Weiss, Lukas; Hebenstreit, Daniel; Greil, Richard; Geisberger, Roland

2014-01-01

The activation-induced cytidine deaminase (AID) mediates somatic hypermutation and class switch recombination of the Ig genes by directly deaminating cytosines to uracils. As AID causes a substantial amount of off-target mutations, its activity has been associated with lymphomagenesis and clonal evolution of B-cell malignancies. Although it has been shown that AID is expressed in B-cell chronic lymphocytic leukemia (CLL), a clear analysis of in vivo AID activity in this B-cell malignancy remained elusive. In this study performed on primary human CLL samples, we report that, despite the presence of a dominant VDJ heavy chain region, a substantial intraclonal diversity was observed at VDJ as well as at IgM switch regions (Sμ), showing ongoing AID activity in vivo during disease progression. This AID-mediated heterogeneity was higher in CLL subclones expressing CD86, which we identified as the proliferative CLL fraction. Finally, CD86 expression correlated with shortened time to first treatment and increased γ-H2AX focus formation. Our data demonstrate that AID is active in CLL in vivo and thus, AID likely contributes to clonal evolution of CLL. PMID:25179679

Evolution in action: climate change, biodiversity dynamics and emerging infectious disease

PubMed Central

Hoberg, Eric P.; Brooks, Daniel R.

2015-01-01

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host–parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)—phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference—provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. PMID:25688014

Understanding the conductive channel evolution in Na:WO(3-x)-based planar devices.

PubMed

Shang, Dashan; Li, Peining; Wang, Tao; Carria, Egidio; Sun, Jirong; Shen, Baogen; Taubner, Thomas; Valov, Ilia; Waser, Rainer; Wuttig, Matthias

2015-04-14

An ion migration process in a solid electrolyte is important for ion-based functional devices, such as fuel cells, batteries, electrochromics, gas sensors, and resistive switching systems. In this study, a planar sandwich structure is prepared by depositing tungsten oxide (WO(3-x)) films on a soda-lime glass substrate, from which Na(+) diffuses into the WO(3-x) films during the deposition. The entire process of Na(+) migration driven by an alternating electric field is visualized in the Na-doped WO(3-x) films in the form of conductive channel by in situ optical imaging combined with infrared spectroscopy and near-field imaging techniques. A reversible change of geometry between a parabolic and a bar channel is observed with the resistance change of the devices. The peculiar channel evolution is interpreted by a thermal-stress-induced mechanical deformation of the films and an asymmetric Na(+) mobility between the parabolic and the bar channels. These results exemplify a typical ion migration process driven by an alternating electric field in a solid electrolyte with a low ion mobility and are expected to be beneficial to improve the controllability of the ion migration in ion-based functional devices, such as resistive switching devices.

Evaluating a Novel Cellular Automata-Based Distributed Power Management Approach for Mobile Wireless Sensor Networks

NASA Astrophysics Data System (ADS)

Adabi, Sepideh; Adabi, Sahar; Rezaee, Ali

According to the traditional definition of Wireless Sensor Networks (WSNs), static sensors have limited the feasibility of WSNs in some kind of approaches, so the mobility was introduced in WSN. Mobile nodes in a WSN come equipped with battery and from the point of deployment, this battery reserve becomes a valuable resource since it cannot be replenished. Hence, maximizing the network lifetime by minimizing the energy is an important challenge in Mobile WSN. Energy conservation can be accomplished by different approaches. In this paper, we presented an energy conservation solution based on Cellular Automata. The main objective of this solution is based on dynamically adjusting the transmission range and switching between operational states of the sensor nodes.

On the Effect of Energy Conservation on Black Hole Evaporation

NASA Astrophysics Data System (ADS)

Torres, R.; Fayos, F.; Lorente-Espín, O.

2013-06-01

We consider the emission of Hawking radiation by black holes as a consequence of a tunneling process. By requiring energy conservation in the derivation of the emission rate we get a well-known deviation from an exact thermal spectrum. A model that takes into account the implications of energy conservation, as well as the back-scattered radiation, is then constructed in order to describe the evolution of black holes as they evaporate. The evaporation process in this model is compared with the results in the standard "thermal" approximation. This allows us to point out the relevance that energy conservation might have in the last stages of black hole evaporation. We also comment about the possible implications of energy conservation in the information loss paradox.

Key technologies and concepts for beyond-3G networks

NASA Astrophysics Data System (ADS)

Pehkonen, Kari; Uskela, Sami; Kalliojarvi, Kari; Oksanen, Lauri; Rikkinen, Kari

2001-10-01

Standardization of 3rd Generation (3G) mobile communication systems has produced the first specification releases and the commercial deployment of the 3G systems has started. Whereas 1G and 2G focused on efficiently providing voice services, in 3G a lot of attention has been devoted to solutions that support both Circuit Switched (CS) and Packet Switched (PS) communication. That has called for very flexible air interface and network solutions. 3G will continue to evolve and there are already on-going standardization activities that will, for example, boost the peak data rates up to 5-10 Mbps and improve spectral efficiency by 2-4 times. In the future, 3G evolution will be going towards 10/100 Mbps peak data rates in wide/local are coverage, respectively. This will take place partly because of technical improvements of 3G radio interface solutions, but also due to network evolution which will allow the integration other radio access methods like radio LANs into the 3G system. In longer term the 3G network evolution will be going towards ALL-IP networks. As 3G evolution seems to be going towards 10 Mbps/100 Mbps peak data rates and ALL-IP networks any beyond 3G air interface or network solution should be clearly better in order to justify its technical and commercial feasibility. Given the long evolution time of 3G and integration of other radio access schemes with 3G radio we may not even see a new, complete beyond 3G system being developed. Maybe we will just witness the emergence of a new, more advanced radio access solution which will then be connected to the evolving 3G network. As 3G evolution will continue for several years to come the research targets for any beyond 3G solutions must be set very high. When it comes to air interface, we should aim at 100 Mbps peak data rates for wide area access with high mobility, and at 1 Gbps for local area access with low mobility. Regarding possible commercial launches of any beyond 3G systems or solutions they could then take place around year 2010 or even later.

Vertical distribution, flight behaviour and evolution of wing morphology in Morpho butterflies.

PubMed

Devries, P J; Penz, Carla M; Hill, Ryan I

2010-09-01

1. Flight is a key innovation in the evolution of insects that is crucial to their dispersal, migration, territoriality, courtship and predator avoidance. Male butterflies have characteristic territoriality and courtship flight behaviours, and females use a characteristic flight behaviour when searching for host plants. This implies that selection acts on wing morphology to maximize flight performance for conducting important behaviours among sexes. 2. Butterflies in the genus Morpho are obvious components of neotropical forests, and many observations indicate that they show two broad categories of flight behaviour and flight height. Although species can be categorized as using gliding or flapping flight, and flying at either canopy or understorey height, the association of flight behaviour and flight height with wing shape evolution has never been explored. 3. Two clades within Morpho differ in flight behaviour and height. Males and females of one clade inhabit the forest understorey and use flapping flight, whereas in the other clade, males use gliding flight at canopy level and females use flapping flight in both canopy and understorey. 4. We used independent contrasts to answer whether wing shape is associated with flight behaviour and height. Given a single switch to canopy habitation and gliding flight, we compared contrasts for the node at which the switch to canopy flight occurred with the distribution of values in the two focal clades. We found significant changes in wing shape at the transition to canopy flight only in males, and no change in size for either sex. A second node within the canopy clade suggests that other factors may also be involved in wing shape evolution. Our results reinforce the hypothesis that natural selection acts differently on male and female butterfly wing shape and indicate that the transition to canopy flight cannot explain all wing shape diversity in Morpho. 5. This study provides a starting point for characterizing evolution of wing morphology in forest butterflies in the contexts of habitat selection and flight behaviour. Further, these observations suggest that exploring wing shape evolution for canopy and understorey species in other insects may help understand the effects of habitat destruction on biological diversity.

Conserved domains and SINE diversity during animal evolution.

PubMed

Luchetti, Andrea; Mantovani, Barbara

2013-10-01

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs. © 2013 Elsevier Inc. All rights reserved.

Sex, genes, and heat: triggers of diversity.

PubMed

Western, P S; Sinclair, A H

2001-11-01

In vertebrates, sex is determined by a surprising variety of mechanisms. In many reptiles, the primary testis or ovary-determining trigger is regulated by egg incubation temperature. This temperature dependent sex determining (TSD) mechanism occurs in all crocodilians and marine turtles examined to date and is common in terrestrial turtles and viviparous lizards (Ewert et al. 1994. J Exp Zool 270:3-15; Lang and Andrews. 1994. J Exp Biol 270:28-44; Mrosovsky. 1994. J Exp Zool 270:16-27; Pieau. 1996. Bioessays 18:19-26; Viets et al. 1994. J Exp Zool 270:45-56; Wibbels et al. 1998. J Exp Zool 281:409-416). In contrast, sex in mammals and birds is determined chromosomally (CSD). Despite these differences, morphological development of the gonads in all these vertebrate groups appears to have been conserved through evolution. Therefore, the genetic mechanisms triggering sex determination appear not to have been conserved through evolution, although the basic genetic pathway controlling the morphological differentiation of the gonads appears to have been conserved. Copyright 2001 Wiley-Liss, Inc.

An Evolutionarily Conserved DOF-CONSTANS Module Controls Plant Photoperiodic Signaling1[OPEN

PubMed Central

2015-01-01

The response to daylength is a crucial process that evolved very early in plant evolution, entitling the early green eukaryote to predict seasonal variability and attune its physiological responses to the environment. The photoperiod responses evolved into the complex signaling pathways that govern the angiosperm floral transition today. The Chlamydomonas reinhardtii DNA-Binding with One Finger (CrDOF) gene controls transcription in a photoperiod-dependent manner, and its misexpression influences algal growth and viability. In short days, CrDOF enhances CrCO expression, a homolog of plant CONSTANS (CO), by direct binding to its promoter, while it reduces the expression of cell division genes in long days independently of CrCO. In Arabidopsis (Arabidopsis thaliana), transgenic plants overexpressing CrDOF show floral delay and reduced expression of the photoperiodic genes CO and FLOWERING LOCUS T. The conservation of the DOF-CO module during plant evolution could be an important clue to understanding diversification by the inheritance of conserved gene toolkits in key developmental programs. PMID:25897001

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

PubMed

Liscovitch-Brauer, Noa; Alon, Shahar; Porath, Hagit T; Elstein, Boaz; Unger, Ron; Ziv, Tamar; Admon, Arie; Levanon, Erez Y; Rosenthal, Joshua J C; Eisenberg, Eli

2017-04-06

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

Mapping behavioural evolution onto brain evolution: the strategic roles of conserved organization in individuals and species.

PubMed

Finlay, Barbara L; Hinz, Flora; Darlington, Richard B

2011-07-27

The pattern of individual variation in brain component structure in pigs, minks and laboratory mice is very similar to variation across species in the same components, at a reduced scale. This conserved pattern of allometric scaling resembles robotic architectures designed to be robust to changes in computing power and task demands, and may reflect the mechanism by which both growing and evolving brains defend basic sensory, motor and homeostatic functions at multiple scales. Conserved scaling rules also have implications for species-specific sensory and social communication systems, motor competencies and cognitive abilities. The role of relative changes in neuron number in the central nervous system in producing species-specific behaviour is thus highly constrained, while changes in the sensory and motor periphery, and in motivational and attentional systems increase in probability as the principal loci producing important changes in functional neuroanatomy between species. By their nature, these loci require renewed attention to development and life history in the initial organization and production of species-specific behavioural abilities.

Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes.

PubMed

Cianciulli, Antonia; Calvello, Rosa; Panaro, Maria A

2015-04-01

In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor. Copyright © 2015 Elsevier Ltd. All rights reserved.

Distinguishing the rates of gene activation from phenotypic variations.

PubMed

Chen, Ye; Lv, Cheng; Li, Fangting; Li, Tiejun

2015-06-18

Stochastic genetic switching driven by intrinsic noise is an important process in gene expression. When the rates of gene activation/inactivation are relatively slow, fast, or medium compared with the synthesis/degradation rates of mRNAs and proteins, the variability of protein and mRNA levels may exhibit very different dynamical patterns. It is desirable to provide a systematic approach to identify their key dynamical features in different regimes, aiming at distinguishing which regime a considered gene regulatory network is in from their phenotypic variations. We studied a gene expression model with positive feedbacks when genetic switching rates vary over a wide range. With the goal of providing a method to distinguish the regime of the switching rates, we first focus on understanding the essential dynamics of gene expression system in different cases. In the regime of slow switching rates, we found that the effective dynamics can be reduced to independent evolutions on two separate layers corresponding to gene activation and inactivation states, and the transitions between two layers are rare events, after which the system goes mainly along deterministic ODE trajectories on a particular layer to reach new steady states. The energy landscape in this regime can be well approximated by using Gaussian mixture model. In the regime of intermediate switching rates, we analyzed the mean switching time to investigate the stability of the system in different parameter ranges. We also discussed the case of fast switching rates from the viewpoint of transition state theory. Based on the obtained results, we made a proposal to distinguish these three regimes in a simulation experiment. We identified the intermediate regime from the fact that the strength of cellular memory is lower than the other two cases, and the fast and slow regimes can be distinguished by their different perturbation-response behavior with respect to the switching rates perturbations. We proposed a simulation experiment to distinguish the slow, intermediate and fast regimes, which is the main point of our paper. In order to achieve this goal, we systematically studied the essential dynamics of gene expression system when the switching rates are in different regimes. Our theoretical understanding provides new insights on the gene expression experiments.

Evolution of epigenetic regulation in vertebrate genomes

PubMed Central

Lowdon, Rebecca F.; Jang, Hyo Sik; Wang, Ting

2016-01-01

Empirical models of sequence evolution have spurred progress in the field of evolutionary genetics for decades. We are now realizing the importance and complexity of the eukaryotic epigenome. While epigenome analysis has been applied to genomes from single cell eukaryotes to human, comparative analyses are still relatively few, and computational algorithms to quantify epigenome evolution remain scarce. Accordingly, a quantitative model of epigenome evolution remains to be established. Here we review the comparative epigenomics literature and synthesize its overarching themes. We also suggest one mechanism, transcription factor binding site turnover, which relates sequence evolution to epigenetic conservation or divergence. Lastly, we propose a framework for how the field can move forward to build a coherent quantitative model of epigenome evolution. PMID:27080453

Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA.

PubMed

Arentson, Benjamin W; Hayes, Erin L; Zhu, Weidong; Singh, Harkewal; Tanner, John J; Becker, Donald F

2016-12-01

Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ 1 -pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon-helix-helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the bifunctional Rhodobacter capsulatus PutA (RcPutA) in order to explore the modular design of functional switching in trifunctional PutAs. The EcRHH-RcPutA chimaera retains the catalytic properties of RcPutA while acquiring the oligomeric state, quaternary structure and DNA-binding properties of EcPutA. Furthermore, the EcRHH-RcPutA chimaera exhibits proline-induced lipid association, which is a fundamental characteristic of functional switching. Unexpectedly, RcPutA lipid binding is also activated by proline, which shows for the first time that bifunctional PutAs exhibit a limited form of functional switching. Altogether, these results suggest that the C-terminal domain (CTD), which is conserved by trifunctional PutAs and certain bifunctional PutAs, is essential for functional switching in trifunctional PutAs. © 2016 The Author(s).

Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA

PubMed Central

Arentson, Benjamin W.; Hayes, Erin L.; Zhu, Weidong; Singh, Harkewal; Tanner, John J.; Becker, Donald F.

2016-01-01

Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ1-pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon–helix–helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the bifunctional Rhodobacter capsulatus PutA (RcPutA) in order to explore the modular design of functional switching in trifunctional PutAs. The EcRHH–RcPutA chimaera retains the catalytic properties of RcPutA while acquiring the oligomeric state, quaternary structure and DNA-binding properties of EcPutA. Furthermore, the EcRHH–RcPutA chimaera exhibits proline-induced lipid association, which is a fundamental characteristic of functional switching. Unexpectedly, RcPutA lipid binding is also activated by proline, which shows for the first time that bifunctional PutAs exhibit a limited form of functional switching. Altogether, these results suggest that the C-terminal domain (CTD), which is conserved by trifunctional PutAs and certain bifunctional PutAs, is essential for functional switching in trifunctional PutAs. PMID:27742866

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

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

PubMed Central

Mahmoudi Saber, Morteza

2017-01-01

Abstract Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes. PMID:28633494

Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine

PubMed Central

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409

Developmental studies of the lamprey and hierarchical evolutionary steps towards the acquisition of the jaw

PubMed Central

Kuratani, Shigeru

2005-01-01

The evolution of animal morphology can be understood as a series of changes in developmental programs. Among vertebrates, some developmental stages are conserved across species, representing particular developmental constraints. One of the most conserved stages is the vertebrate pharyngula, in which similar embryonic morphology is observed and the Hox code is clearly expressed. The oral developmental program also appears to be constrained to some extent, as both its morphology and the the Hox-code-default state of the oropharyngeal region are well conserved between the lamprey and gnathostome embryos. These features do not by themselves explain the evolution of jaws, but should be regarded as a prerequisite for evolutionary diversification of the mandibular arch. By comparing the pharyngula morphology of the lamprey and gnathostomes, it has become clear that the oral pattern is not entirely identical; in particular, the positional differentiation of the rostral ectomesenchyme is shifted between these animals. Therefore, the jaw seems to have arisen as an evolutionary novelty by overriding ancestral constraints, a process in which morphological homologies are partially lost. This change involves the heterotopic shift of tissue interaction, which appears to have been preceded by the transition from monorhiny to diplorhiny, as well as separation of the hypophysis. When gene expression patterns are compared between the lamprey and gnathostomes, cell-autonomously functioning genes tend to be associated with identical cell types or equivalent anatomical domains, whereas growth-factor-encoding genes have changed their expression domains during evolution. Thus, the heterotopic evolution may be based on changes in the regulation of signalling-molecule-encoding genes. PMID:16313390

Analysis of Drosophila TRPA1 reveals an ancient origin for human chemical nociception.

PubMed

Kang, Kyeongjin; Pulver, Stefan R; Panzano, Vincent C; Chang, Elaine C; Griffith, Leslie C; Theobald, Douglas L; Garrity, Paul A

2010-03-25

Chemical nociception, the detection of tissue-damaging chemicals, is important for animal survival and causes human pain and inflammation, but its evolutionary origins are largely unknown. Reactive electrophiles are a class of noxious compounds humans find pungent and irritating, such as allyl isothiocyanate (in wasabi) and acrolein (in cigarette smoke). Diverse animals, from insects to humans, find reactive electrophiles aversive, but whether this reflects conservation of an ancient sensory modality has been unclear. Here we identify the molecular basis of reactive electrophile detection in flies. We demonstrate that Drosophila TRPA1 (Transient receptor potential A1), the Drosophila melanogaster orthologue of the human irritant sensor, acts in gustatory chemosensors to inhibit reactive electrophile ingestion. We show that fly and mosquito TRPA1 orthologues are molecular sensors of electrophiles, using a mechanism conserved with vertebrate TRPA1s. Phylogenetic analyses indicate that invertebrate and vertebrate TRPA1s share a common ancestor that possessed critical characteristics required for electrophile detection. These findings support emergence of TRPA1-based electrophile detection in a common bilaterian ancestor, with widespread conservation throughout vertebrate and invertebrate evolution. Such conservation contrasts with the evolutionary divergence of canonical olfactory and gustatory receptors and may relate to electrophile toxicity. We propose that human pain perception relies on an ancient chemical sensor conserved across approximately 500 million years of animal evolution.

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

An activation switch in the rhodopsin family of G protein-coupled receptors: the thyrotropin receptor.

PubMed

Urizar, Eneko; Claeysen, Sylvie; Deupí, Xavier; Govaerts, Cedric; Costagliola, Sabine; Vassart, Gilbert; Pardo, Leonardo

2005-04-29

We aimed at understanding molecular events involved in the activation of a member of the G protein-coupled receptor family, the thyrotropin receptor. We have focused on the transmembrane region and in particular on a network of polar interactions between highly conserved residues. Using molecular dynamics simulations and site-directed mutagenesis techniques we have identified residue Asn-7.49, of the NPxxY motif of TM 7, as a molecular switch in the mechanism of thyrotropin receptor (TSHr) activation. Asn-7.49 appears to adopt two different conformations in the inactive and active states. These two states are characterized by specific interactions between this Asn and polar residues in the transmembrane domain. The inactive gauche+ conformation is maintained by interactions with residues Thr-6.43 and Asp-6.44. Mutation of these residues into Ala increases the constitutive activity of the receptor by factors of approximately 14 and approximately 10 relative to wild type TSHr, respectively. Upon receptor activation Asn-7.49 adopts the trans conformation to interact with Asp-2.50 and a putatively charged residue that remains to be identified. In addition, the conserved Leu-2.46 of the (N/S)LxxxD motif also plays a significant role in restraining the receptor in the inactive state because the L2.46A mutation increases constitutive activity by a factor of approximately 13 relative to wild type TSHr. As residues Leu-2.46, Asp-2.50, and Asn-7.49 are strongly conserved, this molecular mechanism of TSHr activation can be extended to other members of the rhodopsin-like family of G protein-coupled receptors.

DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

PubMed

Kearney, Bradley M; Johnson, Christian W; Roberts, Daniel M; Swartz, Paul; Mattos, Carla

2014-02-06

Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Wor1-like Protein Fgp1 Regulates Pathogenicity, Toxin Synthesis and Reproduction in the Phytopathogenic Fungus Fusarium graminearum

PubMed Central

Jonkers, Wilfried; Dong, Yanhong; Broz, Karen; Corby Kistler, H.

2012-01-01

WOR1 is a gene for a conserved fungal regulatory protein controlling the dimorphic switch and pathogenicity determents in Candida albicans and its ortholog in the plant pathogen Fusarium oxysporum, called SGE1, is required for pathogenicity and expression of key plant effector proteins. F. graminearum, an important pathogen of cereals, is not known to employ switching and no effector proteins from F. graminearum have been found to date that are required for infection. In this study, the potential role of the WOR1-like gene in pathogenesis was tested in this toxigenic fungus. Deletion of the WOR1 ortholog (called FGP1) in F. graminearum results in greatly reduced pathogenicity and loss of trichothecene toxin accumulation in infected wheat plants and in vitro. The loss of toxin accumulation alone may be sufficient to explain the loss of pathogenicity to wheat. Under toxin-inducing conditions, expression of genes for trichothecene biosynthesis and many other genes are not detected or detected at lower levels in Δfgp1 strains. FGP1 is also involved in the developmental processes of conidium formation and sexual reproduction and modulates a morphological change that accompanies mycotoxin production in vitro. The Wor1-like proteins in Fusarium species have highly conserved N-terminal regions and remarkably divergent C-termini. Interchanging the N- and C- terminal portions of proteins from F. oxysporum and F. graminearum resulted in partial to complete loss of function. Wor1-like proteins are conserved but have evolved to regulate pathogenicity in a range of fungi, likely by adaptations to the C-terminal portion of the protein. PMID:22693448

Protein interactions and ligand binding: from protein subfamilies to functional specificity.

PubMed

Rausell, Antonio; Juan, David; Pazos, Florencio; Valencia, Alfonso

2010-02-02

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as "specificity determining positions" (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.

Progressive Loss of Function in a Limb Enhancer during Snake Evolution.

PubMed

Kvon, Evgeny Z; Kamneva, Olga K; Melo, Uirá S; Barozzi, Iros; Osterwalder, Marco; Mannion, Brandon J; Tissières, Virginie; Pickle, Catherine S; Plajzer-Frick, Ingrid; Lee, Elizabeth A; Kato, Momoe; Garvin, Tyler H; Akiyama, Jennifer A; Afzal, Veena; Lopez-Rios, Javier; Rubin, Edward M; Dickel, Diane E; Pennacchio, Len A; Visel, Axel

2016-10-20

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP. Copyright © 2016 Elsevier Inc. All rights reserved.

Two fundamentally different classes of microbial genes.

PubMed

Wolf, Yuri I; Makarova, Kira S; Lobkovsky, Alexander E; Koonin, Eugene V

2016-11-07

The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss 1-4 . Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species 5,6 . Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes. The results reveal two sharply distinct classes of microbial genes, one of which is characterized by effectively instantaneous gene replacement, and the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes. Furthermore, the same distribution of constraints is shown to govern the evolution of gene complement and gene order, without the need to invoke long-range conservation or the selfish operon concept 7 .

Cost-effective conservation of amphibian ecology and evolution

PubMed Central

Campos, Felipe S.; Lourenço-de-Moraes, Ricardo; Llorente, Gustavo A.; Solé, Mirco

2017-01-01

Habitat loss is the most important threat to species survival, and the efficient selection of priority areas is fundamental for good systematic conservation planning. Using amphibians as a conservation target, we designed an innovative assessment strategy, showing that prioritization models focused on functional, phylogenetic, and taxonomic diversity can include cost-effectiveness–based assessments of land values. We report new key conservation sites within the Brazilian Atlantic Forest hot spot, revealing a congruence of ecological and evolutionary patterns. We suggest payment for ecosystem services through environmental set-asides on private land, establishing potential trade-offs for ecological and evolutionary processes. Our findings introduce additional effective area-based conservation parameters that set new priorities for biodiversity assessment in the Atlantic Forest, validating the usefulness of a novel approach to cost-effectiveness–based assessments of conservation value for other species-rich regions. PMID:28691084

Free-space optics technology employed in an UMTS release 4 bearer independent core network access part

NASA Astrophysics Data System (ADS)

Bibac, Ionut

2005-08-01

The UMTS Bearer Independent Core Network program introduced the 3rd Generation Partnership Program Release 4 BICN architecture into the legacy UMTS TDM-switched network. BICN is the application of calI server archltecture for voice and circuit switched data, enabling the provisioning of traditional circuit-switched services using a packet-switched transport network. Today"s business climate has made it essential for service providers to develop a comprehensive networking strategy that means introduction of RCBICN networks. The R4-BICN solution to the evolution of the Core Network in UMTS will enable operators to significantly reduce the capital and operational costs of delivering both traditional voice sewices and new multimedia services. To build the optical backbone, which can support the third generation (3G) packetized infrastructure, the operators could choose a fibre connection, or they could retain the benefits of a wireless connectivity by using a FSO - Free Space Optical lmk, the only wireless technology available that is capable of achieving data rates up to 2.4 Gbit/s. FSO offers viable alternatives for both core transmission networks and for replacing microwaves links in NodeB - RNC access networks. The paper and presentation aim to demonstrate the manner in which FSO products and networks are employed into R4-BICN design solutions.

Understanding the conductive channel evolution in Na:WO3-x-based planar devices

NASA Astrophysics Data System (ADS)

Shang, Dashan; Li, Peining; Wang, Tao; Carria, Egidio; Sun, Jirong; Shen, Baogen; Taubner, Thomas; Valov, Ilia; Waser, Rainer; Wuttig, Matthias

2015-03-01

An ion migration process in a solid electrolyte is important for ion-based functional devices, such as fuel cells, batteries, electrochromics, gas sensors, and resistive switching systems. In this study, a planar sandwich structure is prepared by depositing tungsten oxide (WO3-x) films on a soda-lime glass substrate, from which Na+ diffuses into the WO3-x films during the deposition. The entire process of Na+ migration driven by an alternating electric field is visualized in the Na-doped WO3-x films in the form of conductive channel by in situ optical imaging combined with infrared spectroscopy and near-field imaging techniques. A reversible change of geometry between a parabolic and a bar channel is observed with the resistance change of the devices. The peculiar channel evolution is interpreted by a thermal-stress-induced mechanical deformation of the films and an asymmetric Na+ mobility between the parabolic and the bar channels. These results exemplify a typical ion migration process driven by an alternating electric field in a solid electrolyte with a low ion mobility and are expected to be beneficial to improve the controllability of the ion migration in ion-based functional devices, such as resistive switching devices.An ion migration process in a solid electrolyte is important for ion-based functional devices, such as fuel cells, batteries, electrochromics, gas sensors, and resistive switching systems. In this study, a planar sandwich structure is prepared by depositing tungsten oxide (WO3-x) films on a soda-lime glass substrate, from which Na+ diffuses into the WO3-x films during the deposition. The entire process of Na+ migration driven by an alternating electric field is visualized in the Na-doped WO3-x films in the form of conductive channel by in situ optical imaging combined with infrared spectroscopy and near-field imaging techniques. A reversible change of geometry between a parabolic and a bar channel is observed with the resistance change of the devices. The peculiar channel evolution is interpreted by a thermal-stress-induced mechanical deformation of the films and an asymmetric Na+ mobility between the parabolic and the bar channels. These results exemplify a typical ion migration process driven by an alternating electric field in a solid electrolyte with a low ion mobility and are expected to be beneficial to improve the controllability of the ion migration in ion-based functional devices, such as resistive switching devices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07545e

Extensive concerted evolution of rice paralogs and the road to regaining independence.

PubMed

Wang, Xiyin; Tang, Haibao; Bowers, John E; Feltus, Frank A; Paterson, Andrew H

2007-11-01

Many genes duplicated by whole-genome duplications (WGDs) are more similar to one another than expected. We investigated whether concerted evolution through conversion and crossing over, well-known to affect tandem gene clusters, also affects dispersed paralogs. Genome sequences for two Oryza subspecies reveal appreciable gene conversion in the approximately 0.4 MY since their divergence, with a gradual progression toward independent evolution of older paralogs. Since divergence from subspecies indica, approximately 8% of japonica paralogs produced 5-7 MYA on chromosomes 11 and 12 have been affected by gene conversion and several reciprocal exchanges of chromosomal segments, while approximately 70-MY-old "paleologs" resulting from a genome duplication (GD) show much less conversion. Sequence similarity analysis in proximal gene clusters also suggests more conversion between younger paralogs. About 8% of paleologs may have been converted since rice-sorghum divergence approximately 41 MYA. Domain-encoding sequences are more frequently converted than nondomain sequences, suggesting a sort of circularity--that sequences conserved by selection may be further conserved by relatively frequent conversion. The higher level of concerted evolution in the 5-7 MY-old segmental duplication may reflect the behavior of many genomes within the first few million years after duplication or polyploidization.

Following the Footsteps of Chlamydial Gene Regulation

PubMed Central

Domman, D.; Horn, M.

2015-01-01

Regulation of gene expression ensures an organism responds to stimuli and undergoes proper development. Although the regulatory networks in bacteria have been investigated in model microorganisms, nearly nothing is known about the evolution and plasticity of these networks in obligate, intracellular bacteria. The phylum Chlamydiae contains a vast array of host-associated microbes, including several human pathogens. The Chlamydiae are unique among obligate, intracellular bacteria as they undergo a complex biphasic developmental cycle in which large swaths of genes are temporally regulated. Coupled with the low number of transcription factors, these organisms offer a model to study the evolution of regulatory networks in intracellular organisms. We provide the first comprehensive analysis exploring the diversity and evolution of regulatory networks across the phylum. We utilized a comparative genomics approach to construct predicted coregulatory networks, which unveiled genus- and family-specific regulatory motifs and architectures, most notably those of virulence-associated genes. Surprisingly, our analysis suggests that few regulatory components are conserved across the phylum, and those that are conserved are involved in the exploitation of the intracellular niche. Our study thus lends insight into a component of chlamydial evolution that has otherwise remained largely unexplored. PMID:26424812

Pathogen evolution and disease emergence in carnivores.

PubMed

McCarthy, Alex J; Shaw, Marie-Anne; Goodman, Simon J

2007-12-22

Emerging infectious diseases constitute some of the most pressing problems for both human and domestic animal health, and biodiversity conservation. Currently it is not clear whether the removal of past constraints on geographical distribution and transmission possibilities for pathogens alone are sufficient to give rise to novel host-pathogen combinations, or whether pathogen evolution is also generally required for establishment in novel hosts. Canine distemper virus (CDV) is a morbillivirus that is prevalent in the world dog population and poses an important conservation threat to a diverse range of carnivores. We performed an extensive phylogenetic and molecular evolution analysis on complete sequences of all CDV genes to assess the role of selection and recombination in shaping viral genetic diversity and driving the emergence of CDV in non-dog hosts. We tested the specific hypothesis that molecular adaptation at known receptor-binding sites of the haemagglutinin gene is associated with independent instances of the spread of CDV to novel non-dog hosts in the wild. This hypothesis was upheld, providing compelling evidence that repeated evolution at known functional sites (in this case residues 530 and 549 of the haemagglutinin molecule) is associated with multiple independent occurrences of disease emergence in a range of novel host species.

Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution.

PubMed

Rogozin, Igor B; Wolf, Yuri I; Sorokin, Alexander V; Mirkin, Boris G; Koonin, Eugene V

2003-09-02

Sequencing of eukaryotic genomes allows one to address major evolutionary problems, such as the evolution of gene structure. We compared the intron positions in 684 orthologous gene sets from 8 complete genomes of animals, plants, fungi, and protists and constructed parsimonious scenarios of evolution of the exon-intron structure for the respective genes. Approximately one-third of the introns in the malaria parasite Plasmodium falciparum are shared with at least one crown group eukaryote; this number indicates that these introns have been conserved through >1.5 billion years of evolution that separate Plasmodium from the crown group. Paradoxically, humans share many more introns with the plant Arabidopsis thaliana than with the fly or nematode. The inferred evolutionary scenario holds that the common ancestor of Plasmodium and the crown group and, especially, the common ancestor of animals, plants, and fungi had numerous introns. Most of these ancestral introns, which are retained in the genomes of vertebrates and plants, have been lost in fungi, nematodes, arthropods, and probably Plasmodium. In addition, numerous introns have been inserted into vertebrate and plant genes, whereas, in other lineages, intron gain was much less prominent.

Time-dependent spectral renormalization method

NASA Astrophysics Data System (ADS)

Cole, Justin T.; Musslimani, Ziad H.

2017-11-01

The spectral renormalization method was introduced by Ablowitz and Musslimani (2005) as an effective way to numerically compute (time-independent) bound states for certain nonlinear boundary value problems. In this paper, we extend those ideas to the time domain and introduce a time-dependent spectral renormalization method as a numerical means to simulate linear and nonlinear evolution equations. The essence of the method is to convert the underlying evolution equation from its partial or ordinary differential form (using Duhamel's principle) into an integral equation. The solution sought is then viewed as a fixed point in both space and time. The resulting integral equation is then numerically solved using a simple renormalized fixed-point iteration method. Convergence is achieved by introducing a time-dependent renormalization factor which is numerically computed from the physical properties of the governing evolution equation. The proposed method has the ability to incorporate physics into the simulations in the form of conservation laws or dissipation rates. This novel scheme is implemented on benchmark evolution equations: the classical nonlinear Schrödinger (NLS), integrable PT symmetric nonlocal NLS and the viscous Burgers' equations, each of which being a prototypical example of a conservative and dissipative dynamical system. Numerical implementation and algorithm performance are also discussed.

Selection platforms for directed evolution in synthetic biology

PubMed Central

Tizei, Pedro A.G.; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B.

2016-01-01

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules–gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function–be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. PMID:27528765

Selection platforms for directed evolution in synthetic biology.

PubMed

Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

2016-08-15

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).

Stability and change in the clinical course of schizoaffective disorder.

PubMed

Durla, Anca; Lenciu, M; Bredicean, C; Papava, I; Cristanovici, M

2013-01-01

Schizoaffective disorder currently raises several questions, one of them being related to the stability of the clinical diagnosis over time. The aim of this study is to identify the clinical and evolutional particularities in the longitudinal course of schizoaffective disorder. 44 subjects with a current diagnosis of schizoaffective disorder have been assessed prospectively. Following parameters were analyzed: socio-demographic (age at onset, gender, educational, professional and marital status at onset) and clinical (total duration of evolution, diagnosis at onset, duration of the evolution until the switch to the schizoaffective disorder diagnosis). Socio-demographic parameters are similar to those in literature and the clinical assessment revealed that schizoaffective disorder is present as a diagnosis along with the longitudinal course of other types of psychosis. Schizoaffective disorder appears as a heterogeneous pathology in terms of the longitudinal course.

Investigation of local thermodynamic equilibrium of laser induced Al{sub 2}O{sub 3}–TiC plasma in argon by spatially resolved optical emission spectroscopy

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

Alnama, K.; Alkhawwam, A.; Jazmati, A. K., E-mail: pscientific5@aec.org.sy

Plasma plume of Al{sub 2}O{sub 3}–TiC is generated by third harmonic Q-switched Nd:YAG nanosecond laser. It is characterized using Optical Emission Spectroscopy (OES) at different argon background gas pressures 10, 10{sup 2}, 10{sup 3}, 10{sup 4} and 10{sup 5} Pa. Spatial evolution of excitation and ionic temperatures is deduced from spectral data analysis. Temporal evolution of Ti I emission originated from different energy states is probed. The correlation between the temporal behavior and the spatial temperature evolution are investigated under LTE condition for the possibility to use the temporal profile of Ti I emission as an indicator for LTE validitymore » in the plasma.« less

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.

PubMed

Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G; Asher, Claire L; Jurkowski, Tomasz P; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O H; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

2015-11-10

Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

PubMed Central

Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G.; Asher, Claire L.; Jurkowski, Tomasz P.; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E.; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S.; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E.; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O. H.; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

2015-01-01

Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity. PMID:26483466

Functional Differentiation of SWI/SNF Remodelers in Transcription and Cell Cycle Control▿ †

PubMed Central

Moshkin, Yuri M.; Mohrmann, Lisette; van Ijcken, Wilfred F. J.; Verrijzer, C. Peter

2007-01-01

Drosophila BAP and PBAP represent two evolutionarily conserved subclasses of SWI/SNF chromatin remodelers. The two complexes share the same core subunits, including the BRM ATPase, but differ in a few signature subunits: OSA defines BAP, whereas Polybromo (PB) and BAP170 specify PBAP. Here, we present a comprehensive structure-function analysis of BAP and PBAP. An RNA interference knockdown survey revealed that the core subunits BRM and MOR are critical for the structural integrity of both complexes. Whole-genome expression profiling suggested that the SWI/SNF core complex is largely dysfunctional in cells. Regulation of the majority of target genes required the signature subunit OSA, PB, or BAP170, suggesting that SWI/SNF remodelers function mostly as holoenzymes. BAP and PBAP execute similar, independent, or antagonistic functions in transcription control and appear to direct mostly distinct biological processes. BAP, but not PBAP, is required for cell cycle progression through mitosis. Because in yeast the PBAP-homologous complex, RSC, controls cell cycle progression, our finding reveals a functional switch during evolution. BAP mediates G2/M transition through direct regulation of string/cdc25. Its signature subunit, OSA, is required for directing BAP to the string/cdc25 promoter. Our results suggest that the core subunits play architectural and enzymatic roles but that the signature subunits determine most of the functional specificity of SWI/SNF holoenzymes in general gene control. PMID:17101803

Evolution of periodicity in periodical cicadas.

PubMed

Ito, Hiromu; Kakishima, Satoshi; Uehara, Takashi; Morita, Satoru; Koyama, Takuya; Sota, Teiji; Cooley, John R; Yoshimura, Jin

2015-09-14

Periodical cicadas (Magicicada spp.) in the USA are famous for their unique prime-numbered life cycles of 13 and 17 years and their nearly perfectly synchronized mass emergences. Because almost all known species of cicada are non-periodical, periodicity is assumed to be a derived state. A leading hypothesis for the evolution of periodicity in Magicicada implicates the decline in average temperature during glacial periods. During the evolution of periodicity, the determinant of maturation in ancestral cicadas is hypothesized to have switched from size dependence to time (period) dependence. The selection for the prime-numbered cycles should have taken place only after the fixation of periodicity. Here, we build an individual-based model of cicadas under conditions of climatic cooling to explore the fixation of periodicity. In our model, under cold environments, extremely long juvenile stages lead to extremely low adult densities, limiting mating opportunities and favouring the evolution of synchronized emergence. Our results indicate that these changes, which were triggered by glacial cooling, could have led to the fixation of periodicity in the non-periodical ancestors.

The Pendulum: From Constrained Fall to the Concept of Potential

NASA Astrophysics Data System (ADS)

Bevilacqua, Fabio; Falomo, Lidia; Fregonese, Lucio; Giannetto, Enrico; Giudice, Franco; Mascheretti, Paolo

2006-08-01

Kuhn underlined the relevance of Galileo’s gestalt switch in the interpretation of a swinging body from constrained fall to time metre. But the new interpretation did not eliminate the older one. The constrained fall, both in the motion of pendulums and along inclined planes, led Galileo to the law of free fall. Experimenting with physical pendulums and assuming the impossibility of perpetual motion Huygens obtained a law of conservation of vis viva at specific positions, beautifully commented by Mach. Daniel Bernoulli generalised Huygens results introducing the concept of potential and the related independence of the ‘work’ done from the trajectories (paths) followed: vis viva conservation at specific positions is now linked with the potential. Feynman’s modern way of teaching the subject shows striking similarities with Bernoulli’s approach. A number of animations and simulations can help to visualise and teach some of the pendulum’s interpretations related to what we now see as instances of energy conservation.

The Biochemistry of Mitosis

PubMed Central

Wieser, Samuel; Pines, Jonathon

2015-01-01

In this article, we will discuss the biochemistry of mitosis in eukaryotic cells. We will focus on conserved principles that, importantly, are adapted to the biology of the organism. It is vital to bear in mind that the structural requirements for division in a rapidly dividing syncytial Drosophila embryo, for example, are markedly different from those in a unicellular yeast cell. Nevertheless, division in both systems is driven by conserved modules of antagonistic protein kinases and phosphatases, underpinned by ubiquitin-mediated proteolysis, which create molecular switches to drive each stage of division forward. These conserved control modules combine with the self-organizing properties of the subcellular architecture to meet the specific needs of the cell. Our discussion will draw on discoveries in several model systems that have been important in the long history of research on mitosis, and we will try to point out those principles that appear to apply to all cells, compared with those in which the biochemistry has been specifically adapted in a particular organism. PMID:25663668

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

PubMed

Glinsky, Gennadi V

2016-09-19

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The yan gene is highly conserved in Drosophila and its expression suggests a complex role throughout development.

PubMed

Price, M D; Lai, Z

1999-04-01

Competence for cell fate determination and cellular differentiation is under tight control of regulatory genes. Yan, a nuclear target of receptor tyrosine kinase (RTK) signaling, is an E twenty six (ETS) DNA-binding protein that functions as a negative regulator of cell differentiation and proliferation in Drosophila. Most members of RTK signaling pathways are highly conserved through evolution, yet no yan orthologues have been identified to date in vertebrates. To investigate the degree of yan conservation during evolution, we have characterized a yan homologue from a sibling species of D. melanogaster, D. virilis. Our results show that the organization, primary structure and expression pattern of yan are highly conserved. Both genes span over 20 kb and contain four exons with introns at identical positions. The areas with highest amino acid similarity include the Pointed and ETS domain but there are other discrete regions with a high degree of similarity. Phylogenetic analysis reveals that yan's closest relative is the human tel gene, a negative regulator of differentiation in hematopoetic precursors. In both species, Yan is dynamically expressed beginning as early as stage 4/5 and persisting throughout embryogenesis. In third instar larvae, Yan is expressed in and behind the morphogenetic furrow of the eye imaginal disc as well as in the laminar precursor cells of the brain. Ovarian follicle cells also contain Yan protein. Conservation of the structure and expression patterns of yan genes strongly suggests that regulatory mechanisms for their expression are also conserved in these two species.

Magnetic drops in a soft-magnetic cylinder

NASA Astrophysics Data System (ADS)

Hertel, Riccardo; Kirschner, Jürgen

2004-07-01

Magnetization reversal in a cylindrical ferromagnetic particle seems to be a simple textbook problem in magnetism. But at a closer look, the magnetization reversal dynamics in a cylinder is far from being trivial. The difficulty arises from the central axis, where the magnetization switches in a discontinuous fashion. Micromagnetic computer simulations allow for a detailed description of the evolution of the magnetic structure on the sub-nanosecond time scale. The switching process involves the injection of a magnetic point singularity (Bloch point) into the cylinder. Further point singularities may be generated and annihilated periodically during the reversal process. This results in the temporary formation of micromagnetic drops, i.e., isolated, non-reversed regions. This surprising feature in dynamic micromagnetism is due to different mobilities of domain wall and Bloch point.

Nanoscale self-recovery of resistive switching in Ar+ irradiated TiO2-x films

NASA Astrophysics Data System (ADS)

Barman, A.; Saini, C. P.; Sarkar, P. K.; Das, D.; Dhar, S.; Singh, M.; Sinha, A. K.; Kanjilal, D.; Gupta, M.; Phase, D. M.; Kanjilal, A.

2017-11-01

Nanoscale evidence of self-recovery in resistive switching (RS) behavior was found in TiO2-x film by conductive atomic force microscopy when exposed to Ar+-ions above a threshold fluence of 1  ×  1016 ions cm-2. This revealed an evolution and gradual disappearance of bipolar RS-loops, followed by reappearance with increasing number of voltage sweep. This was discussed in the realm of oxygen vacancy (OV) driven formation, dissolution and reformation of conducting filaments. The presence of OVs in ion-beam irradiated TiO2-x films was evidenced by decreasing trend of work function in scanning-Kelvin probe microscopy, and was further verified by x-ray absorption near edge spectroscopy at Ti and O-K edges.

Modified unified kinetic scheme for all flow regimes.

PubMed

Liu, Sha; Zhong, Chengwen

2012-06-01

A modified unified kinetic scheme for the prediction of fluid flow behaviors in all flow regimes is described. The time evolution of macrovariables at the cell interface is calculated with the idea that both free transport and collision mechanisms should be considered. The time evolution of macrovariables is obtained through the conservation constraints. The time evolution of local Maxwellian distribution is obtained directly through the one-to-one mapping from the evolution of macrovariables. These improvements provide more physical realities in flow behaviors and more accurate numerical results in all flow regimes especially in the complex transition flow regime. In addition, the improvement steps introduce no extra computational complexity.

Convergent evolution of Y chromosome gene content in flies.

PubMed

Mahajan, Shivani; Bachtrog, Doris

2017-10-04

Sex-chromosomes have formed repeatedly across Diptera from ordinary autosomes, and X-chromosomes mostly conserve their ancestral genes. Y-chromosomes are characterized by abundant gene-loss and an accumulation of repetitive DNA, yet the nature of the gene repertoire of fly Y-chromosomes is largely unknown. Here we trace gene-content evolution of Y-chromosomes across 22 Diptera species, using a subtraction pipeline that infers Y genes from male and female genome, and transcriptome data. Few genes remain on old Y-chromosomes, but the number of inferred Y-genes varies substantially between species. Young Y-chromosomes still show clear evidence of their autosomal origins, but most genes on old Y-chromosomes are not simply remnants of genes originally present on the proto-sex-chromosome that escaped degeneration, but instead were recruited secondarily from autosomes. Despite almost no overlap in Y-linked gene content in different species with independently formed sex-chromosomes, we find that Y-linked genes have evolved convergent gene functions associated with testis expression. Thus, male-specific selection appears as a dominant force shaping gene-content evolution of Y-chromosomes across fly species.While X-chromosome gene content tends to be conserved, Y-chromosome evolution is dynamic and difficult to reconstruct. Here, Mahajan and Bachtrog use a subtraction pipeline to identify Y-linked genes in 22 Diptera species, revealing patterns of Y-chromosome gene-content evolution.

Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution.

PubMed

Duan, Yuange; Dou, Shengqian; Zhang, Hong; Wu, Changcheng; Wu, Mingming; Lu, Jian

2018-01-01

The adenosine-to-inosine (A-to-I) RNA editomes have been systematically characterized in various metazoan species, and many editing sites were found in clusters. However, it remains unclear whether the clustered editing sites tend to be linked in the same RNA molecules or not. By adopting a method originally designed to detect linkage disequilibrium of DNA mutations, we examined the editomes of ten metazoan species and detected extensive linkage of editing in Drosophila and cephalopods. The prevalent linkages of editing in these two clades, many of which are conserved between closely related species and might be associated with the adaptive proteomic recoding, are maintained by natural selection at the cost of genome evolution. Nevertheless, in worms and humans, we only detected modest proportions of linked editing events, the majority of which were not conserved. Furthermore, the linkage of editing in coding regions of worms and humans might be overall deleterious, which drives the evolution of DNA sites to escape promiscuous editing. Altogether, our results suggest that the linkage landscape of A-to-I editing has evolved during metazoan evolution. This present study also suggests that linkage of editing should be considered in elucidating the functional consequences of RNA editing. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Computational Study of Phenotype Switching in Bacillus Subtilis Biofilm

NASA Astrophysics Data System (ADS)

Smith, Howard; Wang, Xiaoling; Jiang, Yi

Bacillus Subtilis (B. Subtilis), is known to differentiate into three main phenotypes during biofilm growth. Novel techniques to track the spatial and temporal evolution of the three main phenotypes exhibited by B. Subtilis have been developed. However, the techniques do not explain the environmental causes of the phenotype switching and how this leads to the spatiotemporal organization of the biofilm. We hypothesize that cells switch their phenotype according to nutrients and autoinducer levels. We test the hypothesis using a hybrid agent-based and continuous model. The bacteria in our model are individual cells that can (i) grow and divide by the intake of nutrients, (ii) produce and secrete EPS, (iii) form spores and (iv) produce an auto inducer. Using a threshold for nutrient and thresholds for autoinducers, we were able to reproduce the experimental spatiotemporal dynamics. From our simulations we observed that in order to reproduce experimental results, two different autoinducers were necessary. The results also suggest that low-EPS producing biofilms generally obtained higher cell populations. Furthermore, most of the cells that become spore forming cells arise from matrix producing cells.

Change deafness, dual-task performance, and domain-specific expertise.

PubMed

Neuhoff, John G; Bochtler, Katharina S

2018-05-01

In a change deafness manipulation using radio broadcasts of sporting events, we show that change deafness to a switch in talker increases when listeners are asked to monitor both lexical and indexical information for change. We held semantic content constant and demonstrated a change deafness rate of 85% when participants listened to the home team broadcast of a hockey game that switched midway to the away team broadcast with a different announcer. In Study 2, participants were asked to monitor either the indexical characteristics ( listen for a change in announcer) or both the indexical and semantic components ( listen for a change in announcer or a goal scored). Monitoring both components led to significantly greater change deafness even though both groups were alerted to the possibility of a change in announcer. In Study 3, we changed both the indexical and the semantic components when the broadcast switched from a hockey game to a basketball game. We found a negative correlation between sports expertise and change deafness. The results are discussed in terms of the nature of perceptual representation and the influence of expertise and evolution on attention allocation.

Black swans, cognition, and the power of learning from failure.

PubMed

Catalano, Allison S; Redford, Kent; Margoluis, Richard; Knight, Andrew T

2018-06-01

Failure carries undeniable stigma and is difficult to confront for individuals, teams, and organizations. Disciplines such as commercial and military aviation, medicine, and business have long histories of grappling with it, beginning with the recognition that failure is inevitable in every human endeavor. Although conservation may arguably be more complex, conservation professionals can draw on the research and experience of these other disciplines to institutionalize activities and attitudes that foster learning from failure, whether they are minor setbacks or major disasters. Understanding the role of individual cognitive biases, team psychological safety, and organizational willingness to support critical self-examination all contribute to creating a cultural shift in conservation to one that is open to the learning opportunity that failure provides. This new approach to managing failure is a necessary next step in the evolution of conservation effectiveness. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail

DOE PAGES

Langan, Patricia S.; Close, Devin W.; Coates, Leighton; ...

2016-03-18

In this paper, we report the engineering of a new reversibly switching chromogenic protein, Dathail. Dathail was evolved from the extremely thermostable fluorescent proteins thermal green protein (TGP) and eCGP123 using directed evolution and ratiometric sorting. Dathail has two spectrally distinct chromogenic states with low quantum yields, corresponding to absorbance in a ground state with a maximum at 389 nm, and a photo-induced metastable state with a maximum at 497 nm. In contrast to all previously described photoswitchable proteins, both spectral states of Dathail are non-fluorescent. The photo-induced chromogenic state of Dathail has a lifetime of ~ 50 min atmore » 293 K and pH 7.5 as measured by UV–Vis spectrophotometry, returning to the ground state through thermal relaxation. X-ray crystallography provided structural insights supporting a change in conformation and coordination in the chromophore pocket as being responsible for Dathail's photoswitching. Neutron crystallography, carried out for the first time on a protein from the green fluorescent protein family, showed a distribution of hydrogen atoms revealing protonation of the chromophore 4-hydroxybenzyl group in the ground state. Additionally, the neutron structure also supports the hypothesis that the photo-induced proton transfer from the chromophore occurs through water-mediated proton relay into the bulk solvent. Beyond its spectroscopic curiosity, Dathail has several characteristics that are improvements for applications, including low background fluorescence, large spectral separation, rapid switching time, and the ability to switch many times. Therefore, Dathail is likely to be extremely useful in the quickly developing fields of imaging and biosensors, including photochromic Förster resonance energy transfer, high-resolution microscopy, and live tracking within the cell.« less

Simulation of the Plasma Density Evolution during Electron Cyclotron Resonance Heating at the T-10 Tokamak

NASA Astrophysics Data System (ADS)

Dnestrovskij, Yu. N.; Vershkov, V. A.; Danilov, A. V.; Dnestrovskij, A. Yu.; Zenin, V. N.; Lysenko, S. E.; Melnikov, A. V.; Shelukhin, D. A.; Subbotin, G. F.; Cherkasov, S. V.

2018-01-01

In ohmically heated (OH) plasma with low recycling, an improved particle confinement (IPC) mode is established during gas puffing. However, after gas puffing is switched off, this mode is retained only for about 100 ms, after which an abrupt phase transition into the low particle confinement (LPC) mode occurs in the entire plasma cross section. During such a transition, energy transport due to heat conduction does not change. The phase transition in OH plasma is similar to the effect of density pump-out from the plasma core, which occurs after electron cyclotron heating (ECH) is switched on. Analysis of the measured plasma pressure profiles in the T-10 tokamak shows that, after gas puffing in the OH mode is switched off, the plasma pressure profile in the IPC stage becomes more peaked and, after the peakedness exceeds a certain critical value, the IPC-LPC transition occurs. Similar processes are also observed during ECH. If the pressure profile is insufficiently peaked during ECH, then the density pump-out effect comes into play only after the critical peakedness of the pressure profile is reached. In the plasma core, the density and pressure profiles are close to the corresponding canonical profiles. This allows one to derive an expression for the particle flux within the canonical profile model and formulate a criterion for the IPC-LPC transition. The time evolution of the plasma density profile during phase transitions was simulated for a number of T-10 shots with ECH and high recycling. The particle transport coefficients in the IPC and LPC phases, as well as the dependences of these coefficients on the ECH power, are determined.

Ferroionic states: coupling between surface electrochemical and bulk ferroelectric functionalities on the nanoscale.

NASA Astrophysics Data System (ADS)

Kalinin, Sergei

Ferroelectricity on the nanoscale has remained a subject of much fascination in condensed matter physics for the last several decades. It is well-recognized that stability of the ferroelectric state necessitates effective polarization screening, and hence screening mechanism and screening charge dynamics become strongly coupled to ferroelectric phase stability and domain behavior. Previously, the role of the screening charge in macroscopic ferroelectrics was observed in phenomena such as potential retention above Curie temperature, back switching of ferroelectric domains, and chaos and intermittency during domain switching. In the last several years, multiple reports claiming ferroelectricity in ultrathin ferroelectrics based on formation of remanent polarization states, local hysteresis loops, and pressure induced switching were made. However, similar phenomena were reported for traditionally non-ferroelectric materials, creating significant level of uncertainty in the field. We pose that in the nanoscale systems, the ferroelectric state is fundamentally inseparable from electrochemical state of the surface, leading to emergence of coupled electrochemical-ferroelectric states. I will present the results of experimental and theoretical work exploring the basic mechanisms of emergence of these coupled states including the basic theory and phase-field formulation for domain evolution. I further discuss the thermodynamics and thickness evolution of this state, and demonstrate the experimental pathway to establish its presence based on spectroscopic version of piezoresponse force microscopy. Finally, the role of chemical screening on domain dynamics is explored using phase-field modelling. This analysis reconciles multiple prior studies, and set forward the predictive pathways for new generations of ferroelectric devices and applications. This research was sponsored by the Division of Materials Sciences and Engineering, BES, DOE, and was conducted at the Center for Nanophase Materials Sciences, sponsored at Oak Ridge National Laboratory by the Scientific User Facilities Division.

Environmental Assessment: Demolish CASS Switch Stations Buildings 644, 645, 646 at Grand Forks Air Force Base

DTIC Science & Technology

2006-06-01

Per Year TSCA Toxic Substance Control Act TSI Thermal System Insulation UAV Unmanned Aerial Vehicle UHF Ultra High Frequency UPS Uninterruptible...Conservation and Recovery Act (RCRA) of 1976 [42 U.S.C. Sec. 6901, et seq.] • Toxic Substances Control Act (TSCA) of 1976 [15 U.S.C. Sec. 2601, et...Corporation (SAIC). Typical hazardous materials include reactive materials such as explosives, ignitables, toxics , and corrosives. Improper storage can

RNA Polymerase Structure, Function, Regulation, Dynamics, Fidelity, and Roles in GENE EXPRESSION | Center for Cancer Research

Cancer.gov

Multi-subunit RNA polymerases (RNAP) are ornate molecular machines that translocate on a DNA template as they generate a complementary RNA chain. RNAPs are highly conserved in evolution among eukarya, eubacteria, archaea, and some viruses. As such, multi-subunit RNAPs appear to be an irreplaceable advance in the evolution of complex life on earth. Because of their stepwise

Dynamic analysis of evolutive conservative systems. Discussion of eigenmode crossings

NASA Technical Reports Server (NTRS)

Morand, H. J. P.

1984-01-01

After an analysis of the close connection between the symmetries of a dynamical system and the multiplicity of its vibrational natural frequencies, it is proved by variational arguments that for a system of invariable symmetry the eigenfrequencies associated with the eigenmodes of a given symmetry type do not cross, in general, during the evolution of this system. The theory is implemented by some numerical calculations applied to the analysis of the evolution of the axisymmetric hydroelastic modes of the Ariane launch vehicle during burning of the first stage.

[Challenges and countermeasures for water conservancy combined with schistosomiasis prevention and control in China in new era].

PubMed

Jia-Sheng, Wang; Jin-You, Lu; Feng-Yang, Min; Kong-Xian, Zhu

2017-04-27

The spread of schistosomiasis seriously threaten the health of people and hinder the economic and social development in China. The water conservancy combined with schistosomiasis prevention and control effectively controlled the spread of schistosomiasis by controlling the spread of Oncomelania hupensis , the only intermediate host of Schistosoma japonicum . This paper reviews the evolution of the strategy of schistosomiasis prevention and control in China and points out the historical role of water conservancy combined with schistosomiasis prevention and control. Furthermore, this article analyzes the problems and challenges of water conservancy combined with schistosomiasis prevention and control in the new period. In response to the challenges, the new strategy of water conservancy combined with schistosomiasis prevention and control is put forward, including: developing the research of the new strategy of water conservancy combined with schistosomiasis prevention and control, enhancing the research of water conservancy technology combined with schistosomiasis prevention and control, improving the efficiency and applicability of water conservancy projects combined with schistosomiasis prevention and control, strengthening the guidance of water conservancy technology combined with schistosomiasis prevention and control, and perfecting the evaluation system.

A Stable Urban Ecosystem

ERIC Educational Resources Information Center

Meier, Richard L.

1976-01-01

Describes a model for the future evolution of a stable ecosystem in a densely-populated society. Discusses designs for limiting population growth, resource-conserving settlements, and ways to feed growing cities. (MLH)

On the Total Variation of High-Order Semi-Discrete Central Schemes for Conservation Laws

NASA Technical Reports Server (NTRS)

Bryson, Steve; Levy, Doron

2004-01-01

We discuss a new fifth-order, semi-discrete, central-upwind scheme for solving one-dimensional systems of conservation laws. This scheme combines a fifth-order WENO reconstruction, a semi-discrete central-upwind numerical flux, and a strong stability preserving Runge-Kutta method. We test our method with various examples, and give particular attention to the evolution of the total variation of the approximations.

mTOR modulates the antibody response to provide cross-protective immunity to lethal influenza infections

PubMed Central

Keating, Rachael; Hertz, Tomer; Wehenkel, Marie; Harris, Tarsha L.; Edwards, Benjamin A.; McClaren, Jennifer L.; Brown, Scott A.; Surman, Sherri; Wilson, Zachary S.; Bradley, Philip; Hurwitz, Julia; Chi, Hongbo; Doherty, Peter C.; Thomas, Paul G.; McGargill, Maureen A.

2013-01-01

Highly pathogenic avian influenza viruses pose a continuing global threat. Current vaccines will not protect against novel pandemic viruses. Creating “universal” vaccines has been unsuccessful because the immunological mechanisms promoting heterosubtypic immunity are incompletely defined. We show that rapamycin, an immunosuppressive drug that inhibits mTOR, promotes cross-strain protection against lethal H5N1 and H7N9 infections when administered during H3N2 virus immunization. Rapamycin reduced germinal center formation and inhibited B cell class-switching, yielding a unique repertoire of antibodies that mediated heterosubtypic protection. Our data establish a requirement for mTORC1 in B cell class-switching and demonstrate that rapamycin skews the antibody response away from high affinity variant epitopes, targeting more conserved elements of hemagglutinin. These findings have intriguing implications for influenza vaccine design. PMID:24141387

Observation of the four wave mixing photonic band gap signal in electromagnetically induced grating.

PubMed

Ullah, Zakir; Wang, Zhiguo; Gao, Mengqin; Zhang, Dan; Zhang, Yiqi; Gao, Hong; Zhang, Yanpeng

2014-12-01

For the first time, we experimentally and theoretically research about the probe transmission signal (PTS), the reflected four wave mixing band gap signal(FWM BGS) and fluorescence signal (FLS) under the double dressing effect in an inverted Y-type four level system. FWM BGS results from photonic band gap structure. We demonstrate that the characteristics of PTS, FWM BGS and FLS can be controlled by power, phase and the frequency detuning of the dressing beams. It is observed in our experiment that FWM BGS switches from suppression to enhancement, corresponding to the switch from transmission enhancement to absorption enhancement in the PTS with changing the relative phase. We also observe the relation among the three signals, which satisfy the law of conservation of energy. Such scheme could have potential applications in optical diodes, amplifiers and quantum information processing.

Hydrogen Bond Switching among Flavin and Amino Acid Side Chains in the BLUF Photoreceptor Observed by Ultrafast Infrared Spectroscopy

PubMed Central

Bonetti, Cosimo; Mathes, Tilo; van Stokkum, Ivo H. M.; Mullen, Katharine M.; Groot, Marie-Louise; van Grondelle, Rienk; Hegemann, Peter; Kennis, John T. M.

2008-01-01

BLUF domains constitute a recently discovered class of photoreceptor proteins found in bacteria and eukaryotic algae. BLUF domains are blue-light sensitive through a FAD cofactor that is involved in an extensive hydrogen-bond network with nearby amino acid side chains, including a highly conserved tyrosine and glutamine. The participation of particular amino acid side chains in the ultrafast hydrogen-bond switching reaction with FAD that underlies photoactivation of BLUF domains is assessed by means of ultrafast infrared spectroscopy. Blue-light absorption by FAD results in formation of FAD•− and a bleach of the tyrosine ring vibrational mode on a picosecond timescale, showing that electron transfer from tyrosine to FAD constitutes the primary photochemistry. This interpretation is supported by the absence of a kinetic isotope effect on the fluorescence decay on H/D exchange. Subsequent protonation of FAD•− to result in FADH• on a picosecond timescale is evidenced by the appearance of a N-H bending mode at the FAD N5 protonation site and of a FADH• C=N stretch marker mode, with tyrosine as the likely proton donor. FADH• is reoxidized in 67 ps (180 ps in D2O) to result in a long-lived hydrogen-bond switched network around FAD. This hydrogen-bond switch shows infrared signatures from the C-OH stretch of tyrosine and the FAD C4=O and C=N stretches, which indicate increased hydrogen-bond strength at all these sites. The results support a previously hypothesized rotation of glutamine by ∼180° through a light-driven radical-pair mechanism as the determinant of the hydrogen-bond switch. PMID:18708458

Adaptive switching of interaction potentials in the time domain: an extended Lagrangian approach tailored to transmute force field to QM/MM simulations and back.

PubMed

Böckmann, Marcus; Doltsinis, Nikos L; Marx, Dominik

2015-06-09

An extended Lagrangian formalism that allows for a smooth transition between two different descriptions of interactions during a molecular dynamics simulation is presented. This time-adaptive method is particularly useful in the context of multiscale simulation as it provides a sound recipe to switch on demand between different hierarchical levels of theory, for instance between ab initio ("QM") and force field ("MM") descriptions of a given (sub)system in the course of a molecular dynamics simulation. The equations of motion can be integrated straightforwardly using the usual propagators, such as the Verlet algorithm. First test cases include a bath of harmonic oscillators, of which a subset is switched to a different force constant and/or equilibrium position, as well as an all-MM to QM/MM transition in a hydrogen-bonded water dimer. The method is then applied to a smectic 8AB8 liquid crystal and is shown to be able to switch dynamically a preselected 8AB8 molecule from an all-MM to a QM/MM description which involves partition boundaries through covalent bonds. These examples show that the extended Lagrangian approach is not only easy to implement into existing code but that it is also efficient and robust. The technique moreover provides easy access to a conserved energy quantity, also in cases when Nosé-Hoover chain thermostatting is used throughout dynamical switching. A simple quadratic driving potential proves to be sufficient to guarantee a smooth transition whose time scale can be easily tuned by varying the fictitious mass parameter associated with the auxiliary variable used to extend the Lagrangian. The method is general and can be applied to time-adaptive switching on demand between two different levels of theory within the framework of hybrid scale-bridging simulations.

Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

PubMed Central

Longo, Mark S; Carone, Dawn M; Green, Eric D; O'Neill, Michael J; O'Neill, Rachel J

2009-01-01

Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB), are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN), euchromatic regions (EU), and an evolutionary breakpoint (EB) that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s) and endogenous retroviruses (ERVs) and a depletion of short interspersed nucleotide elements (SINEs) shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33), known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the divergence of marsupials and eutherians that may have predisposed these genomic regions to large-scale chromosomal instability. PMID:19630942

Evolution of behavior and neural control of the fast-start escape response.

PubMed

Hale, Melina E; Long, John H; McHenry, Matthew J; Westneat, Mark W

2002-05-01

The fast-start startle behavior is the primary mechanism of rapid escape in fishes and is a model system for examining neural circuit design and musculoskeletal function. To develop a dataset for evolutionary analysis of the startle response, the kinematics and muscle activity patterns of the fast-start were analyzed for four fish species at key branches in the phylogeny of vertebrates. Three of these species (Polypterus palmas, Lepisosteus osseus, and Amia calva) represent the base of the actinopterygian radiation. A fourth species (Oncorhynchus mykiss) provided data for a species in the central region of the teleost phylogeny. Using these data, we explored the evolution of this behavior within the phylogeny of vertebrates. To test the hypothesis that startle features are evolutionarily conservative, the variability of motor patterns and kinematics in fast-starts was described. Results show that the evolution of the startle behavior in fishes, and more broadly among vertebrates, is not conservative. The fast-start has undergone substantial change in suites of kinematics and electromyogram features, including the presence of either a one- or a two-stage kinematic response and change in the extent of bilateral muscle activity. Comparative methods were used to test the evolutionary hypothesis that changes in motor control are correlated with key differences in the kinematics and behavior of the fast-start. Significant evolutionary correlations were found between several motor pattern and behavioral characters. These results suggest that the startle neural circuit itself is not conservative. By tracing the evolution of motor pattern and kinematics on a phylogeny, it is shown that major changes in the neural circuit of the startle behavior occur at several levels in the phylogeny of vertebrates.

Physical Mapping and Refinement of the Painted Turtle Genome (Chrysemys picta) Inform Amniote Genome Evolution and Challenge Turtle-Bird Chromosomal Conservation.

PubMed

Badenhorst, Daleen; Hillier, LaDeana W; Literman, Robert; Montiel, Eugenia Elisabet; Radhakrishnan, Srihari; Shen, Yingjia; Minx, Patrick; Janes, Daniel E; Warren, Wesley C; Edwards, Scott V; Valenzuela, Nicole

2015-06-24

Comparative genomics continues illuminating amniote genome evolution, but for many lineages our understanding remains incomplete. Here, we refine the assembly (CPI 3.0.3 NCBI AHGY00000000.2) and develop a cytogenetic map of the painted turtle (Chrysemys picta-CPI) genome, the first in turtles and in vertebrates with temperature-dependent sex determination. A comparison of turtle genomes with those of chicken, selected nonavian reptiles, and human revealed shared and novel genomic features, such as numerous chromosomal rearrangements. The largest conserved syntenic blocks between birds and turtles exist in four macrochromosomes, whereas rearrangements were evident in these and other chromosomes, disproving that turtles and birds retain fully conserved macrochromosomes for greater than 300 Myr. C-banding revealed large heterochromatic blocks in the centromeric region of only few chromosomes. The nucleolar-organizing region (NOR) mapped to a single CPI microchromosome, whereas in some turtles and lizards the NOR maps to nonhomologous sex-chromosomes, thus revealing independent translocations of the NOR in various reptilian lineages. There was no evidence for recent chromosomal fusions as interstitial telomeric-DNA was absent. Some repeat elements (CR1-like, Gypsy) were enriched in the centromeres of five chromosomes, whereas others were widespread in the CPI genome. Bacterial artificial chromosome (BAC) clones were hybridized to 18 of the 25 CPI chromosomes and anchored to a G-banded ideogram. Several CPI sex-determining genes mapped to five chromosomes, and homology was detected between yet other CPI autosomes and the globally nonhomologous sex chromosomes of chicken, other turtles, and squamates, underscoring the independent evolution of vertebrate sex-determining mechanisms. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution of the Karyopherin-β Family of Nucleocytoplasmic Transport Factors; Ancient Origins and Continued Specialization

PubMed Central

O'Reilly, Amanda J.; Dacks, Joel B.; Field, Mark C.

2011-01-01

Background Macromolecular transport across the nuclear envelope (NE) is achieved through nuclear pore complexes (NPCs) and requires karyopherin-βs (KAP-βs), a family of soluble receptors, for recognition of embedded transport signals within cargo. We recently demonstrated, through proteomic analysis of trypanosomes, that NPC architecture is likely highly conserved across the Eukaryota, which in turn suggests conservation of the transport mechanisms. To determine if KAP-β diversity was similarly established early in eukaryotic evolution or if it was subsequently layered onto a conserved NPC, we chose to identify KAP-β sequences in a diverse range of eukaryotes and to investigate their evolutionary history. Results Thirty six predicted proteomes were scanned for candidate KAP-β family members. These resulting sequences were resolved into fifteen KAP-β subfamilies which, due to broad supergroup representation, were most likely represented in the last eukaryotic common ancestor (LECA). Candidate members of each KAP-β subfamily were found in all eukaryotic supergroups, except XPO6, which is absent from Archaeplastida. Phylogenetic reconstruction revealed the likely evolutionary relationships between these different subfamilies. Many species contain more than one representative of each KAP-β subfamily; many duplications are apparently taxon-specific but others result from duplications occurring earlier in eukaryotic history. Conclusions At least fifteen KAP-β subfamilies were established early in eukaryote evolution and likely before the LECA. In addition we identified expansions at multiple stages within eukaryote evolution, including a multicellular plant-specific KAP-β, together with frequent secondary losses. Taken with evidence for early establishment of NPC architecture, these data demonstrate that multiple pathways for nucleocytoplasmic transport were established prior to the radiation of modern eukaryotes but that selective pressure continues to sculpt the KAP-β family. PMID:21556326

On the timing properties of SAX J1808.4-3658 during its 2015 outburst

NASA Astrophysics Data System (ADS)

Sanna, A.; Di Salvo, T.; Burderi, L.; Riggio, A.; Pintore, F.; Gambino, A. F.; Iaria, R.; Tailo, M.; Scarano, F.; Papitto, A.

2017-10-01

We present a timing analysis of the 2015 outburst of the accreting millisecond X-ray pulsar SAX J1808.4-3658, using non-simultaneous XMM-Newton and NuSTAR observations. We estimate the pulsar spin frequency and update the system orbital solution. Combining the average spin frequency from the previous observed, we confirm the long-term spin-down at an average rate \\dot{ν }_{SD}=1.5(2)× 10^{-15} Hz s-1. We also discuss possible corrections to the spin-down rate accounting for mass accretion on to the compact object when the system is X-ray active. Finally, combining the updated ephemerides with those of the previous outbursts, we find a long-term orbital evolution compatible with a binary expansion at a mean rate \\dot{P}_{orb}=3.6(4)× 10^{-12} s s-1, in agreement with previously reported values. This fast evolution is incompatible with an evolution driven by angular momentum losses caused by gravitational radiation under the hypothesis of conservative mass transfer. We discuss the observed orbital expansion in terms of non-conservative mass transfer and gravitational quadrupole coupling mechanism. We find that the latter can explain, under certain conditions, small fluctuations (of the order of few seconds) of the orbital period around a global parabolic trend. At the same time, a non-conservative mass transfer is required to explain the observed fast orbital evolution, which likely reflects ejection of a large fraction of mass from the inner Lagrangian point caused by the irradiation of the donor by the magnetodipole rotator during quiescence (radio-ejection model). This strong outflow may power tidal dissipation in the companion star and be responsible of the gravitational quadrupole change oscillations.

Examining the Evolution of the Regulatory Circuit Controlling Secondary Metabolism and Development in the Fungal Genus Aspergillus

PubMed Central

Lind, Abigail L.; Wisecaver, Jennifer H.; Smith, Timothy D.; Feng, Xuehuan; Calvo, Ana M.; Rokas, Antonis

2015-01-01

Filamentous fungi produce diverse secondary metabolites (SMs) essential to their ecology and adaptation. Although each SM is typically produced by only a handful of species, global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes, such as development. We examined the interplay between the taxonomic narrowness of SM distribution and the broad conservation of global regulation of SM and development in Aspergillus, a diverse fungal genus whose members produce well-known SMs such as penicillin and gliotoxin. Evolutionary analysis of the 2,124 genes comprising the 262 SM pathways in four Aspergillus species showed that most SM pathways were species-specific, that the number of SM gene orthologs was significantly lower than that of orthologs in primary metabolism, and that the few conserved SM orthologs typically belonged to non-homologous SM pathways. RNA sequencing of two master transcriptional regulators of SM and development, veA and mtfA, showed that the effects of deletion of each gene, especially veA, on SM pathway regulation were similar in A. fumigatus and A. nidulans, even though the underlying genes and pathways regulated in each species differed. In contrast, examination of the role of these two regulators in development, where 94% of the underlying genes are conserved in both species showed that whereas the role of veA is conserved, mtfA regulates development in the homothallic A. nidulans but not in the heterothallic A. fumigatus. Thus, the regulation of these highly conserved developmental genes is divergent, whereas–despite minimal conservation of target genes and pathways–the global regulation of SM production is largely conserved. We suggest that the evolution of the transcriptional regulation of secondary metabolism in Aspergillus represents a novel type of regulatory circuit rewiring and hypothesize that it has been largely driven by the dramatic turnover of the target genes involved in the process. PMID:25786130

Enlightening Butterfly Conservation Efforts: The Importance of Natural Lighting for Butterfly Behavioral Ecology and Conservation

PubMed Central

2018-01-01

Light is arguably the most important abiotic factor for living organisms. Organisms evolved under specific lighting conditions and their behavior, physiology, and ecology are inexorably linked to light. Understanding light effects on biology could not be more important as present anthropogenic effects are greatly changing the light environments in which animals exist. The two biggest anthropogenic contributors changing light environments are: (1) anthropogenic lighting at night (i.e., light pollution); and (2) deforestation and the built environment. I highlight light importance for butterfly behavior, physiology, and ecology and stress the importance of including light as a conservation factor for conserving butterfly biodiversity. This review focuses on four parts: (1) Introducing the nature and extent of light. (2) Visual and non-visual light reception in butterflies. (3) Implications of unnatural lighting for butterflies across several different behavioral and ecological contexts. (4). Future directions for quantifying the threat of unnatural lighting on butterflies and simple approaches to mitigate unnatural light impacts on butterflies. I urge future research to include light as a factor and end with the hopeful thought that controlling many unnatural light conditions is simply done by flipping a switch. PMID:29439549

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.

Host switch during evolution of a genetically distinct hantavirus in the American shrew mole (Neurotrichus gibbsii)

PubMed Central

Kang, Hae Ji; Bennett, Shannon N.; Dizney, Laurie; Sumibcay, Laarni; Arai, Satoru; Ruedas, Luis A.; Song, Jin-Won; Yanagihara, Richard

2009-01-01

A genetically distinct hantavirus, designated Oxbow virus (OXBV), was detected in tissues of an American shrew mole (Neurotrichus gibbsii), captured in Gresham, Oregon, in September 2003. Pairwise analysis of full-length S- and M- and partial L-segment nucleotide and amino acid sequences of OXBV indicated low sequence similarity with rodent-borne hantaviruses. Phylogenetic analyses using maximum-likelihood and Bayesian methods, and host-parasite evolutionary comparisons, showed that OXBV and Asama virus, a hantavirus recently identified from the Japanese shrew mole (Urotrichus talpoides), were related to soricine shrew-borne hantaviruses from North America and Eurasia, respectively, suggesting parallel evolution associated with cross-species transmission. PMID:19394994

Eco-evolutionary feedbacks drive species interactions

PubMed Central

Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

2014-01-01

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

Evolving nutritional strategies in the presence of competition: a geometric agent-based model.

PubMed

Senior, Alistair M; Charleston, Michael A; Lihoreau, Mathieu; Buhl, Jerome; Raubenheimer, David; Simpson, Stephen J

2015-03-01

Access to nutrients is a key factor governing development, reproduction and ultimately fitness. Within social groups, contest-competition can fundamentally affect nutrient access, potentially leading to reproductive asymmetry among individuals. Previously, agent-based models have been combined with the Geometric Framework of nutrition to provide insight into how nutrition and social interactions affect one another. Here, we expand this modelling approach by incorporating evolutionary algorithms to explore how contest-competition over nutrient acquisition might affect the evolution of animal nutritional strategies. Specifically, we model tolerance of nutrient excesses and deficits when ingesting nutritionally imbalanced foods, which we term 'nutritional latitude'; a higher degree of nutritional latitude constitutes a higher tolerance of nutritional excess and deficit. Our results indicate that a transition between two alternative strategies occurs at moderate to high levels of competition. When competition is low, individuals display a low level of nutritional latitude and regularly switch foods in search of an optimum. When food is scarce and contest-competition is intense, high nutritional latitude appears optimal, and individuals continue to consume an imbalanced food for longer periods before attempting to switch to an alternative. However, the relative balance of nutrients within available foods also strongly influences at what levels of competition, if any, transitions between these two strategies occur. Our models imply that competition combined with reproductive skew in social groups can play a role in the evolution of diet breadth. We discuss how the integration of agent-based, nutritional and evolutionary modelling may be applied in future studies to further understand the evolution of nutritional strategies across social and ecological contexts.

Electric-Field-Driven Dual Vacancies Evolution in Ultrathin Nanosheets Realizing Reversible Semiconductor to Half-Metal Transition.

PubMed

Lyu, Mengjie; Liu, Youwen; Zhi, Yuduo; Xiao, Chong; Gu, Bingchuan; Hua, Xuemin; Fan, Shaojuan; Lin, Yue; Bai, Wei; Tong, Wei; Zou, Youming; Pan, Bicai; Ye, Bangjiao; Xie, Yi

2015-12-02

Fabricating a flexible room-temperature ferromagnetic resistive-switching random access memory (RRAM) device is of fundamental importance to integrate nonvolatile memory and spintronics both in theory and practice for modern information technology and has the potential to bring about revolutionary new foldable information-storage devices. Here, we show that a relatively low operating voltage (+1.4 V/-1.5 V, the corresponding electric field is around 20,000 V/cm) drives the dual vacancies evolution in ultrathin SnO2 nanosheets at room temperature, which causes the reversible transition between semiconductor and half-metal, accompanyied by an abrupt conductivity change up to 10(3) times, exhibiting room-temperature ferromagnetism in two resistance states. Positron annihilation spectroscopy and electron spin resonance results show that the Sn/O dual vacancies in the ultrathin SnO2 nanosheets evolve to isolated Sn vacancy under electric field, accounting for the switching behavior of SnO2 ultrathin nanosheets; on the other hand, the different defect types correspond to different conduction natures, realizing the transition between semiconductor and half-metal. Our result represents a crucial step to create new a information-storage device realizing the reversible transition between semiconductor and half-metal with flexibility and room-temperature ferromagnetism at low energy consumption. The as-obtained half-metal in the low-resistance state broadens the application of the device in spintronics and the semiconductor to half-metal transition on the basis of defects evolution and also opens up a new avenue for exploring random access memory mechanisms and finding new half-metals for spintronics.

We know in part: James McCosh on evolution and Christian faith.

PubMed

Morris, Matthew

2014-01-01

James McCosh (1811–1894), president of Princeton College from 1868 to 1888, played a significant role in the American reception of evolution in the late 1800s – he was one of the more prominent clergyman to assuage the public’s fears of evolution while incorporating evolution into a conservative Christian worldview. McCosh was a prolific writer, whose books document his intellectual journey from hostility to acceptance of evolution. Three things will stand out in this overview that have not been emphasized in detail in other works: (1) James McCosh’s perspective on evolution dramatically changed over time; (2) McCosh’s motivations for engaging in the evolution-religion debate serve to clear up confusion regarding McCosh’s final position on evolution; and (3) the theological and philosophical basis for McCosh’s acceptance of evolution was established while McCosh was still hostile to evolution. His theological background therefore ‘pre-adapted’ him for evolution, and he was able to preach theology and evolution without substantially altering his theology.

Conservation and divergence of plant LHP1 protein sequences and expression patterns in angiosperms and gymnosperms.

PubMed

Guan, Hexin; Zheng, Zhengui; Grey, Paris H; Li, Yuhua; Oppenheimer, David G

2011-05-01

Floral transition is a critical and strictly regulated developmental process in plants. Mutations in Arabidopsis LIKE HETEROCHROMATIN PROTEIN 1 (AtLHP1)/TERMINAL FLOWER 2 (TFL2) result in early and terminal flowers. Little is known about the gene expression, function and evolution of plant LHP1 homologs, except for Arabidopsis LHP1. In this study, the conservation and divergence of plant LHP1 protein sequences was analyzed by sequence alignments and phylogeny. LHP1 expression patterns were compared among taxa that occupy pivotal phylogenetic positions. Several relatively conserved new motifs/regions were identified among LHP1 homologs. Phylogeny of plant LHP1 proteins agreed with established angiosperm relationships. In situ hybridization unveiled conserved expression of plant LHP1 in the axillary bud/tiller, vascular bundles, developing stamens, and carpels. Unlike AtLHP1, cucumber CsLHP1-2, sugarcane SoLHP1 and maize ZmLHP1, rice OsLHP1 is not expressed in the shoot apical meristem (SAM) and the OsLHP1 transcript level is consistently low in shoots. "Unequal crossover" might have contributed to the divergence in the N-terminal and hinge region lengths of LHP1 homologs. We propose an "insertion-deletion" model for soybean (Glycine max L.) GmLHP1s evolution. Plant LHP1 homologs are more conserved than previously expected, and may favor vegetative meristem identity and primordia formation. OsLHP1 may not function in rice SAM during floral induction.

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

PubMed

Dong, Zheng; Zhou, Hongyu; Tao, Peng

2018-02-01

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

PubMed Central

Mohammed, Jaaved; Flynt, Alex S.; Siepel, Adam; Lai, Eric C.

2013-01-01

The molecular evolutionary signatures of miRNAs inform our understanding of their emergence, biogenesis, and function. The known signatures of miRNA evolution have derived mostly from the analysis of deeply conserved, canonical loci. In this study, we examine the impact of age, biogenesis pathway, and genomic arrangement on the evolutionary properties of Drosophila miRNAs. Crucial to the accuracy of our results was our curation of high-quality miRNA alignments, which included nearly 150 corrections to ortholog calls and nucleotide sequences of the global 12-way Drosophilid alignments currently available. Using these data, we studied primary sequence conservation, normalized free-energy values, and types of structure-preserving substitutions. We expand upon common miRNA evolutionary patterns that reflect fundamental features of miRNAs that are under functional selection. We observe that melanogaster-subgroup-specific miRNAs, although recently emerged and rapidly evolving, nonetheless exhibit evolutionary signatures that are similar to well-conserved miRNAs and distinct from other structured noncoding RNAs and bulk conserved non-miRNA hairpins. This provides evidence that even young miRNAs may be selected for regulatory activities. More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth. These studies highlight the previously unappreciated impact of biogenesis strategy and genomic location on the evolutionary dynamics of miRNAs, and affirm that miRNAs do not evolve as a unitary class. PMID:23882112

An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

PubMed Central

Hung, Li-Yuan; Chen, Yen-Ju; Mai, Te-Lun; Chen, Chia-Ying; Yang, Min-Yu; Chiang, Tai-Wei; Wang, Yi-Da

2018-01-01

Abstract Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization. PMID:29294013

Network evolution model for supply chain with manufactures as the core.

PubMed

Fang, Haiyang; Jiang, Dali; Yang, Tinghong; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model.

Network evolution model for supply chain with manufactures as the core

PubMed Central

Jiang, Dali; Fang, Ling; Yang, Jian; Li, Wu; Zhao, Jing

2018-01-01

Building evolution model of supply chain networks could be helpful to understand its development law. However, specific characteristics and attributes of real supply chains are often neglected in existing evolution models. This work proposes a new evolution model of supply chain with manufactures as the core, based on external market demand and internal competition-cooperation. The evolution model assumes the external market environment is relatively stable, considers several factors, including specific topology of supply chain, external market demand, ecological growth and flow conservation. The simulation results suggest that the networks evolved by our model have similar structures as real supply chains. Meanwhile, the influences of external market demand and internal competition-cooperation to network evolution are analyzed. Additionally, 38 benchmark data sets are applied to validate the rationality of our evolution model, in which, nine manufacturing supply chains match the features of the networks constructed by our model. PMID:29370201

Life cycles, fitness decoupling and the evolution of multicellularity.

PubMed

Hammerschmidt, Katrin; Rose, Caroline J; Kerr, Benjamin; Rainey, Paul B

2014-11-06

Cooperation is central to the emergence of multicellular life; however, the means by which the earliest collectives (groups of cells) maintained integrity in the face of destructive cheating types is unclear. One idea posits cheats as a primitive germ line in a life cycle that facilitates collective reproduction. Here we describe an experiment in which simple cooperating lineages of bacteria were propagated under a selective regime that rewarded collective-level persistence. Collectives reproduced via life cycles that either embraced, or purged, cheating types. When embraced, the life cycle alternated between phenotypic states. Selection fostered inception of a developmental switch that underpinned the emergence of collectives whose fitness, during the course of evolution, became decoupled from the fitness of constituent cells. Such development and decoupling did not occur when groups reproduced via a cheat-purging regime. Our findings capture key events in the evolution of Darwinian individuality during the transition from single cells to multicellularity.

A novel coupled system of non-local integro-differential equations modelling Young's modulus evolution, nutrients' supply and consumption during bone fracture healing

NASA Astrophysics Data System (ADS)

Lu, Yanfei; Lekszycki, Tomasz

2016-10-01

During fracture healing, a series of complex coupled biological and mechanical phenomena occurs. They include: (i) growth and remodelling of bone, whose Young's modulus varies in space and time; (ii) nutrients' diffusion and consumption by living cells. In this paper, we newly propose to model these evolution phenomena. The considered features include: (i) a new constitutive equation for growth simulation involving the number of sensor cells; (ii) an improved equation for nutrient concentration accounting for the switch between Michaelis-Menten kinetics and linear consumption regime; (iii) a new constitutive equation for Young's modulus evolution accounting for its dependence on nutrient concentration and variable number of active cells. The effectiveness of the model and its predictive capability are qualitatively verified by numerical simulations (using COMSOL) describing the healing of bone in the presence of damaged tissue between fractured parts.

An Evolutionarily Conserved DOF-CONSTANS Module Controls Plant Photoperiodic Signaling.

PubMed

Lucas-Reina, Eva; Romero-Campero, Francisco J; Romero, José M; Valverde, Federico

2015-06-01

The response to daylength is a crucial process that evolved very early in plant evolution, entitling the early green eukaryote to predict seasonal variability and attune its physiological responses to the environment. The photoperiod responses evolved into the complex signaling pathways that govern the angiosperm floral transition today. The Chlamydomonas reinhardtii DNA-Binding with One Finger (CrDOF) gene controls transcription in a photoperiod-dependent manner, and its misexpression influences algal growth and viability. In short days, CrDOF enhances CrCO expression, a homolog of plant CONSTANS (CO), by direct binding to its promoter, while it reduces the expression of cell division genes in long days independently of CrCO. In Arabidopsis (Arabidopsis thaliana), transgenic plants overexpressing CrDOF show floral delay and reduced expression of the photoperiodic genes CO and FLOWERING LOCUS T. The conservation of the DOF-CO module during plant evolution could be an important clue to understanding diversification by the inheritance of conserved gene toolkits in key developmental programs. © 2015 American Society of Plant Biologists. All Rights Reserved.

The origin, current diversity and future conservation of the modern lion (Panthera leo)

PubMed Central

Barnett, Ross; Yamaguchi, Nobuyuki; Barnes, Ian; Cooper, Alan

2006-01-01

Understanding the phylogeographic processes affecting endangered species is crucial both to interpreting their evolutionary history and to the establishment of conservation strategies. Lions provide a key opportunity to explore such processes; however, a lack of genetic diversity and shortage of suitable samples has until now hindered such investigation. We used mitochondrial control region DNA (mtDNA) sequences to investigate the phylogeographic history of modern lions, using samples from across their entire range. We find the sub-Saharan African lions are basal among modern lions, supporting a single African origin model of modern lion evolution, equivalent to the ‘recent African origin’ model of modern human evolution. We also find the greatest variety of mtDNA haplotypes in the centre of Africa, which may be due to the distribution of physical barriers and continental-scale habitat changes caused by Pleistocene glacial oscillations. Our results suggest that the modern lion may currently consist of three geographic populations on the basis of their recent evolutionary history: North African–Asian, southern African and middle African. Future conservation strategies should take these evolutionary subdivisions into consideration. PMID:16901830

Genetics, evolution and conservation of Bromeliaceae

PubMed Central

Zanella, Camila M.; Janke, Aline; Palma-Silva, Clarisse; Kaltchuk-Santos, Eliane; Pinheiro, Felipe G.; Paggi, Gecele M.; Soares, Luis E.S.; Goetze, Márcia; Büttow, Miriam V.; Bered, Fernanda

2012-01-01

Bromeliaceae is a morphologically distinctive and ecologically diverse family originating in the New World. Three centers of diversity, 58 genera, and about 3,140 bromeliad species are currently recognized. We compiled all of the studies related to the reproductive biology, genetic diversity, and population structure of the Bromeliaceae, and discuss the evolution and conservation of this family. Bromeliads are preferentially pollinated by vertebrates and show marked variation in breeding systems, from predominant inbreeding to predominant outcrossing, as well as constancy in chromosome number (2n = 2x = 50). Autogamous or mixed mating system bromeliads have a high inbreeding coefficient (FIS), while outcrossing species show low FIS. The degree of differentiation among populations (FST)of species ranges from 0.043 to 0.961, which can be influenced by pollen and seed dispersal effects, clonal growth, gene flow rates, and connectivity among populations. The evolutionary history of the Bromeliaceae is poorly known, although some studies have indicated that the family arose in the Guayana Shield roughly 100 Mya. We believe that genetic, cytogenetic, and reproductive data will be essential for diagnosing species status and for assisting conservation programs. PMID:23412953

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower

PubMed Central

Chanderbali, André S.; Yoo, Mi-Jeong; Zahn, Laura M.; Brockington, Samuel F.; Wall, P. Kerr; Gitzendanner, Matthew A.; Albert, Victor A.; Leebens-Mack, James; Altman, Naomi S.; Ma, Hong; dePamphilis, Claude W.; Soltis, Douglas E.; Soltis, Pamela S.

2010-01-01

The origin and rapid diversification of the angiosperms (Darwin's “Abominable Mystery”) has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants. PMID:21149731

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower.

PubMed

Chanderbali, André S; Yoo, Mi-Jeong; Zahn, Laura M; Brockington, Samuel F; Wall, P Kerr; Gitzendanner, Matthew A; Albert, Victor A; Leebens-Mack, James; Altman, Naomi S; Ma, Hong; dePamphilis, Claude W; Soltis, Douglas E; Soltis, Pamela S

2010-12-28

The origin and rapid diversification of the angiosperms (Darwin's "Abominable Mystery") has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants.

Evolution in action: climate change, biodiversity dynamics and emerging infectious disease.

PubMed

Hoberg, Eric P; Brooks, Daniel R

2015-04-05

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host-parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)--phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference--provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Investigation of the nanodomain structure formation by piezoelectric force microscopy and Raman confocal microscopy in LiNbO3 and LiTaO3 crystals

NASA Astrophysics Data System (ADS)

Shur, V. Ya.; Zelenovskiy, P. S.; Nebogatikov, M. S.; Alikin, D. O.; Sarmanova, M. F.; Ievlev, A. V.; Mingaliev, E. A.; Kuznetsov, D. K.

2011-09-01

Piezoelectric force microscopy (PFM) and Raman confocal microscopy have been used for studying the nanodomain structures in congruent LiNbO3 and LiTaO3 crystals. The high-resolution nanodomain images at the surface were observed via PFM. Raman confocal microscopy has been used for the visualization of the nanodomain structures in the bulk via layer-by-layer scanning at various depths. It has been shown experimentally that the nanodomain images obtained at different depths correspond to domain images at the polar surface obtained at different moments: the deeper the nanodomain, the earlier the moment. Such a correlation was applied for the reconstruction of the evolution of the domain structures with charged domain walls. The studied domain structures were obtained in highly non-equilibrium switching conditions realized in LiNbO3 and LiTaO3 via pulse laser irradiation and the electric field poling of LiNbO3, with the surface layer modified by ion implantation. The revealed main stages of the domain structure evolution allow the authors to demonstrate that all geometrically different nanodomain structures observed in LiNbO3 and LiTaO3 appeared as a result of discrete switching.

Assessment of the costs, risks and benefits of selected integrated policy options to adapt to flood and drought in the water and agricultural sectors of the Warta River Basin

NASA Astrophysics Data System (ADS)

Sendzimir, Jan; Dubel, Anna; Linnerooth-Bayer, Joanne; Damurski, Jakub; Schroeter, Dagmar

2014-05-01

Historically large reservoirs have been the dominant strategy to counter flood and drought risk in Europe. However, a number of smaller-scale approaches have emerged as alternative strategies. To compare the cost effectiveness of reservoirs and these alternatives, we calculated the Investment & maintenance costs in terms of (euros) /m3 water stored or annual runoff reduced for five different strategies: large reservoirs (1.68 euros), large on-farm ponds (5.88 euros), small on-farm ponds (558.00 euros), shelterbelts (6.86 euros), switching to conservation tillage (-9.20 euros). The most cost effective measure for reducing runoff is switching to conservation tillage practices because this switch reduces machinery and labor costs in addition to reducing water runoff. Although shelterbelts that reduce annual runoff cannot be directly compared to ponds and reservoirs that store water, our estimates show that they likely compare favorably as a natural water retention measure, especially when taking account of their co-benefits in terms of erosion control, biodiversity and pollination. Another useful result is our demonstration of the economies of scale among reservoirs and ponds for storing water. Small ponds are two orders of magnitude more costly to construct and maintain as a flood and drought prevention measure than large reservoirs. Here, again, there are large co-benefits that should be factored into the cost-benefit equation, including especially the value of small ponds in promoting corridors for migration. This analysis shows the importance of carrying out more extensive cost-benefit estimates across on-farm and off-farm measures for tackling drought and flood risk in the context of a changing climate. While concrete recommendations for supporting water retention measures will depend on a more detailed investigation of their costs and benefits, this research highlights the potential of natural water retention measures as a complement to conventional investments in large reservoirs.

Two-dimensional solitons in conservative and parity-time-symmetric triple-core waveguides with cubic-quintic nonlinearity

NASA Astrophysics Data System (ADS)

Feijoo, David; Zezyulin, Dmitry A.; Konotop, Vladimir V.

2015-12-01

We analyze a system of three two-dimensional nonlinear Schrödinger equations coupled by linear terms and with the cubic-quintic (focusing-defocusing) nonlinearity. We consider two versions of the model: conservative and parity-time (PT ) symmetric. These models describe triple-core nonlinear optical waveguides, with balanced gain and losses in the PT -symmetric case. We obtain families of soliton solutions and discuss their stability. The latter study is performed using a linear stability analysis and checked with direct numerical simulations of the evolutional system of equations. Stable solitons are found in the conservative and PT -symmetric cases. Interactions and collisions between the conservative and PT -symmetric solitons are briefly investigated, as well.

Ionic Liquid Gating Control of Spin Reorientation Transition and Switching of Perpendicular Magnetic Anisotropy.

PubMed

Zhao, Shishun; Wang, Lei; Zhou, Ziyao; Li, Chunlei; Dong, Guohua; Zhang, Le; Peng, Bin; Min, Tai; Hu, Zhongqiang; Ma, Jing; Ren, Wei; Ye, Zuo-Guang; Chen, Wei; Yu, Pu; Nan, Ce-Wen; Liu, Ming

2018-05-29

Electric field (E-field) modulation of perpendicular magnetic anisotropy (PMA) switching, in an energy-efficient manner, is of great potential to realize magnetoelectric (ME) memories and other ME devices. Voltage control of the spin-reorientation transition (SRT) that allows the magnetic moment rotating between the out-of-plane and the in-plane direction is thereby crucial. In this work, a remarkable magnetic anisotropy field change up to 1572 Oe is achieved under a small operation voltage of 4 V through ionic liquid (IL) gating control of SRT in Au/[DEME] + [TFSI] - /Pt/(Co/Pt) 2 /Ta capacitor heterostructures at room temperature, corresponding to a large ME coefficient of 378 Oe V -1 . As revealed by both ferromagnetic resonance measurements and magnetic domain evolution observation, the magnetization can be switched stably and reversibly between the out-of-plane and in-plane directions via IL gating. The key mechanism, revealed by the first-principles calculation, is that the IL gating process influences the interfacial spin-orbital coupling as well as net Rashba magnetic field between the Co and Pt layers, resulting in the modulation of the SRT and in-plane/out-of-plane magnetization switching. This work demonstrates a unique IL-gated PMA with large ME tunability and paves a way toward IL gating spintronic/electronic devices such as voltage tunable PMA memories. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evolution: Tracing the origins of centrioles, cilia, and flagella.

PubMed

Carvalho-Santos, Zita; Azimzadeh, Juliette; Pereira-Leal, José B; Bettencourt-Dias, Mónica

2011-07-25

Centrioles/basal bodies (CBBs) are microtubule-based cylindrical organelles that nucleate the formation of centrosomes, cilia, and flagella. CBBs, cilia, and flagella are ancestral structures; they are present in all major eukaryotic groups. Despite the conservation of their core structure, there is variability in their architecture, function, and biogenesis. Recent genomic and functional studies have provided insight into the evolution of the structure and function of these organelles.

The evolution and function of protein tandem repeats in plants.

PubMed

Schaper, Elke; Anisimova, Maria

2015-04-01

Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Extensive Concerted Evolution of Rice Paralogs and the Road to Regaining Independence

PubMed Central

Wang, Xiyin; Tang, Haibao; Bowers, John E.; Feltus, Frank A.; Paterson, Andrew H.

2007-01-01

Many genes duplicated by whole-genome duplications (WGDs) are more similar to one another than expected. We investigated whether concerted evolution through conversion and crossing over, well-known to affect tandem gene clusters, also affects dispersed paralogs. Genome sequences for two Oryza subspecies reveal appreciable gene conversion in the ∼0.4 MY since their divergence, with a gradual progression toward independent evolution of older paralogs. Since divergence from subspecies indica, ∼8% of japonica paralogs produced 5–7 MYA on chromosomes 11 and 12 have been affected by gene conversion and several reciprocal exchanges of chromosomal segments, while ∼70-MY-old “paleologs” resulting from a genome duplication (GD) show much less conversion. Sequence similarity analysis in proximal gene clusters also suggests more conversion between younger paralogs. About 8% of paleologs may have been converted since rice–sorghum divergence ∼41 MYA. Domain-encoding sequences are more frequently converted than nondomain sequences, suggesting a sort of circularity—that sequences conserved by selection may be further conserved by relatively frequent conversion. The higher level of concerted evolution in the 5–7 MY-old segmental duplication may reflect the behavior of many genomes within the first few million years after duplication or polyploidization. PMID:18039882

Neutral biogeography and the evolution of climatic niches.

PubMed

Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien

2014-05-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.

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

Comparative Analysis of Gene Expression for Convergent Evolution of Camera Eye Between Octopus and Human

PubMed Central

Ogura, Atsushi; Ikeo, Kazuho; Gojobori, Takashi

2004-01-01

Although the camera eye of the octopus is very similar to that of humans, phylogenetic and embryological analyses have suggested that their camera eyes have been acquired independently. It has been known as a typical example of convergent evolution. To study the molecular basis of convergent evolution of camera eyes, we conducted a comparative analysis of gene expression in octopus and human camera eyes. We sequenced 16,432 ESTs of the octopus eye, leading to 1052 nonredundant genes that have matches in the protein database. Comparing these 1052 genes with 13,303 already-known ESTs of the human eye, 729 (69.3%) genes were commonly expressed between the human and octopus eyes. On the contrary, when we compared octopus eye ESTs with human connective tissue ESTs, the expression similarity was quite low. To trace the evolutionary changes that are potentially responsible for camera eye formation, we also compared octopus-eye ESTs with the completed genome sequences of other organisms. We found that 1019 out of the 1052 genes had already existed at the common ancestor of bilateria, and 875 genes were conserved between humans and octopuses. It suggests that a larger number of conserved genes and their similar gene expression may be responsible for the convergent evolution of the camera eye. PMID:15289475

Linkage of A-to-I RNA Editing in Metazoans and the Impact on Genome Evolution

PubMed Central

Duan, Yuange; Dou, Shengqian; Zhang, Hong; Wu, Changcheng; Wu, Mingming

2018-01-01

Abstract The adenosine-to-inosine (A-to-I) RNA editomes have been systematically characterized in various metazoan species, and many editing sites were found in clusters. However, it remains unclear whether the clustered editing sites tend to be linked in the same RNA molecules or not. By adopting a method originally designed to detect linkage disequilibrium of DNA mutations, we examined the editomes of ten metazoan species and detected extensive linkage of editing in Drosophila and cephalopods. The prevalent linkages of editing in these two clades, many of which are conserved between closely related species and might be associated with the adaptive proteomic recoding, are maintained by natural selection at the cost of genome evolution. Nevertheless, in worms and humans, we only detected modest proportions of linked editing events, the majority of which were not conserved. Furthermore, the linkage of editing in coding regions of worms and humans might be overall deleterious, which drives the evolution of DNA sites to escape promiscuous editing. Altogether, our results suggest that the linkage landscape of A-to-I editing has evolved during metazoan evolution. This present study also suggests that linkage of editing should be considered in elucidating the functional consequences of RNA editing. PMID:29048557

Neutral biogeography and the evolution of climatic niches

PubMed Central

Boucher, Florian C.; Thuiller, Wilfried; Davies, T. Jonathan; Lavergne, Sébastien

2014-01-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than adaptive scenarios. We develop a model inspired by Neutral Biodiversity Theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sample the climatic niches of species according to their geographic position and show that even when species evolved independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism, but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191

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.