Live concerts reduce cancer inpatients' anxiety.

PubMed

Toccafondi, A; Bonacchi, A; Mambrini, A; Miccinesi, G; Prosseda, R; Cantore, M

2017-11-01

In Italy a new experience of music medicine called "The Music Givers" is spreading among Oncology Units; it aims to organise weekly live concerts (length 45-60 min) followed by a buffet. Purpose of the present study is to evaluate the effect of the format of The Music Givers on cancer in-patients' anxiety. State-Trait Anxiety Inventory (STAI-Y) was administered to 111 in-patients before and after the concerts. After the concerts we observed a 3.87 point decrease in state anxiety (p < .001) and statistically significant differences in most of the domains assessed by STAI-Y. These results invite a reflection on the importance of offering to inpatients events such as live music concerts, in order to improve their psychological condition during hospitalisation. © 2016 John Wiley & Sons Ltd.

Transcriptomic evidence for the evolution of shoot meristem function in sporophyte-dominant land plants through concerted selection of ancestral gametophytic and sporophytic genetic programs.

PubMed

Frank, Margaret H; Scanlon, Michael J

2015-02-01

Alternation of generations, in which the haploid and diploid stages of the life cycle are each represented by multicellular forms that differ in their morphology, is a defining feature of the land plants (embryophytes). Anciently derived lineages of embryophytes grow predominately in the haploid gametophytic generation from apical cells that give rise to the photosynthetic body of the plant. More recently evolved plant lineages have multicellular shoot apical meristems (SAMs), and photosynthetic shoot development is restricted to the sporophyte generation. The molecular genetic basis for this evolutionary shift from gametophyte-dominant to sporophyte-dominant life cycles remains a major question in the study of land plant evolution. We used laser microdissection and next generation RNA sequencing to address whether angiosperm meristem patterning genes expressed in the sporophytic SAM of Zea mays are expressed in the gametophytic apical cells, or in the determinate sporophytes, of the model bryophytes Marchantia polymorpha and Physcomitrella patens. A wealth of upregulated genes involved in stem cell maintenance and organogenesis are identified in the maize SAM and in both the gametophytic apical cell and sporophyte of moss, but not in Marchantia. Significantly, meiosis-specific genetic programs are expressed in bryophyte sporophytes, long before the onset of sporogenesis. Our data suggest that this upregulated accumulation of meiotic gene transcripts suppresses indeterminate cell fate in the Physcomitrella sporophyte, and overrides the observed accumulation of meristem patterning genes. A model for the evolution of indeterminate growth in the sporophytic generation through the concerted selection of ancestral meristem gene programs from gametophyte-dominant lineages is proposed. © The Author 2014. 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.

Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.

PubMed

Ibstedt, Sebastian; Stenberg, Simon; Bagés, Sara; Gjuvsland, Arne B; Salinas, Francisco; Kourtchenko, Olga; Samy, Jeevan K A; Blomberg, Anders; Omholt, Stig W; Liti, Gianni; Beltran, Gemma; Warringer, Jonas

2015-01-01

Exposing natural selection driving phenotypic and genotypic adaptive differentiation is an extraordinary challenge. Given that an organism's life stages are exposed to the same environmental variations, we reasoned that fitness components, such as the lag, rate, and efficiency of growth, directly reflecting performance in these life stages, should often be selected in concert. We therefore conjectured that correlations between fitness components over natural isolates, in a particular environmental context, would constitute a robust signal of recent selection. Critically, this test for selection requires fitness components to be determined by different genetic loci. To explore our conjecture, we exhaustively evaluated the lag, rate, and efficiency of asexual population growth of natural isolates of the model yeast Saccharomyces cerevisiae in a large variety of nitrogen-limited environments. Overall, fitness components were well correlated under nitrogen restriction. Yeast isolates were further crossed in all pairwise combinations and coinheritance of each fitness component and genetic markers were traced. Trait variations tended to map to quantitative trait loci (QTL) that were private to a single fitness component. We further traced QTLs down to single-nucleotide resolution and uncovered loss-of-function mutations in RIM15, PUT4, DAL1, and DAL4 as the genetic basis for nitrogen source use variations. Effects of SNPs were unique for a single fitness component, strongly arguing against pleiotropy between lag, rate, and efficiency of reproduction under nitrogen restriction. The strong correlations between life stage performances that cannot be explained by pleiotropy compellingly support adaptive differentiation of yeast nitrogen source use and suggest a generic approach for detecting selection. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e

Concert hall acoustics

NASA Astrophysics Data System (ADS)

Schroeder, Manfred

2004-05-01

I will review some work at Bell Laboratories on artificial reverberation and concert hall acoustics including Philharmonic Hall (Lincoln Center for the Performing Arts, New York). I will also touch on sound diffusion by number-theoretic surfaces and the measurement of reverberation time using the music as played in the hall as a ``test'' signal.

Drug use patterns at major rock concert events.

PubMed

Erickson, T B; Aks, S E; Koenigsberg, M; Bunney, E B; Schurgin, B; Levy, P

1996-07-01

To describe alcohol and drug use patterns in patients presenting to first aid stations at major rock concerts. We retrospectively reviewed all charts generated at the first aid stations of five major rock concerts featuring the rock groups Pink Floyd, the Grateful Dead, and the Rolling Stones. The first aid stations, located at a sports stadium, were staffed by paramedics, emergency medicine nurses, and physicians. We recorded the following data: patient demographics, history of drug or ethanol use, time spent by patient in first aid station, treatment rendered, diagnosis, and patient disposition. A total of 253, 286 spectators attended the five concert events. The rate of use of the first aid station was 1.2 per 1,000 patrons. The average age of the patrons was 26.3 +/- 7.9 years (range, 3 to 56 years). The most common diagnoses were minor trauma 130 (42%) and ethanol or illicit drug intoxication 98 (32%). Of the patients treated, 147 (48%) admitted to using illicit drugs or ethanol while attending the concerts. The median time spent in the first aid station was 15 +/- 22.5 minutes (range, 5 to 150 minutes). One hundred patients (32.5%) were treated and released, 98 (32%) were transported to emergency departments, and 110 (35.5%) signed out against medical advice. Minor trauma and the use of illicit drugs and ethanol were common in spectators presenting to first aid stations at these concert events. Physicians and paramedical personnel working at rock concerts should be aware of the current drug use patterns and should be trained in treating such drug use.

Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences.

PubMed

Chen, Sunlu; Zheng, Huizhen; Kishima, Yuji

2017-06-01

The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.

Prehospital severity scoring at major rock concert events.

PubMed

Erickson, T B; Koenigsberg, M; Bunney, E B; Schurgin, B; Levy, P; Willens, J; Tanner, L

1997-01-01

Rock and contemporary music concerts are popular, recurrent events requiring on-site medical staffing. To describe a novel severity score used to stratify the level of acuity of patients presenting to first-aid stations at these events. Retrospective review of charts generated at the first-aid stations of five major rock concerts within a 60,000 spectator capacity, outdoor, professional sports stadium. Participants included all concert patrons presenting to the stadium's first-aid stations as patients. Data were collected on patient demographics, history of drug or ethanol usage while at the concert event, first-aid station time, treatment rendered, diagnosis, and disposition. All patients evaluated were retrospectively assigned a "DRUG-ROCK" Injury Severity Score (DRISS) to stratify their level of acuity. Individual concert events and patient dispositions were compared statistically using chi-square, Fisher's exact, and the ANOVA Mean tests. Approximately 250,000 spectators attended the five concert events. First-aid stations evaluated 308 patients (utilization rate of 1.2 per 1,000 patrons). The most common diagnosis was minor trauma (130; 42%), followed in frequency by ethanol/illicit drug intoxication (98; 32%). The average time in the first-aid station was 23.5 +/- 22.5 minutes (+/- standard deviation; range: 5-150 minutes). Disposition of patients included 100 (32.5%) who were treated and released; 98 (32%) were transported by paramedics to emergency departments (EDs); and 110 (35.5%) signed-out against medical advise (AMA), refusing transport. The mean DRISS was 4.1 (+/- 2.65). Two-thirds (67%) of the study population were ranked as mild by DRISS criteria (score = 1-4), with 27% rated as moderate (score = 5-9), and 6% severe (score > 10). The average of severity scores was highest (6.5) for patients transported to hospitals, and statistically different from the scores of the average of the treated and released and AMA groups (p < 0.005). The DRISS was useful

Cosmos in Concert: Combining astronomy and classical music

NASA Astrophysics Data System (ADS)

Kremer, Kyle

2018-01-01

Cosmos in Concert is an outreach initiative designed to combine astronomy education with classical music. Over the past several years, this program has presented large-scale multimedia shows for symphony orchestras, educational programs at K-12 schools, and research-oriented university collaborations designed to develop techniques for the sonification of data. Cosmos in Concert has collaborated with institutions including Fermi National Lab, the Adler Planetarium, the Bienen School of Music, and the Colburn School of Music. In this talk, I will give a brief overview of some of the main Cosmos in Concert initiatives and discuss ways these initiatives may be implemented at other institutions.

Mini-Concerts: Creating Space for Student-Initiated Performance

ERIC Educational Resources Information Center

Gifford, Cody; Johnson, Erik

2015-01-01

Mini-concerts are regularly occurring, low-stakes curricular events in the classroom where students perform music of their choice for their peers. An idea generated by music educators in domestic and international K-12 schools who strive to meet the needs of diverse student populations, mini-concerts have helped generate student excitement and…

Substance use patterns and in-hospital care of adolescents and young adults attending music concerts.

PubMed

Ruest, Stephanie M; Stephan, Alexander M; Masiakos, Peter T; Biddinger, Paul D; Camargo, Carlos A; Kharasch, Sigmund

2018-01-09

Few studies describe medical complaints and substance use patterns related to attending music concerts. As such, the objective of this study is to describe patient demographics, substance use and intoxication patterns, and medical interventions provided to adolescents and young adults assessed in an emergency department (ED) for complaints directly related to concert attendance. A retrospective chart review of patients 13-30 years old who were transported to the ED directly from music concerts between January 2011 and December 2015 was conducted. Descriptive statistics and logistic regression were used to analyze patient demographic, intervention, and substance use data. There were 115 concerts identified, of which 48 (42%) were linked to 142 relevant ED visits; the total number of attendees at each concert is unknown. The mean age of the 142 described patients was 19.5 years (SD 3.3) with 72% < 21 and 33% < 18; 71% of patients were female and 96% of visits were substance-use related. Mean blood alcohol level was 242 mg/dL (range 104-412, SD 70). Glasgow Coma Scale (GCS) scores ranged from 3 to 15, with a mean of 14. Two patients required intubation and 61% of patients received interventions, including medications (47%), intravenous fluids (46%), specialty consultation (20%), restraints (14%), imaging (6%), and laceration repair (3%). Attendance at pop and electronic dance music concerts was associated with the widest ranges of GCS scores (8-15 and 6-14 respectively), mass casualty incident declarations, and among the highest mean blood alcohol levels (246 and 244 mg/dL, respectively). Substance use is the predominant reason for music concert related ED visits and patients may have serious levels of intoxication, receiving multiple medical interventions. These data demonstrate the need for additional large-scale studies to confirm trends and increase awareness of this important public health problem.

Concerted evolution of the tandem array encoding primate U2 snRNA occurs in situ, without changing the cytological context of the RNU2 locus.

PubMed Central

Pavelitz, T; Rusché, L; Matera, A G; Scharf, J M; Weiner, A M

1995-01-01

In primates, the tandemly repeated genes encoding U2 small nuclear RNA evolve concertedly, i.e. the sequence of the U2 repeat unit is essentially homogeneous within each species but differs somewhat between species. Using chromosome painting and the NGFR gene as an outside marker, we show that the U2 tandem array (RNU2) has remained at the same chromosomal locus (equivalent to human 17q21) through multiple speciation events over > 35 million years leading to the Old World monkey and hominoid lineages. The data suggest that the U2 tandem repeat, once established in the primate lineage, contained sequence elements favoring perpetuation and concerted evolution of the array in situ, despite a pericentric inversion in chimpanzee, a reciprocal translocation in gorilla and a paracentric inversion in orang utan. Comparison of the 11 kb U2 repeat unit found in baboon and other Old World monkeys with the 6 kb U2 repeat unit in humans and other hominids revealed that an ancestral U2 repeat unit was expanded by insertion of a 5 kb retrovirus bearing 1 kb long terminal repeats (LTRs). Subsequent excision of the provirus by homologous recombination between the LTRs generated a 6 kb U2 repeat unit containing a solo LTR. Remarkably, both junctions between the human U2 tandem array and flanking chromosomal DNA at 17q21 fall within the solo LTR sequence, suggesting a role for the LTR in the origin or maintenance of the primate U2 array. Images PMID:7828589

Perception of music dynamics in concert hall acoustics.

PubMed

Pätynen, Jukka; Lokki, Tapio

2016-11-01

Dynamics is one of the principal means of expressivity in Western classical music. Still, preceding research on room acoustics has mostly neglected the contribution of music dynamics to the acoustic perception. This study investigates how the different concert hall acoustics influence the perception of varying music dynamics. An anechoic orchestra signal, containing a step in music dynamics, was rendered in the measured acoustics of six concert halls at three seats in each. Spatial sound was reproduced through a loudspeaker array. By paired comparison, naive subjects selected the stimuli that they considered to change more during the music. Furthermore, the subjects described their foremost perceptual criteria for each selection. The most distinct perceptual factors differentiating the rendering of music dynamics between halls include the dynamic range, and varying width of sound and reverberance. The results confirm the hypothesis that the concert halls render the performed music dynamics differently, and with various perceptual aspects. The analysis against objective room acoustic parameters suggests that the perceived dynamic contrasts are pronounced by acoustics that provide stronger sound and more binaural incoherence by a lateral sound field. Concert halls that enhance the dynamics have been found earlier to elicit high subjective preference.

National Symphony Orchestra Concert

NASA Image and Video Library

2010-09-04

National Symphony Orchestra Conductor Emil de Cou leads the National Symphony Orchestra during the Labor Day Weekend concert on the West Lawn of the U.S. Capitol, Sunday, September 5, 2010 in Washington. NASA Administrator Charles Bolden joined the Orchestra to introduce one the program's segments, music from the film "Apollo 13". Photo Credit: (NASA/Bill Ingalls)

Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation.

PubMed

Chan, Yvonne L; Schanzenbach, David; Hickerson, Michael J

2014-09-01

Methods that integrate population-level sampling from multiple taxa into a single community-level analysis are an essential addition to the comparative phylogeographic toolkit. Detecting how species within communities have demographically tracked each other in space and time is important for understanding the effects of future climate and landscape changes and the resulting acceleration of extinctions, biological invasions, and potential surges in adaptive evolution. Here, we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage. Our method combines population genetic data sets from multiple taxa into a single analysis to estimate: 1) the proportion of a community sample that demographically expanded in a temporally clustered pulse and 2) when the pulse occurred. To validate the accuracy and utility of this new approach, we use simulation cross-validation experiments and subsequently analyze an empirical data set of 32 avian populations from Australia that are hypothesized to have expanded from smaller refugia populations in the late Pleistocene. The method can accommodate data set heterogeneity such as variability in effective population size, mutation rates, and sample sizes across species and exploits the statistical strength from the simultaneous analysis of multiple species. This hABC framework used in a multitaxa demographic context can increase our understanding of the impact of historical climate change by determining what proportion of the community responded in concert or independently and can be used with a wide variety of comparative phylogeographic data sets as biota-wide DNA barcoding data sets accumulate. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Concert halls with strong lateral reflections enhance musical dynamics.

PubMed

Pätynen, Jukka; Tervo, Sakari; Robinson, Philip W; Lokki, Tapio

2014-03-25

One of the most thrilling cultural experiences is to hear live symphony-orchestra music build up from a whispering passage to a monumental fortissimo. The impact of such a crescendo has been thought to depend only on the musicians' skill, but here we show that interactions between the concert-hall acoustics and listeners' hearing also play a major role in musical dynamics. These interactions contribute to the shoebox-type concert hall's established success, but little prior research has been devoted to dynamic expression in this three-part transmission chain as a complete system. More forceful orchestral playing disproportionately excites high frequency harmonics more than those near the note's fundamental. This effect results in not only more sound energy, but also a different tone color. The concert hall transmits this sound, and the room geometry defines from which directions acoustic reflections arrive at the listener. Binaural directional hearing emphasizes high frequencies more when sound arrives from the sides of the head rather than from the median plane. Simultaneously, these same frequencies are emphasized by higher orchestral-playing dynamics. When the room geometry provides reflections from these directions, the perceived dynamic range is enhanced. Current room-acoustic evaluation methods assume linear behavior and thus neglect this effect. The hypothesis presented here is that the auditory excitation by reflections is emphasized with an orchestra forte most in concert halls with strong lateral reflections. The enhanced dynamic range provides an explanation for the success of rectangularly shaped concert-hall geometry.

The evolution of increased competitive ability, innate competitive advantages, and novel biochemical weapons act in concert for a tropical invader.

PubMed

Qin, Rui-Min; Zheng, Yu-Long; Valiente-Banuet, Alfonso; Callaway, Ragan M; Barclay, Gregor F; Pereyra, Carlos Silva; Feng, Yu-Long

2013-02-01

There are many non-mutually exclusive mechanisms for exotic invasions but few studies have concurrently tested more than one hypothesis for the same species. Here, we tested the evolution of increased competitive ability (EICA) hypothesis in two common garden experiments in which Chromolaena odorata plants originating from native and nonnative ranges were grown in competition with natives from each range, and the novel weapons hypothesis in laboratory experiments with leachates from C. odorata. Compared with conspecifics originating from the native range, C. odorata plants from the nonnative range were stronger competitors at high nutrient concentrations in the nonnative range in China and experienced far more herbivore damage in the native range in Mexico. In both China and Mexico, C. odorata was more suppressed by species native to Mexico than by species native to China. Species native to China were much more inhibited by leaf extracts from C. odorata than species from Mexico, and this difference in allelopathic effects may provide a possible explanation for the biogeographic differences in competitive ability. Our results indicate that EICA, innate competitive advantages, and novel biochemical weapons may act in concert to promote invasion by C. odorata, and emphasize the importance of exploring multiple, non-mutually exclusive mechanisms for invasions. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

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

PubMed Central

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

2014-01-01

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

Teaching Bioinformatics in Concert

PubMed Central

Goodman, Anya L.; Dekhtyar, Alex

2014-01-01

Can biology students without programming skills solve problems that require computational solutions? They can if they learn to cooperate effectively with computer science students. The goal of the in-concert teaching approach is to introduce biology students to computational thinking by engaging them in collaborative projects structured around the software development process. Our approach emphasizes development of interdisciplinary communication and collaboration skills for both life science and computer science students. PMID:25411792

Concerted orientation induced unidirectional water transport through nanochannels.

PubMed

Wan, Rongzheng; Lu, Hangjun; Li, Jinyuan; Bao, Jingdong; Hu, Jun; Fang, Haiping

2009-11-14

The dynamics of water inside nanochannels is of great importance for biological activities as well as for the design of molecular sensors, devices, and machines, particularly for sea water desalination. When confined in specially sized nanochannels, water molecules form a single-file structure with concerted dipole orientations, which collectively flip between the directions along and against the nanotube axis. In this paper, by using molecular dynamics simulations, we observed a net flux along the dipole-orientation without any application of an external electric field or external pressure difference during the time period of the particular concerted dipole orientations of the molecules along or against the nanotube axis. We found that this unique special-directional water transportation resulted from the asymmetric potential of water-water interaction along the nanochannel, which originated from the concerted dipole orientation of the water molecules that breaks the symmetry of water orientation distribution along the channel within a finite time period. This finding suggests a new mechanism for achieving high-flux water transportation, which may be useful for nanotechnology and biological applications.

Item Feature Effects in Evolution Assessment

ERIC Educational Resources Information Center

Nehm, Ross H.; Ha, Minsu

2011-01-01

Despite concerted efforts by science educators to understand patterns of evolutionary reasoning in science students and teachers, the vast majority of evolution education studies have failed to carefully consider or control for item feature effects in knowledge measurement. Our study explores whether robust contextualization patterns emerge within…

Reaction mechanism of guanidinoacetate methyltransferase, concerted or step-wise.

PubMed

Zhang, Xiaodong; Bruice, Thomas C

2006-10-31

We describe a quantum mechanics/molecular mechanics investigation of the guanidinoacetate methyltransferase catalyzed reaction, which shows that proton transfer from guanidinoacetate (GAA) to Asp-134 and methyl transfer from S-adenosyl-L-methionine (AdoMet) to GAA are concerted. By self-consistent-charge density functional tight binding/molecular mechanics, the bond lengths in the concerted mechanism's transition state are 1.26 A for both the OD1 (Asp-134)-H(E) (GAA) and H(E) (GAA)-N(E) (GAA) bonds, and 2.47 and 2.03 A for the S8 (AdoMet)-C9 (AdoMet) and C9 (AdoMet)-N(E) (GAA) bonds, respectively. The potential-energy barrier (DeltaE++) determined by single-point B3LYP/6-31+G*//MM is 18.9 kcal/mol. The contributions of the entropy (-TDeltaS++) and zero-point energy corrections Delta(ZPE)++ by normal mode analysis are 2.3 kcal/mol and -1.7 kcal/mol, respectively. Thus, the activation enthalpy of this concerted mechanism is predicted to be DeltaH++ = DeltaE++ plus Delta(ZPE)++ = 17.2 kcal/mol. The calculated free-energy barrier for the concerted mechanism is DeltaG++ = 19.5 kcal/mol, which is in excellent agreement with the value of 19.0 kcal/mol calculated from the experimental rate constant (3.8 +/- 0.2.min(-1)).

Reaction mechanism of guanidinoacetate methyltransferase, concerted or step-wise

PubMed Central

Zhang, Xiaodong; Bruice, Thomas C.

2006-01-01

We describe a quantum mechanics/molecular mechanics investigation of the guanidinoacetate methyltransferase catalyzed reaction, which shows that proton transfer from guanidinoacetate (GAA) to Asp-134 and methyl transfer from S-adenosyl-l-methionine (AdoMet) to GAA are concerted. By self-consistent-charge density functional tight binding/molecular mechanics, the bond lengths in the concerted mechanism's transition state are 1.26 Å for both the OD1 (Asp-134)–HE (GAA) and HE (GAA)–NE (GAA) bonds, and 2.47 and 2.03 Å for the S8 (AdoMet)–C9 (AdoMet) and C9 (AdoMet)–NE (GAA) bonds, respectively. The potential-energy barrier (ΔE‡) determined by single-point B3LYP/6–31+G*//MM is 18.9 kcal/mol. The contributions of the entropy (−TΔS‡) and zero-point energy corrections Δ(ZPE)‡ by normal mode analysis are 2.3 kcal/mol and −1.7 kcal/mol, respectively. Thus, the activation enthalpy of this concerted mechanism is predicted to be ΔH‡ = ΔE‡ + Δ(ZPE)‡ = 17.2 kcal/mol. The calculated free-energy barrier for the concerted mechanism is ΔG‡ = 19.5 kcal/mol, which is in excellent agreement with the value of 19.0 kcal/mol calculated from the experimental rate constant (3.8 ± 0.2·min−1). PMID:17053070

Evolution of Protein Domain Repeats in Metazoa

PubMed Central

Schüler, Andreas; Bornberg-Bauer, Erich

2016-01-01

Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a significant fraction of noteworthy volatile outliers with very high indel rates. Analysis of structural data indicates that repeats with an open structure and independently folding units are more volatile and more likely to be intrinsically disordered. Such disordered repeats are also significantly enriched in sites with a high functional potential such as linear motifs. Furthermore, the most volatile repeats have a high sequence similarity between their units. Since many volatile repeats also show signs of recombination, we conclude they are often shaped by concerted evolution. Intriguingly, many of these conserved yet volatile repeats are involved in host-pathogen interactions where they might foster fast but subtle adaptation in biological arms races. Key Words: protein evolution, domain rearrangements, protein repeats, concerted evolution. PMID:27671125

Interrupting the Symphony: Unpacking the Importance Placed on Classical Concert Experiences

ERIC Educational Resources Information Center

Hess, Juliet

2018-01-01

The Toronto Symphony Orchestra presents a series of youth concerts each year to introduce and attract younger audiences to the symphony. Music teachers often attend these concerts with students, and the importance of such experiences is frequently emphasised and normalised. This article explores the historical roots of the following relations,…

Is High Primordial Deuterium Consistent with Galactic Evolution?

NASA Astrophysics Data System (ADS)

Tosi, Monica; Steigman, Gary; Matteucci, Francesca; Chiappini, Cristina

1998-05-01

Galactic destruction of primordial deuterium is inevitably linked through star formation to the chemical evolution of the Galaxy. The relatively high present gas content and low metallicity suggest only modest D destruction. In concert with deuterium abundances derived from solar system and/or interstellar observations, this suggests a primordial deuterium abundance in possible conflict with data from some high-redshift, low-metallicity QSO absorbers. We have explored a variety of chemical evolution models including infall of processed material and early, supernovae-driven winds with the aim of identifying models with large D destruction that are consistent with the observations of stellar-produced heavy elements. When such models are confronted with data, we reconfirm that only modest destruction of deuterium (less than a factor of 3) is permitted. When combined with solar system and interstellar data, these results favor the low deuterium abundances derived for the QSO absorbers by Tytler et al.

A molecular phylogeny of rose chafers (Coleoptera: Scarabaeidae: Cetoniinae) reveals a complex and concerted morphological evolution related to their flight mode.

PubMed

Šípek, Petr; Fabrizi, Silvia; Eberle, Jonas; Ahrens, Dirk

2016-08-01

Rose chafers (Cetoniinae) are a large group of flower visitors within the pleurostict Scarabaeidae that are characterized by their distinctive flight mode with nearly closed forewings. Despite their popularity, this is the first study to use molecular data to infer their phylogenetic relationships. We used partial gene sequences for 28S rRNA, cytochrome oxidase I (cox1) and 16S rRNA (rrnL) for 299 species, representing most recognized subfamilies of Scarabaeidae, including 125 species of Cetoniinae. Combined analyses using maximum parsimony, maximum likelihood and Bayesian inferences recovered Cetoniinae as monophyletic in all analyses, with the sister clade composed of Rutelinae and Dynastinae. Rutelinae was always recovered as paraphyletic with respect to Dynastinae. Trichiini sensu lato (s.l.) was recovered as a polyphyletic clade, while Cetoniini s.l. was recovered as paraphyletic. The inferred topologies were also supported by site bootstrapping of the ML trees. With the exception of Cremastochelini, most tribes of Cetoniinae were poly- or paraphyletic, indicating the critical need for a careful revision of rose chafer classification. Analysis of elytral base structure (including 11 scored characters) in the context of phylogeny, revealed a complex, concerted and rapid transformation of the single trait elements linked to a modified flight mode with closed elytra. This appears to be unlinked to the lateral sinuation of the elytra, which originated independently several times at later stages in the evolution of the group. Copyright © 2016 Elsevier Inc. All rights reserved.

Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes.

PubMed

Nikolaidis, Nikolas; Nei, Masatoshi

2004-03-01

We have identified the Hsp70 gene superfamily of the nematode Caenorhabditis briggsae and investigated the evolution of these genes in comparison with Hsp70 genes from C. elegans, Drosophila, and yeast. The Hsp70 genes are classified into three monophyletic groups according to their subcellular localization, namely, cytoplasm (CYT), endoplasmic reticulum (ER), and mitochondria (MT). The Hsp110 genes can be classified into the polyphyletic CYT group and the monophyletic ER group. The different Hsp70 and Hsp110 groups appeared to evolve following the model of divergent evolution. This model can also explain the evolution of the ER and MT genes. On the other hand, the CYT genes are divided into heat-inducible and constitutively expressed genes. The constitutively expressed genes have evolved more or less following the birth-and-death process, and the rates of gene birth and gene death are different between the two nematode species. By contrast, some heat-inducible genes show an intraspecies phylogenetic clustering. This suggests that they are subject to sequence homogenization resulting from gene conversion-like events. In addition, the heat-inducible genes show high levels of sequence conservation in both intra-species and inter-species comparisons, and in most cases, amino acid sequence similarity is higher than nucleotide sequence similarity. This indicates that purifying selection also plays an important role in maintaining high sequence similarity among paralogous Hsp70 genes. Therefore, we suggest that the CYT heat-inducible genes have been subjected to a combination of purifying selection, birth-and-death process, and gene conversion-like events.

Operational modal analysis applied to the concert harp

NASA Astrophysics Data System (ADS)

Chomette, B.; Le Carrou, J.-L.

2015-05-01

Operational modal analysis (OMA) methods are useful to extract modal parameters of operating systems. These methods seem to be particularly interesting to investigate the modal basis of string instruments during operation to avoid certain disadvantages due to conventional methods. However, the excitation in the case of string instruments is not optimal for OMA due to the presence of damped harmonic components and low noise in the disturbance signal. Therefore, the present study investigates the least-square complex exponential (LSCE) and the modified least-square complex exponential methods in the case of a string instrument to identify modal parameters of the instrument when it is played. The efficiency of the approach is experimentally demonstrated on a concert harp excited by some of its strings and the two methods are compared to a conventional modal analysis. The results show that OMA allows us to identify modes particularly present in the instrument's response with a good estimation especially if they are close to the excitation frequency with the modified LSCE method.

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution.

PubMed

Mendizabal, Isabel; Shi, Lei; Keller, Thomas E; Konopka, Genevieve; Preuss, Todd M; Hsieh, Tzung-Fu; Hu, Enzhi; Zhang, Zhe; Su, Bing; Yi, Soojin V

2016-11-01

How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further examining 38 human-specific DMRs using targeted deep genomic and bisulfite sequencing in an independent panel of 37 individuals from five primate species. Our unbiased genome-scan identified human brain differentially methylated regions (DMRs), irrespective of their associations with annotated genes. Remarkably, over half of the newly identified DMRs locate in intergenic regions or gene bodies. Nevertheless, their regulatory potential is on par with those of promoter DMRs. An intriguing observation is that DMRs are enriched in active chromatin loops, suggesting human-specific evolutionary remodeling at a higher-order chromatin structure. These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The concerted trimerization of ethyne to benzene revisited

NASA Astrophysics Data System (ADS)

Cioslowski, Jerzy; Liu, Guanghua; Moncrieff, David

2000-01-01

CCSD(T)/6-311G ∗∗//QCISD/6-311G ∗∗ calculations on the concerted [2+2+2] trimerization of ethyne to benzene yield Δ Htrimo (HCCH)=-140.2 kcal/mol and Δ Hacto(HCCH)=53.1 kcal/mol. The corresponding transition state (TS) possesses C 2 symmetry, although both the planar D 3h and nonplanar D 3 structures are negligibly higher in energy, indicating extreme flatness of the potential energy hypersurface along the distortion paths. The analogous trimerizations of HCCCl and ClCCCl are predicted to be considerably more exothermic. As the respective TSs cannot be located and the planar pseudo-TSs that possess several imaginary vibrational frequencies are associated with high reaction barriers, the concerted mechanism can be ruled out for these reactions.

Science 101: How Do Acoustics Dictate the Design of a Concert Hall?

ERIC Educational Resources Information Center

Robertson, Bill

2015-01-01

This column provides background science information for elementary teachers. When the author was young he used to think that the ideal design for a concert hall would contain walls that were composed of sound-absorbing material, like foam or egg cartons or such. He noticed, though, that this was not the case. Most concert halls contain curtains…

Synergistic Synthetic Biology: Units in Concert

PubMed Central

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

Synergistic Synthetic Biology: Units in Concert.

PubMed

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

"Iitaohkanao'pi--The Meeting Place Project": An Alternative Approach to Young People's Concerts

ERIC Educational Resources Information Center

Wasiak, Edwin B.

2005-01-01

This study explored alternative approaches to young people's concerts aimed at extending musical appreciations and cultural understandings while promoting interest in concert attendance among upper elementary students. The project, an artistic and cross-cultural collaboration grounded in a spirit of mutual respect, consisted of three components:…

[Public music concerts in a psychiatric hospital: effects on public opinion and as therapy for patients].

PubMed

Takasaka, Y; Yokota, O; Tanioka, T; Nagata, K; Yasuoka, K; Toda, H

2001-01-01

We investigate the effects of music therapy concerts, which were held 60 times over a four year period, 1992 to 1996, in Geiyo Psychiatric Hospital, Kochi Prefecture and found that; 1) Musicians who performed at the concerts were not only from Kochi prefecture but also from other prefectures (10 times) and from four foreign countries (7 times). 2) Live concerts in a small hall had a positive influence on patients and drew the patient's attention and interest away from their hallucinations and delusions to the real world. Moreover, the concerts provided the patients with chances to acquire social graces such as being well-groomed. 3) Explanations by the musicians, interviews with the musicians and the seasonal choruses accompanied by the musicians were helpful to give the patients motives for recovering communication skills and to interact with society. 4) Inquiries to the patients about the concerts indicated discrepancies between the poor observed estimations during the concerts (83.3%) and the good subjective impressions expressed by the patients (82.0%), suggesting that the patients were not good at expressing their internal emotions through facial expressions or attitudes. 5) Many citizens including children came to the concerts and/or gave aid to the hospital because the concerts were open to the public and we suggest that this contributed to improving the general publics' image of psychiatric hospitals. Questionnaires revealed that 90% of people in a control group had a bad image of psychiatric hospitals in Japan, but only 32% of the members of the general public who attended our concerts had a bad image of psychiatric hospitals. In addition, the revolving ratio of the hospital beds rose from 0.4 to 1.2 over the four years, which also suggests a beneficial effect on the patients.

Concert halls with strong and lateral sound increase the emotional impact of orchestra music.

PubMed

Pätynen, Jukka; Lokki, Tapio

2016-03-01

An audience's auditory experience during a thrilling and emotive live symphony concert is an intertwined combination of the music and the acoustic response of the concert hall. Music in itself is known to elicit emotional pleasure, and at best, listening to music may evoke concrete psychophysiological responses. Certain concert halls have gained a reputation for superior acoustics, but despite the continuous research by a multitude of objective and subjective studies on room acoustics, the fundamental reason for the appreciation of some concert halls remains elusive. This study demonstrates that room acoustic effects contribute to the overall emotional experience of a musical performance. In two listening tests, the subjects listen to identical orchestra performances rendered in the acoustics of several concert halls. The emotional excitation during listening is measured in the first experiment, and in the second test, the subjects assess the experienced subjective impact by paired comparisons. The results showed that the sound of some traditional rectangular halls provides greater psychophysiological responses and subjective impact. These findings provide a quintessential explanation for these halls' success and reveal the overall significance of room acoustics for emotional experience in music performance.

Energy, time, and channel evolution in catastrophically disturbed fluvial systems

USGS Publications Warehouse

Simon, A.

1992-01-01

Specific energy is shown to decrease nonlinearly with time during channel evolution and provides a measure of reductions in available energy at the channel bed. Data from two sites show convergence towards a minimum specific energy with time. Time-dependent reductions in specific energy at a point act in concert with minimization of the rate of energy dissipation over a reach during channel evolution as the fluvial systems adjust to a new equilibrium.

The 2003 Music in Our School's Month and World's Largest Concert Teacher's Guide.

ERIC Educational Resources Information Center

Music Educators National Conference, Reston, VA.

On March 13, 2003 millions of school children, teachers, and citizens from around the world participate simultaneously in the "World's Largest Concert" (WLC). This concert, a sing-along program, is broadcast on PBS and the Armed Forces Radio and Television Network overseas. Participating in the WLC is a way to celebrate Music in Our…

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

PubMed Central

Mendizabal, Isabel; Shi, Lei; Keller, Thomas E.; Konopka, Genevieve; Preuss, Todd M.; Hsieh, Tzung-Fu; Hu, Enzhi; Zhang, Zhe; Su, Bing; Yi, Soojin V.

2016-01-01

How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further examining 38 human-specific DMRs using targeted deep genomic and bisulfite sequencing in an independent panel of 37 individuals from five primate species. Our unbiased genome-scan identified human brain differentially methylated regions (DMRs), irrespective of their associations with annotated genes. Remarkably, over half of the newly identified DMRs locate in intergenic regions or gene bodies. Nevertheless, their regulatory potential is on par with those of promoter DMRs. An intriguing observation is that DMRs are enriched in active chromatin loops, suggesting human-specific evolutionary remodeling at a higher-order chromatin structure. These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions. PMID:27563052

Exploring the impact of music concerts in promoting well-being in dementia care.

PubMed

Shibazaki, Kagari; Marshall, Nigel A

2017-05-01

This study explores the specific effects of live music concerts on the clients with dementia, their families and nursing staff/caregivers. Researchers attended 22 concerts in care facilities in England and Japan. Interviews were carried out with clients with dementia, nursing staff and family members. Observations were also carried out before, during and after the concerts. All observations were recorded in field notes. The effect of the concerts in both countries was seen to be beneficial to all clients and nursing staff, whether or not they attended the concert. Interviews with clients with mild to mid-stage dementia noted increased levels of cooperation, interaction and conversation. Those with more advanced forms of dementia exhibited decreased levels of agitation and anti-social behaviour. Staff members reported increased levels of care, cooperation and opportunities for assessment. Family members noted an increase in the levels of well-being in their partner/parent as well as in themselves. The study also suggested that the knowledge of musical components, an awareness of the rules of music and specific musical preferences appear to remain well beyond the time when other cognitive skills and abilities have disappeared. This initial study provided some further indication in terms of the uses of music as a non-pharmacological intervention for those living with all stages of dementia. These included opportunities for assessment of physical abilities as well as facilitating an increasing level of care.

The Concerted Services Approach to Developmental Change in Rural Areas: An Interim Evaluation. Center Research and Development Report No. 1.

ERIC Educational Resources Information Center

Griessman, B. Eugene, Ed.

In 1965 Concerted Services in Training and Education (CSTE) began operation in three selected rural counties of New Mexico, Arkansas, and Minnesota with objectives of: (1) developing general operational patterns for alleviation and solution of occupational education problems, (2) identifying employment opportunities and occupational education…

Risks to hearing from a rock concert.

PubMed Central

Yassi, A.; Pollock, N.; Tran, N.; Cheang, M.

1993-01-01

We measured noise exposure and temporary threshold shift (TTS) from a rock concert for 22 volunteers, using dosimetry, questionnaires, and audiometry. Most (81%) participants showed TTS of 10 dB or more 5 to 25 minutes after exposure; of these, 76% showed continued TTS at 40 to 60 minutes. Family physicians should counsel patients about the risks of recreational noise. PMID:8499785

Identifying and exploiting genes that potentiate the evolution of antibiotic resistance.

PubMed

Gifford, Danna R; Furió, Victoria; Papkou, Andrei; Vogwill, Tom; Oliver, Antonio; MacLean, R Craig

2018-06-01

There is an urgent need to develop novel approaches for predicting and preventing the evolution of antibiotic resistance. Here, we show that the ability to evolve de novo resistance to a clinically important β-lactam antibiotic, ceftazidime, varies drastically across the genus Pseudomonas. This variation arises because strains possessing the ampR global transcriptional regulator evolve resistance at a high rate. This does not arise because of mutations in ampR. Instead, this regulator potentiates evolution by allowing mutations in conserved peptidoglycan biosynthesis genes to induce high levels of β-lactamase expression. Crucially, blocking this evolutionary pathway by co-administering ceftazidime with the β-lactamase inhibitor avibactam can be used to eliminate pathogenic P. aeruginosa populations before they can evolve resistance. In summary, our study shows that identifying potentiator genes that act as evolutionary catalysts can be used to both predict and prevent the evolution of antibiotic resistance.

Brain evolution and development: adaptation, allometry and constraint

PubMed Central

Barton, Robert A.

2016-01-01

Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns. PMID:27629025

Diels–Alder Reactions of Allene with Benzene and Butadiene: Concerted, Stepwise, and Ambimodal Transition States

PubMed Central

2015-01-01

Multiconfigurational complete active space methods (CASSCF and CASPT2) have been used to investigate the (4 + 2) cycloadditions of allene with butadiene and with benzene. Both concerted and stepwise radical pathways were examined to determine the mechanism of the Diels–Alder reactions with an allene dienophile. Reaction with butadiene occurs via a single ambimodal transition state that can lead to either the concerted or stepwise trajectories along the potential energy surface, while reaction with benzene involves two separate transition states and favors the concerted mechanism relative to the stepwise mechanism via a diradical intermediate. PMID:25216056

Music Genre as a Predictor of Resource Utilization at Outdoor Music Concerts.

PubMed

Westrol, Michael S; Koneru, Susmith; McIntyre, Norah; Caruso, Andrew T; Arshad, Faizan H; Merlin, Mark A

2017-06-01

The aim of this study was to examine the various modern music genres and their effect on the utilization of medical resources with analysis and adjustment for potential confounders. A retrospective review of patient logs from an open-air, contemporary amphitheater over a period of 10 years was performed. Variables recorded by the medical personnel for each concert included the attendance, description of the weather, and a patient log in which nature and outcome were recorded. The primary outcomes were associations of genres with the medical usage rate (MUR). Secondary outcomes investigated were the association of confounders and the influences on the level of care provided, the transport rate, and the nature of medical complaint. A total of 2,399,864 concert attendees, of which 4,546 patients presented to venue Emergency Medical Services (EMS) during 403 concerts with an average of 11.4 patients (annual range 7.1-17.4) each concert. Of potential confounders, only the heat index ≥90°F (32.2°C) and whether the event was a festival were significant (P=.027 and .001, respectively). After adjustment, the genres with significantly increased MUR in decreasing order were: alternative rock, hip-hop/rap, modern rock, heavy metal/hard rock, and country music (P<.05). Medical complaints were significantly increased with alternative rock or when the heat index was ≥90°F (32.2°C; P<.001). Traumatic injuries were most significantly increased with alternative rock (P<.001). Alcohol or drug intoxication was significantly more common in hip-hop/rap (P<.001). Transport rates were highest with alcohol/drug intoxicated patients (P<.001), lowest with traumatic injuries (P=.004), and negatively affected by heat index ≥90°F (32.2°C; P=.008), alternative rock (P=.017), and country music (P=.033). Alternative rock, hip-hop/rap, modern rock, heavy metal/hard rock, and country music concerts had higher levels of medical resource utilization. High heat indices and music festivals

Parenting Priorities and Pressures: Furthering Understanding of "Concerted Cultivation"

ERIC Educational Resources Information Center

Vincent, Carol; Maxwell, Claire

2016-01-01

This paper re-examines the purposes of a planned and intentional parenting style--"concerted cultivation"--for different middle-class groups, highlighting that social class fraction, ethnicity, and also individual family disposition, guides understandings of the purposes of enrolling children in particular enrichment activities. We…

Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms.

PubMed

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

2013-09-01

The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.

Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi).

PubMed

Lloyd, Graeme T; Wang, Steve C; Brusatte, Stephen L

2012-02-01

Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as "living fossils" due to an apparent slowdown in rates since the Devonian. We find that morphological rates are highly heterogeneous across the phylogeny and recover a general pattern of decreasing rates along the phylogenetic backbone toward living taxa, from the Devonian until the present. Compared with previous work, we are able to report a more nuanced picture of lungfish evolution using these new methods. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Neutral and Non-Neutral Evolution of Duplicated Genes with Gene Conversion

PubMed Central

Fawcett, Jeffrey A.; Innan, Hideki

2011-01-01

Gene conversion is one of the major mutational mechanisms involved in the DNA sequence evolution of duplicated genes. It contributes to create unique patters of DNA polymorphism within species and divergence between species. A typical pattern is so-called concerted evolution, in which the divergence between duplicates is maintained low for a long time because of frequent exchanges of DNA fragments. In addition, gene conversion affects the DNA evolution of duplicates in various ways especially when selection operates. Here, we review theoretical models to understand the evolution of duplicates in both neutral and non-neutral cases. We also explain how these theories contribute to interpreting real polymorphism and divergence data by using some intriguing examples. PMID:24710144

Understanding the evolution of Mammalian brain structures; the need for a (new) cerebrotype approach.

PubMed

Willemet, Romain

2012-05-18

The mammalian brain varies in size by a factor of 100,000 and is composed of anatomically and functionally distinct structures. Theoretically, the manner in which brain composition can evolve is limited, ranging from highly modular ("mosaic evolution") to coordinated changes in brain structure size ("concerted evolution") or anything between these two extremes. There is a debate about the relative importance of these distinct evolutionary trends. It is shown here that the presence of taxa-specific allometric relationships between brain structures makes a taxa-specific approach obligatory. In some taxa, the evolution of the size of brain structures follows a unique, coordinated pattern, which, in addition to other characteristics at different anatomical levels, defines what has been called here a "taxon cerebrotype". In other taxa, no clear pattern is found, reflecting heterogeneity of the species' lifestyles. These results suggest that the evolution of brain size and composition depends on the complex interplay between selection pressures and constraints that have changed constantly during mammalian evolution. Therefore the variability in brain composition between species should not be considered as deviations from the normal, concerted mammalian trend, but in taxa and species-specific versions of the mammalian brain. Because it forms homogenous groups of species within this complex "space" of constraints and selection pressures, the cerebrotype approach developed here could constitute an adequate level of analysis for evo-devo studies, and by extension, for a wide range of disciplines related to brain evolution.

A Theoretical Structure of High School Concert Band Performance

ERIC Educational Resources Information Center

Bergee, Martin J.

2015-01-01

This study used exploratory (EFA) and confirmatory factor analysis (CFA) to verify a theoretical structure for high school concert band performance and to test that structure for viability, generality, and invariance. A total of 101 university students enrolled in two different bands rated two high school band performances (a "first"…

Exposure and materiality of the secondary room and its impact on the impulse response of coupled-volume concert halls

NASA Astrophysics Data System (ADS)

Ermann, Michael; Johnson, Marty

2005-06-01

How does sound decay when one room is partially exposed to another (acoustically coupled)? More specifically, this research aims to quantify how operational and design decisions impact sound fields in the design of concert halls with acoustical coupling. By adding a second room to a concert hall, and designing doors to control the sonic transparency between the two rooms, designers can create a new, coupled acoustic. Concert halls use coupling to achieve a variable, longer, and distinct reverberant quality for their musicians and listeners. For this study a coupled-volume shoebox concert hall is conceived with a fixed geometric volume, form, and primary-room sound absorption. Aperture size and secondary-room sound absorption levels are established as variables. Statistical analysis of sound decay in this simulated hall suggests a highly sensitive relationship between the double-sloped condition and (1) architectural composition, as defined by the aperture size exposing the chamber and (2) materiality, as defined by the sound absorptance in the coupled volume. The theoretical, mathematical predictions are compared with coupled-volume concert hall field measurements and guidelines are suggested for future designs of coupled-volume concert halls.

Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution.

PubMed

Francis, Andrew; Moulton, Vincent

2018-06-07

Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we reliably identify the phylogenetic network that gave rise to the observed data? Recently, identifiability results have appeared for networks relative to a model of sequence evolution that generalizes the standard Markov models used for phylogenetic trees. However, these results are quite limited in terms of the complexity of the networks that are considered. In this paper, by introducing an alternative probabilistic model for evolution along a network that is based on some ground-breaking work by Thatte for pedigrees, we are able to obtain an identifiability result for a much larger class of phylogenetic networks (essentially the class of so-called tree-child networks). To prove our main theorem, we derive some new results for identifying tree-child networks combinatorially, and then adapt some techniques developed by Thatte for pedigrees to show that our combinatorial results imply identifiability in the probabilistic setting. We hope that the introduction of our new model for networks could lead to new approaches to reliably construct phylogenetic networks. Copyright © 2018 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.

The ozone acetylene reaction: concerted or non-concerted reaction mechanism? A quantum chemical investigation

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Kraka, Elfi; Crehuet, Ramon; Anglada, Josep; Gräfenstein, Jürgen

2001-10-01

The ozone-acetylene reaction is found to proceed via an intermediate van der Waals complex (rather than a biradical), which is the precursor for a concerted symmetry-allowed [4+2] cycloaddition reaction leading to 1,2,3-trioxolene. CCSD(T)/6-311G+(2d, 2p) and CCSD(T)/CBS (complete basis set) calculations predict the ozone-acetylene van der Waals complex to be stable by 2.2 kcal mol -1, the calculated activation enthalpy for the cycloaddition reaction is 9.6 kcal mol -1 and the reaction enthalpy -55.5 kcal mol -1. Calculated kinetic data for the overall reaction ( k=0.8 l mol -1 s-1, A=1.71×10 6 l mol -1 s-1, E a=8.6 kcal mol -1) suggest that there is a need for refined kinetic measurements.

Using experimental evolution to identify druggable targets that could inhibit the evolution of antimicrobial resistance

PubMed Central

Mehta, Heer H.; Prater, Amy G.; Shamoo, Yousif

2017-01-01

With multi-drug and pan-drug resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics. A critical step in the development of such strategies lies in understanding the critical evolutionary trajectories responsible for resistance and which proteins or biochemical pathways within those trajectories would be good candidates for co-drug discovery. We identify the most important steps in the evolution of resistance for a specific pathogen and antibiotic combination by evolving highly polymorphic populations of pathogens to resistance in a novel bioreactor that favors biofilm development. As the populations evolve to increasing drug concentrations, we use deep sequencing to elucidate the network of genetic changes responsible for resistance and subsequent in vitro biochemistry and often structure determination to determine how the adaptive mutations produce resistance. Importantly, the identification of the molecular steps, their frequency within the populations and their chronology within the evolutionary trajectory toward resistance is critical to assessing their relative importance. In this work, we discuss findings from the evolution of the ESKAPE pathogen, Pseudomonas aeruginosa to the drug of last resort, colistin to illustrate the power of this approach. PMID:28928474

Duplication and concerted evolution of MiSp-encoding genes underlie the material properties of minor ampullate silks of cobweb weaving spiders.

PubMed

Vienneau-Hathaway, Jannelle M; Brassfield, Elizabeth R; Lane, Amanda Kelly; Collin, Matthew A; Correa-Garhwal, Sandra M; Clarke, Thomas H; Schwager, Evelyn E; Garb, Jessica E; Hayashi, Cheryl Y; Ayoub, Nadia A

2017-03-14

Orb-web weaving spiders and their relatives use multiple types of task-specific silks. The majority of spider silk studies have focused on the ultra-tough dragline silk synthesized in major ampullate glands, but other silk types have impressive material properties. For instance, minor ampullate silks of orb-web weaving spiders are as tough as draglines, due to their higher extensibility despite lower strength. Differences in material properties between silk types result from differences in their component proteins, particularly members of the spidroin (spider fibroin) gene family. However, the extent to which variation in material properties within a single silk type can be explained by variation in spidroin sequences is unknown. Here, we compare the minor ampullate spidroins (MiSp) of orb-weavers and cobweb weavers. Orb-web weavers use minor ampullate silk to form the auxiliary spiral of the orb-web while cobweb weavers use it to wrap prey, suggesting that selection pressures on minor ampullate spidroins (MiSp) may differ between the two groups. We report complete or nearly complete MiSp sequences from five cobweb weaving spider species and measure material properties of minor ampullate silks in a subset of these species. We also compare MiSp sequences and silk properties of our cobweb weavers to published data for orb-web weavers. We demonstrate that all our cobweb weavers possess multiple MiSp loci and that one locus is more highly expressed in at least two species. We also find that the proportion of β-spiral-forming amino acid motifs in MiSp positively correlates with minor ampullate silk extensibility across orb-web and cobweb weavers. MiSp sequences vary dramatically within and among spider species, and have likely been subject to multiple rounds of gene duplication and concerted evolution, which have contributed to the diverse material properties of minor ampullate silks. Our sequences also provide templates for recombinant silk proteins with tailored

Three-body dissociation of OCS3+: Separating sequential and concerted pathways

NASA Astrophysics Data System (ADS)

Kumar, Herendra; Bhatt, Pragya; Safvan, C. P.; Rajput, Jyoti

2018-02-01

Events from the sequential and concerted modes of the fragmentation of OCS3+ that result in coincident detection of fragments C+, O+, and S+ have been separated using a newly proposed representation. An ion beam of 1.8 MeV Xe9+ is used to make the triply charged molecular ion, with the fragments being detected by a recoil ion momentum spectrometer. By separating events belonging exclusively to the sequential mode of breakup, the electronic states of the intermediate molecular ion (CO2+ or CS2+) involved are determined, and from the kinetic energy release spectra, it is shown that the low lying excited states of the parent OCS3+ are responsible for this mechanism. An estimate of branching ratios of events coming from sequential versus concerted mode is presented.

Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

PubMed

Campo, Daniel; García-Vázquez, Eva

2012-01-01

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).

Electronic Performance Monitoring: An Organizational Justice and Concertive Control Perspective.

ERIC Educational Resources Information Center

Alder, G. Stoney; Tompkins, Phillip K.

1997-01-01

Applies theories of organizational justice/concertive control to account for contradictions inherent in electronic monitoring of workers by organizations. Argues that results are usually positive when workers are involved in the design and implementation of monitoring systems, and monitoring is restricted to performance-related activities with…

Tightening the Iron Cage: Concertive Control in Self-Managing Teams.

ERIC Educational Resources Information Center

Barker, James R.

1993-01-01

Describes how an (industrial) organization's control system evolved in response to a managerial change from hierarchical, bureaucratic control to concertive control via self-management teams. The organization's members developed a system of value-based normative rules that controlled their actions more powerfully and completely than did the former…

Concerted hydrogen atom exchange between three HF molecules

NASA Technical Reports Server (NTRS)

Komornicki, Andrew; Dixon, David A.; Taylor, Peter R.

1992-01-01

We have investigated the termolecular reaction involving concerted hydrogen exchange between three HF molecules, with particular emphasis on the effects of correlation at the various stationary points along the reaction. Using an extended basis, we have located the geometries of the stable hydrogen-bonded trimer, which is of C(sub 3h) symmetry, and the transition state for hydrogen exchange, which is of D(sub 3h) symmetry. The energies of the exchange reation were then evaluated at the correlated level, using a large atomic natural orbital basis and correlating all valence electrons. Several correlation treatments were used, namely, configration interaction with single and double excitations, coupled-pair functional, and coupled-cluster methods. We are thus able to measure the effect of accounting for size-extensivity. Zero-point corrections to the correlated level energetics were determined using analytic second derivative techniques at the SCF level. Our best calculations, which include the effects of connected triple excitations in the coupled-cluster procedure, indicate that the trimer is bound by 9 +/- 1 kcal/mol relative to three separate monomers, in excellent agreement with previous estimates. The barrier to concerted hydrogen exchange is 15 kcal/mol above the trimer, or only 4.7 kcal/mol above three separated monomers. Thus the barrier to hydrogen exchange between HF molecules via this termolecular process is very low.

Concerted Cultivation and Music Learning: Global Issues and Local Variations

ERIC Educational Resources Information Center

Ilari, Beatriz

2013-01-01

"Concerted cultivation" has been described as a common, urban middle-class practice concerning the enrollment of children in a variety of age-specific activities that may promote the learning of valuable life skills as well as the development of individual abilities (Lareau, 2003). Music is one such activity. This study investigated the…

Impact-induced concerted mass transport on W surfaces by a voidion mechanism

NASA Astrophysics Data System (ADS)

Mazilova, T. I.; Sadanov, E. V.; Voyevodin, V. N.; Ksenofontov, V. A.; Mikhailovskij, I. M.

2018-03-01

Using low-temperature field ion microscope techniques, we studied at the atomic level morphological evolution of the W surface through bombardment by a beam of several keV He atoms. This technique allows the direct observation of the results of the high energy He atom impact on the elementary damage stages. The formation of the 〈110〉 and 〈100〉 linear vacancy chains and the high relaxation of the near-neighbors of the surface vacancy clusters were revealed. Performed molecular dynamics simulations shows that a single He atom impact triggers the relaxation process of the linear vacancy chain by a substantial decrease of the distance between atoms at both sides of the chain. The observed inward relaxations in W and Mo are an order of magnitude more than that for a single vacancy. It was revealed a novel highly cooperative impact-induced mass transport mechanism on the stepped surface: the formation and motion of a surface spatially delocalized vacancies (voidions). Surface voidions are extremely mobile: the mean velocity of atoms in voidions equals to a substantial portion of the sound velocity. Successive collective translations of the 〈111〉 lines of atoms in adjacent voidions give rise to a concerted gliding motion of great atomic clusters.

Community trees: Identifying codiversification in the Páramo dipteran community.

PubMed

Carstens, Bryan C; Gruenstaeudl, Michael; Reid, Noah M

2016-05-01

Groups of codistributed species that responded in a concerted manner to environmental events are expected to share patterns of evolutionary diversification. However, the identification of such groups has largely been based on qualitative, post hoc analyses. We develop here two methods (posterior predictive simulation [PPS], Kuhner-Felsenstein [K-F] analysis of variance [ANOVA]) for the analysis of codistributed species that, given a group of species with a shared pattern of diversification, allow empiricists to identify those taxa that do not codiversify (i.e., "outlier" species). The identification of outlier species makes it possible to jointly estimate the evolutionary history of co-diversifying taxa. To evaluate the approaches presented here, we collected data from Páramo dipterans, identified outlier species, and estimated a "community tree" from species that are identified as having codiversified. Our results demonstrate that dipteran communities from different Páramo habitats in the same mountain range are more closely related than communities in other ranges. We also conduct simulation testing to evaluate this approach. Results suggest that our approach provides a useful addition to comparative phylogeographic methods, while identifying aspects of the analysis that require careful interpretation. In particular, both the PPS and K-F ANOVA perform acceptably when there are one or two outlier species, but less so as the number of outliers increases. This is likely a function of the corresponding degradation of the signal of community divergence; without a strong signal from a codiversifying community, there is no dominant pattern from which to detect an outlier species. For this reason, both the magnitude of K-F distance distribution and outside knowledge about the phylogeographic history of each putative member of the community should be considered when interpreting the results. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Epideictic Rhetoric in the Context of Ritual Behavior: Rock Concerts.

ERIC Educational Resources Information Center

Purnell, Sandra E.

This study focuses upon the rock concert as a ceremonial or epideictic rhetoric. A major function of rhetoric, Kenneth Burke suggests, is to achieve a symbolic transcendence of the sense of division among men. Rock music, the author contends, fulfills this Burkean definition and serves the dual function of identification and unification for the…

Family Music Concerts: Bringing Families, Music Students, and Music Together

ERIC Educational Resources Information Center

Kenney, Susan Hobson

2014-01-01

This article describes how conductors of the top performing groups and music education faculty at one university collaborated to create a Family Concert Series for parents and children of all ages, including infants in arms. Recognizing the conflict between "The first three years of life are the most important for educating a young child in…

The Concert system - Compiler and runtime technology for efficient concurrent object-oriented programming

NASA Technical Reports Server (NTRS)

Chien, Andrew A.; Karamcheti, Vijay; Plevyak, John; Sahrawat, Deepak

1993-01-01

Concurrent object-oriented languages, particularly fine-grained approaches, reduce the difficulty of large scale concurrent programming by providing modularity through encapsulation while exposing large degrees of concurrency. Despite these programmability advantages, such languages have historically suffered from poor efficiency. This paper describes the Concert project whose goal is to develop portable, efficient implementations of fine-grained concurrent object-oriented languages. Our approach incorporates aggressive program analysis and program transformation with careful information management at every stage from the compiler to the runtime system. The paper discusses the basic elements of the Concert approach along with a description of the potential payoffs. Initial performance results and specific plans for system development are also detailed.

Reaction of Chlorosulfonyl Isocyanate (CSI) with Fluorosubstituted Alkenes: Evidence of a Concerted Pathway for Reaction of CSI with Fluorosubstituted Alkenes (Preprint)

DTIC Science & Technology

2010-06-01

ABSTRACT Concerted reactions are indicated for the electrophilic addition of chlorosulfonyl isocyanate with monofluoroalkenes. A vinyl fluorine atom on...SO2Cl R F O ‡ N SO2Cl F R O Abstract: Concerted reactions are indicated for the electrophilic addition of chlorosulfonyl isocyanate with...monofluoroalkenes. A vinyl fluorine atom on an alkene raises the energy of a step-wise transition state more than the energy of the competing concerted

Outdoor concert hall sound design: idea and possible solutions

NASA Astrophysics Data System (ADS)

Kim, Yang-Hann; Lee, Jung-Min; Kim, Wanjung; Kim, Hwan; Choi, Jung-Woo; Wang, Semyung

Sound design of outdoor concert halls needs to satisfy two contradictory objectives: good sound reproduction within the hall, as well as the minimization of external sound radiation. Outdoor concert hall usually has open space, therefore good sound for the listeners can be bad sound for its neighborhood. It would be a good attempt to have a virtual sound wall that can reflect all sound, therefore making a relatively quiet zone in the outside. This attempt can be possible if we could produce invisible but very high impedance mismatch around the hall, for a selected frequency band. This can be possible if we can generate an acoustically bright zone inside and a dark (quite) zone outside. Earlier work [Choi, J.-W. and Kim, Y.-H. (2002). J. Acoust. Soc. Am. 111, 1695-1700], at least, assures it is possible for a selected region and frequencies. Simulations show that it is possible for a two-dimensional case. Experimental verification has been also tried. The discrepancies have been explained in terms of the number of loudspeakers, their spatial distributions, spacing with regard to wavelength. The dependency of its performances with respect to the size of bright and dark zone scaled by wavelength of interest has also been explained.

Understanding the Evolution of Mammalian Brain Structures; the Need for a (New) Cerebrotype Approach

PubMed Central

Willemet, Romain

2012-01-01

The mammalian brain varies in size by a factor of 100,000 and is composed of anatomically and functionally distinct structures. Theoretically, the manner in which brain composition can evolve is limited, ranging from highly modular (“mosaic evolution”) to coordinated changes in brain structure size (“concerted evolution”) or anything between these two extremes. There is a debate about the relative importance of these distinct evolutionary trends. It is shown here that the presence of taxa-specific allometric relationships between brain structures makes a taxa-specific approach obligatory. In some taxa, the evolution of the size of brain structures follows a unique, coordinated pattern, which, in addition to other characteristics at different anatomical levels, defines what has been called here a “taxon cerebrotype”. In other taxa, no clear pattern is found, reflecting heterogeneity of the species’ lifestyles. These results suggest that the evolution of brain size and composition depends on the complex interplay between selection pressures and constraints that have changed constantly during mammalian evolution. Therefore the variability in brain composition between species should not be considered as deviations from the normal, concerted mammalian trend, but in taxa and species-specific versions of the mammalian brain. Because it forms homogenous groups of species within this complex “space” of constraints and selection pressures, the cerebrotype approach developed here could constitute an adequate level of analysis for evo-devo studies, and by extension, for a wide range of disciplines related to brain evolution. PMID:24962772

Measured Early Lateral Energy Fractions in Concert Halls and Opera Houses

NASA Astrophysics Data System (ADS)

BARRON, M.

2000-04-01

In the 30 years since early lateral reflections were first suggested as important for concert halls, spatial impression and source broadening have become almost universally accepted as essential characteristics of halls with good acoustics. Two objective measures of source broadening have been proposed. Measured values of the best defined of these measures, the early lateral energy fraction (LF), are considered here. Results from two independent measurement surveys are discussed. Comparisons of LF values by hall show a significant link between hall mean LF and hall width. There is however considerable overlap between measured LF values in different halls so the relevance of describing halls by their mean early lateral energy fraction values is questionable. The behaviour of LF values within auditoria is discussed for different concert hall plan forms and within opera houses. A measure of source broadening including sound level is proposed and results considered in the context of auditorium design.

Resolution of concerted versus sequential mechanisms in photo-induced double-proton transfer reaction in 7-azaindole H-bonded dimer

PubMed Central

Catalán, Javier; del Valle, Juan Carlos; Kasha, Michael

1999-01-01

The experimental and theoretical bases for a synchronous or concerted double-proton transfer in centro-symmetric H-bonded electronically excited molecular dimers are presented. The prototype model is the 7-azaindole dimer. New research offers confirmation of a concerted mechanism for excited-state biprotonic transfer. Recent femtosecond photoionization and coulombic explosion techniques have given rise to time-of-flight MS observations suggesting sequential two-step biprotonic transfer for the same dimer. We interpret the overall species observed in the time-of-flight experiments as explicable without conflict with the concerted mechanism of proton transfer. PMID:10411876

Multisensory integration and the concert experience: An overview of how visual stimuli can affect what we hear

NASA Astrophysics Data System (ADS)

Hyde, Jerald R.

2004-05-01

It is clear to those who ``listen'' to concert halls and evaluate their degree of acoustical success that it is quite difficult to separate the acoustical response at a given seat from the multi-modal perception of the whole event. Objective concert hall data have been collected for the purpose of finding a link with their related subjective evaluation and ultimately with the architectural correlates which produce the sound field. This exercise, while important, tends to miss the point that a concert or opera event utilizes all the senses of which the sound field and visual stimuli are both major contributors to the experience. Objective acoustical factors point to visual input as being significant in the perception of ``acoustical intimacy'' and with the perception of loudness versus distance in large halls. This paper will review the evidence of visual input as a factor in what we ``hear'' and introduce concepts of perceptual constancy, distance perception, static and dynamic visual stimuli, and the general process of the psychology of the integrated experience. A survey of acousticians on their opinions about the auditory-visual aspects of the concert hall experience will be presented. [Work supported in part from the Veneklasen Research Foundation and Veneklasen Associates.

Identifying Major Transitions in the Evolution of Lithic Cutting Edge Production Rates

PubMed Central

Clarkson, Chris

2016-01-01

The notion that the evolution of core reduction strategies involved increasing efficiency in cutting edge production is prevalent in narratives of hominin technological evolution. Yet a number of studies comparing two different knapping technologies have found no significant differences in edge production. Using digital analysis methods we present an investigation of raw material efficiency in eight core technologies broadly representative of the long-term evolution of lithic technology. These are bipolar, multiplatform, discoidal, biface, Levallois, prismatic blade, punch blade and pressure blade production. Raw material efficiency is assessed by the ratio of cutting edge length to original core mass. We also examine which flake attributes contribute to maximising raw material efficiency, as well as compare the difference between expert and intermediate knappers in terms of cutting edge produced per gram of core. We identify a gradual increase in raw material efficiency over the broad sweep of lithic technological evolution. The results indicate that the most significant transition in efficiency likely took place with the introduction of small foliate biface, Levallois and prismatic blade knapping, all introduced in the Middle Stone Age / Middle Palaeolithic among early Homo sapiens and Neanderthals. This suggests that no difference in raw material efficiency existed between these species. With prismatic blade technology securely dated to the Middle Palaeolithic, by including the more recent punch and pressure blade technology our results dispel the notion that the transition to the Upper Palaeolithic was accompanied by an increase in efficiency. However, further increases in cutting edge efficiency are evident, with pressure blades possessing the highest efficiency in this study, indicating that late/epi-Palaeolithic and Neolithic blade technologies further increased efficiency. PMID:27936135

Identifying Major Transitions in the Evolution of Lithic Cutting Edge Production Rates.

PubMed

Muller, Antoine; Clarkson, Chris

2016-01-01

The notion that the evolution of core reduction strategies involved increasing efficiency in cutting edge production is prevalent in narratives of hominin technological evolution. Yet a number of studies comparing two different knapping technologies have found no significant differences in edge production. Using digital analysis methods we present an investigation of raw material efficiency in eight core technologies broadly representative of the long-term evolution of lithic technology. These are bipolar, multiplatform, discoidal, biface, Levallois, prismatic blade, punch blade and pressure blade production. Raw material efficiency is assessed by the ratio of cutting edge length to original core mass. We also examine which flake attributes contribute to maximising raw material efficiency, as well as compare the difference between expert and intermediate knappers in terms of cutting edge produced per gram of core. We identify a gradual increase in raw material efficiency over the broad sweep of lithic technological evolution. The results indicate that the most significant transition in efficiency likely took place with the introduction of small foliate biface, Levallois and prismatic blade knapping, all introduced in the Middle Stone Age / Middle Palaeolithic among early Homo sapiens and Neanderthals. This suggests that no difference in raw material efficiency existed between these species. With prismatic blade technology securely dated to the Middle Palaeolithic, by including the more recent punch and pressure blade technology our results dispel the notion that the transition to the Upper Palaeolithic was accompanied by an increase in efficiency. However, further increases in cutting edge efficiency are evident, with pressure blades possessing the highest efficiency in this study, indicating that late/epi-Palaeolithic and Neolithic blade technologies further increased efficiency.

Not your grandfather's concert hall

NASA Astrophysics Data System (ADS)

Cooper, Russell; Malenka, Richard; Griffith, Charles; Friedlander, Steven

2004-05-01

The opening of Judy and Arthur Zankel Hall on 12 September 2003, restores Andrew Carnegie's original 1891 concept of having three outstanding auditoriums of different sizes under one roof, and creates a 21st-century venue for music performance and education. With concerts ranging from early music to avant-garde multimedia productions, from jazz to world music, and from solo recitals to chamber music, Zankel Hall expands the breadth and depth of Carnegie Hall's offerings. It allows for the integration of programming across three halls with minifestivals tailored both to the size and strengths of each hall and to the artists and music to be performed. The new flexible space also provides Carnegie Hall with an education center equipped with advanced communications technology. This paper discusses the unique program planned for this facility and how the architects, theatre consultants, and acousticians developed a design that fulfilled the client's expectations and coordinated the construction of the facility under the floor of the main Isaac Stern Auditorium without having to cancel a single performance.

Living Room vs. Concert Hall: Patterns of Music Consumption in Flanders

ERIC Educational Resources Information Center

Roose, Henk; Stichele, Alexander Vander

2010-01-01

In this article we probe the interplay between public and private music consumption using a large-scale survey of the Flemish population in Belgium. We analyze whether public and private music consumption have different correlates and to what extent there is convergence between the genres that people listen to at home and at concerts. Results show…

Distinct mechanisms act in concert to mediate cell cycle arrest.

PubMed

Toettcher, Jared E; Loewer, Alexander; Ostheimer, Gerard J; Yaffe, Michael B; Tidor, Bruce; Lahav, Galit

2009-01-20

In response to DNA damage, cells arrest at specific stages in the cell cycle. This arrest must fulfill at least 3 requirements: it must be activated promptly; it must be sustained as long as damage is present to prevent loss of genomic information; and after the arrest, cells must re-enter into the appropriate cell cycle phase to ensure proper ploidy. Multiple molecular mechanisms capable of arresting the cell cycle have been identified in mammalian cells; however, it is unknown whether each mechanism meets all 3 requirements or whether they act together to confer specific functions to the arrest. To address this question, we integrated mathematical models describing the cell cycle and the DNA damage signaling networks and tested the contributions of each mechanism to cell cycle arrest and re-entry. Predictions from this model were then tested with quantitative experiments to identify the combined action of arrest mechanisms in irradiated cells. We find that different arrest mechanisms serve indispensable roles in the proper cellular response to DNA damage over time: p53-independent cyclin inactivation confers immediate arrest, whereas p53-dependent cyclin downregulation allows this arrest to be sustained. Additionally, p21-mediated inhibition of cyclin-dependent kinase activity is indispensable for preventing improper cell cycle re-entry and endoreduplication. This work shows that in a complex signaling network, seemingly redundant mechanisms, acting in a concerted fashion, can achieve a specific cellular outcome.

Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called "species signal".

PubMed

Musser, Jacob M; Wagner, Günter P

2015-11-01

We elaborate a framework for investigating the evolutionary history of morphological characters. We argue that morphological character trees generated by phylogenetic analysis of transcriptomes provide a useful tool for identifying causal gene expression differences underlying the development and evolution of morphological characters. They also enable rigorous testing of different models of morphological character evolution and origination, including the hypothesis that characters originate via divergence of repeated ancestral characters. Finally, morphological character trees provide evidence that character transcriptomes undergo concerted evolution. We argue that concerted evolution of transcriptomes can explain the so-called "species signal" found in several recent comparative transcriptome studies. The species signal is the phenomenon that transcriptomes cluster by species rather than character type, even though the characters are older than the respective species. We suggest the species signal is a natural consequence of concerted gene expression evolution resulting from mutations that alter gene regulatory network interactions shared by the characters under comparison. Thus, character trees generated from transcriptomes allow us to investigate the variational independence, or individuation, of morphological characters at the level of genetic programs. © 2015 Wiley Periodicals, Inc.

Concerted dihedral rotations give rise to internal friction in unfolded proteins.

PubMed

Echeverria, Ignacia; Makarov, Dmitrii E; Papoian, Garegin A

2014-06-18

Protein chains undergo conformational diffusion during folding and dynamics, experiencing both thermal kicks and viscous drag. Recent experiments have shown that the corresponding friction can be separated into wet friction, which is determined by the solvent viscosity, and dry friction, where frictional effects arise due to the interactions within the protein chain. Despite important advances, the molecular origins underlying dry friction in proteins have remained unclear. To address this problem, we studied the dynamics of the unfolded cold-shock protein at different solvent viscosities and denaturant concentrations. Using extensive all-atom molecular dynamics simulations we estimated the internal friction time scales and found them to agree well with the corresponding experimental measurements (Soranno et al. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 17800-17806). Analysis of the reconfiguration dynamics of the unfolded chain further revealed that hops in the dihedral space provide the dominant mechanism of internal friction. Furthermore, the increased number of concerted dihedral moves at physiological conditions suggest that, in such conditions, the concerted motions result in higher frictional forces. These findings have important implications for understanding the folding kinetics of proteins as well as the dynamics of intrinsically disordered proteins.

Concerted copy number variation balances ribosomal DNA dosage in human and mouse genomes

PubMed Central

Gibbons, John G.; Branco, Alan T.; Godinho, Susana A.; Yu, Shoukai; Lemos, Bernardo

2015-01-01

Tandemly repeated ribosomal DNA (rDNA) arrays are among the most evolutionary dynamic loci of eukaryotic genomes. The loci code for essential cellular components, yet exhibit extensive copy number (CN) variation within and between species. CN might be partly determined by the requirement of dosage balance between the 5S and 45S rDNA arrays. The arrays are nonhomologous, physically unlinked in mammals, and encode functionally interdependent RNA components of the ribosome. Here we show that the 5S and 45S rDNA arrays exhibit concerted CN variation (cCNV). Despite 5S and 45S rDNA elements residing on different chromosomes and lacking sequence similarity, cCNV between these loci is strong, evolutionarily conserved in humans and mice, and manifested across individual genotypes in natural populations and pedigrees. Finally, we observe that bisphenol A induces rapid and parallel modulation of 5S and 45S rDNA CN. Our observations reveal a novel mode of genome variation, indicate that natural selection contributed to the evolution and conservation of cCNV, and support the hypothesis that 5S CN is partly determined by the requirement of dosage balance with the 45S rDNA array. We suggest that human disease variation might be traced to disrupted rDNA dosage balance in the genome. PMID:25583482

Evolution of genes and repeats in the Nimrod superfamily.

PubMed

Somogyi, Kálmán; Sipos, Botond; Pénzes, Zsolt; Kurucz, Eva; Zsámboki, János; Hultmark, Dan; Andó, István

2008-11-01

The recently identified Nimrod superfamily is characterized by the presence of a special type of EGF repeat, the NIM repeat, located right after a typical CCXGY/W amino acid motif. On the basis of structural features, nimrod genes can be divided into three types. The proteins encoded by Draper-type genes have an EMI domain at the N-terminal part and only one copy of the NIM motif, followed by a variable number of EGF-like repeats. The products of Nimrod B-type and Nimrod C-type genes (including the eater gene) have different kinds of N-terminal domains, and lack EGF-like repeats but contain a variable number of NIM repeats. Draper and Nimrod C-type (but not Nimrod B-type) proteins carry a transmembrane domain. Several members of the superfamily were claimed to function as receptors in phagocytosis and/or binding of bacteria, which indicates an important role in the cellular immunity and the elimination of apoptotic cells. In this paper, the evolution of the Nimrod superfamily is studied with various methods on the level of genes and repeats. A hypothesis is presented in which the NIM repeat, along with the EMI domain, emerged by structural reorganizations at the end of an EGF-like repeat chain, suggesting a mechanism for the formation of novel types of repeats. The analyses revealed diverse evolutionary patterns in the sequences containing multiple NIM repeats. Although in the Nimrod B and Nimrod C proteins show characteristics of independent evolution, many internal NIM repeats in Eater sequences seem to have undergone concerted evolution. An analysis of the nimrod genes has been performed using phylogenetic and other methods and an evolutionary scenario of the origin and diversification of the Nimrod superfamily is proposed. Our study presents an intriguing example how the evolution of multigene families may contribute to the complexity of the innate immune response.

Density functional theory study of the concerted pyrolysis mechanism for lignin models

Treesearch

Thomas Elder; Ariana Beste

2014-01-01

ABSTRACT: Studies on the pyrolysis mechanisms of lignin model compounds have largely focused on initial homolytic cleavage reactions. It has been noted, however, that concerted mechanisms may also account for observed product formation. In the current work, the latter processes are examined and compared to the former, by the application of density functional theory...

A continued role for signaling functions in the early evolution of feathers.

PubMed

Ruxton, Graeme D; Persons Iv, W Scott; Currie, Philip J

2017-03-01

Persons and Currie (2015) argued against either flight, thermoregulation, or signaling as a functional benefit driving the earliest evolution of feathers; rather, they favored simple feathers having an initial tactile sensory function, which changed to a thermoregulatory function as density increased. Here, we explore the relative merits of early simple feathers that may have originated as tactile sensors progressing instead toward a signaling, rather than (or in addition to) a thermoregulatory function. We suggest that signaling could act in concert with a sensory function more naturally than could thermoregulation. As such, the dismissal of a possible signaling function and the presumption that an initial sensory function led directly to a thermoregulatory function (implicit in the title "bristles before down") are premature. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Rates of morphological evolution, asymmetry and morphological integration of shell shape in scallops.

PubMed

Sherratt, Emma; Serb, Jeanne M; Adams, Dean C

2017-12-08

Rates of morphological evolution vary across different taxonomic groups, and this has been proposed as one of the main drivers for the great diversity of organisms on Earth. Of the extrinsic factors pertaining to this variation, ecological hypotheses feature prominently in observed differences in phenotypic evolutionary rates across lineages. But complex organisms are inherently modular, comprising distinct body parts that can be differentially affected by external selective pressures. Thus, the evolution of trait covariation and integration in modular systems may also play a prominent role in shaping patterns of phenotypic diversity. Here we investigate the role ecological diversity plays in morphological integration, and the tempo of shell shape evolution and of directional asymmetry in bivalved scallops. Overall, the shape of both valves and the magnitude of asymmetry of the whole shell (difference in shape between valves) are traits that are evolving fast in ecomorphs under strong selective pressures (gliders, recessers and nestling), compared to low rates observed in other ecomorphs (byssal-attaching, free-living and cementing). Given that different parts of an organism can be under different selective pressures from the environment, we also examined the degree of evolutionary integration between the valves as it relates to ecological shifts. We find that evolutionary morphological integration is consistent and surprisingly high across species, indicating that while the left and right valves of a scallop shell are diversifying in accordance with ecomorphology, they are doing so in a concerted fashion. Our study on scallops adds another strong piece of evidence that ecological shifts play an important role in the tempo and mode of morphological evolution. Strong selective pressures from the environment, inferred from the repeated evolution of distinct ecomorphs, have influenced the rate of morphological evolution in valve shape and the magnitude of asymmetry

Evolution of self-reporting methods for identifying discrete emotions in science classrooms

NASA Astrophysics Data System (ADS)

Ritchie, Stephen M.; Hudson, Peter; Bellocchi, Alberto; Henderson, Senka; King, Donna; Tobin, Kenneth

2016-09-01

Emotion researchers have grappled with challenging methodological issues in capturing emotions of participants in naturalistic settings such as school or university classrooms. Self-reporting methods have been used frequently, yet these methods are inadequate when used alone. We argue that the self-reporting methods of emotion diaries and cogenerative dialogues can be helpful in identifying in-the-moment emotions when used in conjunction with the microanalysis of video recordings of classroom events. We trace the evolution of our use of innovative self-reporting methods through three cases from our research projects, and propose new directions for our ongoing development and application of these methods in both school and university classrooms.

Identifying innovation in laboratory studies of cultural evolution: rates of retention and measures of adaptation

PubMed Central

Caldwell, Christine A.; Cornish, Hannah; Kandler, Anne

2016-01-01

In recent years, laboratory studies of cultural evolution have become increasingly prevalent as a means of identifying and understanding the effects of cultural transmission on the form and functionality of transmitted material. The datasets generated by these studies may provide insights into the conditions encouraging, or inhibiting, high rates of innovation, as well as the effect that this has on measures of adaptive cultural change. Here we review recent experimental studies of cultural evolution with a view to elucidating the role of innovation in generating observed trends. We first consider how tasks are presented to participants, and how the corresponding conceptualization of task success is likely to influence the degree of intent underlying any deviations from perfect reproduction. We then consider the measures of interest used by the researchers to track the changes that occur as a result of transmission, and how these are likely to be affected by differing rates of retention. We conclude that considering studies of cultural evolution from the perspective of innovation provides us with valuable insights that help to clarify important differences in research designs, which have implications for the likely effects of variation in retention rates on measures of cultural adaptation. PMID:26926283

Ecological constraint and the evolution of sexual dichromatism in darters.

PubMed

Bossu, Christen M; Near, Thomas J

2015-05-01

It is not known how environmental pressures and sexual selection interact to influence the evolution of extravagant male traits. Sexual and natural selection are often viewed as antagonistic forces shaping the evolution of visual signals, where conspicuousness is favored by sexual selection and crypsis is favored by natural selection. Although typically investigated independently, the interaction between natural and sexual selection remains poorly understood. Here, we investigate whether sexual dichromatism evolves stochastically, independent from, or in concert with habitat use in darters, a species-rich lineage of North American freshwater fish. We find the evolution of sexual dichromatism is coupled to habitat use in darter species. Comparative analyses reveal that mid-water darter lineages exhibit a narrow distribution of dichromatism trait space surrounding a low optimum, suggesting a constraint imposed on the evolution of dichromatism, potentially through predator-mediated selection. Alternatively, the transition to benthic habitats coincides with greater variability in the levels of dichromatism that surround a higher optimum, likely due to relaxation of the predator-mediated selection and heterogeneous microhabitat dependent selection regimes. These results suggest a complex interaction of sexual selection with potentially two mechanisms of natural selection, predation and sensory drive, that influence the evolution of diverse male nuptial coloration in darters. © 2015 The Author(s).

Ethanol dehydration in HZSM-5 studied by density functional theory: evidence for a concerted process.

PubMed

Kim, Seonah; Robichaud, David J; Beckham, Gregg T; Paton, Robert S; Nimlos, Mark R

2015-04-16

Dehydration over acidic zeolites is an important reaction class for the upgrading of biomass pyrolysis vapors to hydrocarbon fuels or to precursors for myriad chemical products. Here, we examine the dehydration of ethanol at a Brønsted acid site, T12, found in HZSM-5 using density functional theory (DFT). The geometries of both cluster and mixed quantum mechanics/molecular mechanics (QM:MM) models are prepared from the ZSM-5 crystal structure. Comparisons between these models and different DFT methods are conducted to show similar results among the models and methods used. Inclusion of the full catalyst cavity through a QM:MM approach is found to be important, since activation barriers are computed on average as 7 kcal mol(-1) lower than those obtained with a smaller cluster model. Two different pathways, concerted and stepwise, have been considered when examining dehydration and deprotonation steps. The current study shows that a concerted dehydration process is possible with a lower (4-5 kcal mol(-1)) activation barrier while previous literature studies have focused on a stepwise mechanism. Overall, this work demonstrates that fairly high activation energies (∼50 kcal mol(-1)) are required for ethanol dehydration. A concerted mechanism is favored over a stepwise mechanism because charge separation in the transition state is minimized. QM:MM approaches appear to provide superior results to cluster calculations due to a more accurate representation of charges on framework oxygen atoms.

Correlated evolution of body and fin morphology in the cichlid fishes.

PubMed

Feilich, Kara L

2016-10-01

Body and fin shapes are chief determinants of swimming performance in fishes. Different configurations of body and fin shapes can suit different locomotor specializations. The success of any configuration is dependent upon the hydrodynamic interactions between body and fins. Despite the importance of body-fin interactions for swimming, there are few data indicating whether body and fin configurations evolve in concert, or whether these structures vary independently. The cichlid fishes are a diverse family whose well-studied phylogenetic relationships make them ideal for the study of macroevolution of ecomorphology. This study measured body, and caudal and median fin morphology from radiographs of 131 cichlid genera, using morphometrics and phylogenetic comparative methods to determine whether these traits exhibit correlated evolution. Partial least squares canonical analysis revealed that body, caudal fin, dorsal fin, and anal fin shapes all exhibited strong correlated evolution consistent with locomotor ecomorphology. Major patterns included the evolution of deep body profiles with long fins, suggestive of maneuvering specialization; and the evolution of narrow, elongate caudal peduncles with concave tails, a combination that characterizes economical cruisers. These results demonstrate that body shape evolution does not occur independently of other traits, but among a suite of other morphological changes that augment locomotor specialization. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies.

PubMed

Daane, Jacob M; Rohner, Nicolas; Konstantinidis, Peter; Djuranovic, Sergej; Harris, Matthew P

2016-01-01

The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus. As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes. © The Author 2015. 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.

Catalysis of concerted reactions by antibodies: the Claisen rearrangement.

PubMed Central

Hilvert, D; Carpenter, S H; Nared, K D; Auditor, M T

1988-01-01

Monoclonal antibodies were prepared against a transition state analog inhibitor of chorismate mutase (EC 5.4.99.5). One of the antibodies catalyzes the rearrangement of chorismate to prephenate with rate accelerations of more than 2 orders of magnitude compared to the uncatalyzed reaction. Saturation kinetics were observed, and at 25 degrees C the values of kcat and Km were 1.2 X 10(-3) s-1 and 5.1 X 10(-5) M respectively. The transition state analog was shown to be a competitive inhibitor of the reaction with Ki equal to 0.6 microM. These results demonstrate the feasibility of using rationally designed immunogens to generate antibodies that catalyze concerted reactions. PMID:3393525

Subjective ranking of concert halls substantiated through orthogonal objective parameters.

PubMed

Cerdá, Salvador; Giménez, Alicia; Cibrián, Rosa; Girón, Sara; Zamarreño, Teófilo

2015-02-01

This paper studies the global subjective assessment, obtained from mean values of the results of surveys addressed to members of the audience of live concerts in Spanish auditoriums, through the mean values of the three orthogonal objective parameters (Tmid, IACCE3, and LEV), expressed in just noticeable differences (JNDs), regarding the best-valued hall. Results show that a linear combination of the relative variations of orthogonal parameters can largely explain the overall perceived quality of the sample. However, the mean values of certain orthogonal parameters are not representative, which shows that an alternative approach to the problem is necessary. Various possibilities are proposed.

Pilot study: Exposure and materiality of the secondary room and its impact in the impulse response of coupled-volume concert halls

NASA Astrophysics Data System (ADS)

Ermann, Michael; Johnson, Marty E.

2002-05-01

What does one room sound like when it is partially exposed to another (acoustically coupled)? More specifically, this research aims to quantify how operational and design decisions impact aural impressions in the design of concert halls with acoustical coupling. By adding a second room to a concert hall, and designing doors to control the sonic transparency between the two rooms, designers can create a new, coupled acoustic. Concert halls use coupling to achieve a variable, longer, and distinct reverberant quality for their musicians and listeners. For this study, a coupled-volume shoebox concert hall was conceived with a fixed geometric volume, form, and primary-room sound absorption. Aperture size and secondary-room sound-absorption levels were established as variables. Statistical analysis of sound decay in this simulated hall suggests a highly sensitive relationship between the double-sloped condition and (1) Architectural composition, as defined by the aperture size exposing the chamber and (2) Materiality, as defined by the sound absorbance in the coupled volume. Preliminary calculations indicate that the double-sloped sound decay condition only appears when the total aperture area is less than 1.5% of the total shoebox surface area and the average absorption coefficient of the coupled volume is less than 0.07.

Inactivation gating of Kv7.1 channels does not involve concerted cooperative subunit interactions.

PubMed

Meisel, Eshcar; Tobelaim, William; Dvir, Meidan; Haitin, Yoni; Peretz, Asher; Attali, Bernard

2018-01-01

Inactivation is an intrinsic property of numerous voltage-gated K + (Kv) channels and can occur by N-type or/and C-type mechanisms. N-type inactivation is a fast, voltage independent process, coupled to activation, with each inactivation particle of a tetrameric channel acting independently. In N-type inactivation, a single inactivation particle is necessary and sufficient to occlude the pore. C-type inactivation is a slower process, involving the outermost region of the pore and is mediated by a concerted, highly cooperative interaction between all four subunits. Inactivation of Kv7.1 channels does not exhibit the hallmarks of N- and C-type inactivation. Inactivation of WT Kv7.1 channels can be revealed by hooked tail currents that reflects the recovery from a fast and voltage-independent inactivation process. However, several Kv7.1 mutants such as the pore mutant L273F generate an additional voltage-dependent slow inactivation. The subunit interactions during this slow inactivation gating remain unexplored. The goal of the present study was to study the nature of subunit interactions along Kv7.1 inactivation gating, using concatenated tetrameric Kv7.1 channel and introducing sequentially into each of the four subunits the slow inactivating pore mutation L273F. Incorporating an incremental number of inactivating mutant subunits did not affect the inactivation kinetics but slowed down the recovery kinetics from inactivation. Results indicate that Kv7.1 inactivation gating is not compatible with a concerted cooperative process. Instead, adding an inactivating subunit L273F into the Kv7.1 tetramer incrementally stabilizes the inactivated state, which suggests that like for activation gating, Kv7.1 slow inactivation gating is not a concerted process.

Evolution of thorax architecture in ant castes highlights trade-off between flight and ground behaviors

PubMed Central

Keller, Roberto A; Peeters, Christian; Beldade, Patrícia

2014-01-01

The concerted evolution of morphological and behavioral specializations has compelling examples in ant castes. Unique to ants is a marked divergence between winged queens and wingless workers, but morphological specializations for behaviors on the ground have been overlooked. We analyzed thorax morphology of queens and workers in species from 21 of the 25 ant subfamilies. We uncovered unique skeletomuscular modifications in workers that presumably increase power and flexibility of head–thorax articulation, emphasizing that workers are not simply wingless versions of queens. We also identified two distinct types of queens and showed repeated evolutionary associations with strategies of colony foundation. Solitary founding queens that hunt have a more worker-like thorax. Our results reveal that ants invest in the relative size of thorax segments according to their tasks. Versatility of head movements allows for better manipulation of food and objects, which arguably contributed to the ants’ ecological and evolutionary success. DOI: http://dx.doi.org/10.7554/eLife.01539.001 PMID:24399458

Evolution of thorax architecture in ant castes highlights trade-off between flight and ground behaviors.

PubMed

Keller, Roberto A; Peeters, Christian; Beldade, Patrícia

2014-01-01

The concerted evolution of morphological and behavioral specializations has compelling examples in ant castes. Unique to ants is a marked divergence between winged queens and wingless workers, but morphological specializations for behaviors on the ground have been overlooked. We analyzed thorax morphology of queens and workers in species from 21 of the 25 ant subfamilies. We uncovered unique skeletomuscular modifications in workers that presumably increase power and flexibility of head-thorax articulation, emphasizing that workers are not simply wingless versions of queens. We also identified two distinct types of queens and showed repeated evolutionary associations with strategies of colony foundation. Solitary founding queens that hunt have a more worker-like thorax. Our results reveal that ants invest in the relative size of thorax segments according to their tasks. Versatility of head movements allows for better manipulation of food and objects, which arguably contributed to the ants' ecological and evolutionary success. DOI: http://dx.doi.org/10.7554/eLife.01539.001.

Managing Risk in Producing Concerts and Other Major Campus Events: A Guide for Student Programmers.

ERIC Educational Resources Information Center

German, Carol J.

1999-01-01

Offers suggestions for campus-activities programmers on how to minimize liability for problems with concerts and other student-planned campus events. Discussion covers prevention of monetary loss, breach of contract issues, and preventing personal injuries and property damage. Specific preventive actions and policies are discussed. (MSE)

Evolution and development of fetal membranes and placentation in amniote vertebrates.

PubMed

Ferner, Kirsten; Mess, Andrea

2011-08-31

We review aspects of fetal membrane evolution and patterns of placentation within amniotes, the most successful land vertebrates. Special reference is given to embryonic gas supply. The evolution of fetal membranes is a prerequisite for reproduction independent from aquatic environments. Starting from a basically similar repertoire of fetal membranes - the amnion, chorion, allantois and yolk sac, which form the cleidoic egg - different structural solutions for embryonic development have evolved. In oviparous amniotes the chorioallantoic membrane is the major site for the exchange of respiratory gases between fetus and outer environment. The richly vascularised yolk sac and allantois in concert with the chorion play an important role in the evolution of placentation in various viviparous amniotes. Highly complex placentas have evolved independently among squamate sauropsids and in marsupial and placental mammals. In conclusion, there seems to be a natural force to improve gas exchange processes in intrauterine environments by reducing the barrier between the blood systems and optimising the exchange areas. Copyright © 2011 Elsevier B.V. All rights reserved.

Concert hall acoustics: Repertoire, listening position, and individual taste of the listeners influence the qualitative attributes and preferences.

PubMed

Lokki, Tapio; Pätynen, Jukka; Kuusinen, Antti; Tervo, Sakari

2016-07-01

Some studies of concert hall acoustics consider the acoustics in a hall as a single entity. Here, it is shown that the acoustics vary between different seats, and the choice of music also influences the perceived acoustics. The presented study compared the acoustics of six unoccupied concert halls with extensive listening tests, applying two different music excerpts on three different seats. Twenty eight assessors rated the halls according to the subjective preference of the assesors and individual attributes with a paired comparison method. Results show that assessors can be classified into two preference groups, which prioritize different perceptual factors. In addition, the individual attributes elicited by assessors were clustered into three latent classes.

Unequal Academic Achievement in High School: The Mediating Roles of Concerted Cultivation and Close Friends

ERIC Educational Resources Information Center

Carolan, Brian V.

2016-01-01

Building from the classic Wisconsin model of status attainment, this study examines whether a specific style of parenting, concerted cultivation, and a close friend's school-related attitudes and behaviors mediate the relationship between a family's socioeconomic status and their child's academic achievement in the United States. Using a recursive…

Concerted control of Escherichia coli cell division

PubMed Central

Osella, Matteo; Nugent, Eileen; Cosentino Lagomarsino, Marco

2014-01-01

The coordination of cell growth and division is a long-standing problem in biology. Focusing on Escherichia coli in steady growth, we quantify cell division control using a stochastic model, by inferring the division rate as a function of the observable parameters from large empirical datasets of dividing cells. We find that (i) cells have mechanisms to control their size, (ii) size control is effected by changes in the doubling time, rather than in the single-cell elongation rate, (iii) the division rate increases steeply with cell size for small cells, and saturates for larger cells. Importantly, (iv) the current size is not the only variable controlling cell division, but the time spent in the cell cycle appears to play a role, and (v) common tests of cell size control may fail when such concerted control is in place. Our analysis illustrates the mechanisms of cell division control in E. coli. The phenomenological framework presented is sufficiently general to be widely applicable and opens the way for rigorous tests of molecular cell-cycle models. PMID:24550446

Concerted formation of macromolecular Suppressor–mutator transposition complexes

PubMed Central

Raina, Ramesh; Schläppi, Michael; Karunanandaa, Balasulojini; Elhofy, Adam; Fedoroff, Nina

1998-01-01

Transposition of the maize Suppressor–mutator (Spm) transposon requires two element-encoded proteins, TnpA and TnpD. Although there are multiple TnpA binding sites near each element end, binding of TnpA to DNA is not cooperative, and the binding affinity is not markedly affected by the number of binding sites per DNA fragment. However, intermolecular complexes form cooperatively between DNA fragments with three or more TnpA binding sites. TnpD, itself not a sequence-specific DNA-binding protein, binds to TnpA and stabilizes the TnpA–DNA complex. The high redundancy of TnpA binding sites at both element ends and the protein–protein interactions between DNA-bound TnpA complexes and between these and TnpD imply a concerted transition of the element from a linear to a protein crosslinked transposition complex within a very narrow protein concentration range. PMID:9671711

Crisis behavior: An exploration of theories in concert.

PubMed

McConnell, Jason B; Crudo, Christine

2015-01-01

How might prominent existing communication theory better explain behavior in a crisis context, when considered in concert with one another? This theoretical work highlights the insight to be gained using Situational Crisis Communication Theory and Bandura's notions of self-efficacy to heighten the explanatory power of the Theory of Planned Behavior as applied to communication during times of crisis. Situational Crisis Communication Theory better explains how past experience with crisis influences the attitudes and social norms of crisis behavior, while Bandura's notion of self-efficacy speaks more directly to the availability of resources as contributing factors to perceived behavioral control in a crisis situation. As such, the incorporation of these well-developed notions into the broader framework of the Theory of Planned Behavior affords greater understanding of the relationship between communication and behavior during a crisis. Further exploration of this theoretical relationship is warranted.

Dust sources and atmospheric circulation in concert controlling Saharan dust emission and transport towards the Western Mediterranean Basin

NASA Astrophysics Data System (ADS)

Schepanski, Kerstin; Mallet, Marc; Heinold, Bernd; Ulrich, Max

2017-04-01

Dust transported from north African source regions towards Europe is a ubiquitous phenomenon in the Mediterranean region, a geographic region that is in part densely populated. Besides its impacts on the atmospheric radiation budget, dust suspended in the atmosphere results in reduced air quality, which is generally sensed as a reduction in quality of life. Furthermore, the exposure to dust aerosols enhances the prevalence of respiratory diseases, which reduces the general human wellbeing, and ultimately results in an increased loss of working hours due to illness and hospitalization rates. Characteristics of the atmospheric dust life cycle that determine dust transport will be presented with focus on the ChArMEx special observation period in June and July 2013 using the atmosphere-dust model COSMO-MUSCAT (COSMO: Consortium for Small-scale MOdeling; MUSCAT: MUltiScale Chemistry Aerosol Transport Model). Modes of atmospheric circulation were identified from empirical orthogonal function (EOF) analysis of the geopotential height at 850 hPa for summer 2013 and compared to EOFs calculated from 1979-2015 ERA-Interim reanalysis. Generally, two different phases were identified. They are related to the eastward propagation of the subtropical ridge into the Mediterranean basin, the position of the Saharan heat low, and the predominant Iberian heat low. The relation of these centres of action illustrates a dipole pattern for enhanced (reduced) dust emission fluxes, stronger (weaker) meridional dust transport, and consequent increase (decrease) atmospheric dust concentrations and deposition fluxes. In concert, the results from this study aim at illustrating the relevance of knowing the dust source locations in concert with the atmospheric circulation. Ultimately, this study addresses the question of what is finally transported towards the Mediterranean basin and Europe from which source regions - and fostered by which atmospheric circulation pattern. Outcomes from this study

Role of transcriptional regulation in the evolution of plant phenotype: A dynamic systems approach.

PubMed

Rodríguez-Mega, Emiliano; Piñeyro-Nelson, Alma; Gutierrez, Crisanto; García-Ponce, Berenice; Sánchez, María De La Paz; Zluhan-Martínez, Estephania; Álvarez-Buylla, Elena R; Garay-Arroyo, Adriana

2015-03-02

A growing body of evidence suggests that alterations in transcriptional regulation of genes involved in modulating development are an important part of phenotypic evolution, and this can be documented among species and within populations. While the effects of differential transcriptional regulation in organismal development have been preferentially studied in animal systems, this phenomenon has also been addressed in plants. In this review, we summarize evidence for cis-regulatory mutations, trans-regulatory changes and epigenetic modifications as molecular events underlying important phenotypic alterations, and thus shaping the evolution of plant development. We postulate that a mechanistic understanding of why such molecular alterations have a key role in development, morphology and evolution will have to rely on dynamic models of complex regulatory networks that consider the concerted action of genetic and nongenetic components, and that also incorporate the restrictions underlying the genotype to phenotype mapping process. Developmental Dynamics, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Iterative key-residues interrogation of a phytase with thermostability increasing substitutions identified in directed evolution.

PubMed

Shivange, Amol V; Roccatano, Danilo; Schwaneberg, Ulrich

2016-01-01

Bacterial phytases have attracted industrial interest as animal feed supplement due to their high activity and sufficient thermostability (required for feed pelleting). We devised an approach named KeySIDE,  an iterative Key-residues interrogation of the wild type with Substitutions Identified in Directed Evolution for improving Yersinia mollaretii phytase (Ymphytase) thermostability by combining key beneficial substitutions and elucidating their individual roles. Directed evolution yielded in a discovery of nine positions in Ymphytase and combined iteratively to identify key positions. The "best" combination (M6: T77K, Q154H, G187S, and K289Q) resulted in significantly improved thermal resistance; the residual activity improved from 35 % (wild type) to 89 % (M6) at 58 °C and 20-min incubation. Melting temperature increased by 3 °C in M6 without a loss of specific activity. Molecular dynamics simulation studies revealed reduced flexibility in the loops located next to helices (B, F, and K) which possess substitutions (Helix-B: T77K, Helix-F: G187S, and Helix-K: K289E/Q). Reduced flexibility in the loops might be caused by strengthened hydrogen bonding network (e.g., G187S and K289E/K289Q) and a salt bridge (T77K). Our results demonstrate a promising approach to design phytases in food research, and we hope that the KeySIDE might become an attractive approach for understanding of structure-function relationships of enzymes.

Repetitive sequences in plant nuclear DNA: types, distribution, evolution and function.

PubMed

Mehrotra, Shweta; Goyal, Vinod

2014-08-01

Repetitive DNA sequences are a major component of eukaryotic genomes and may account for up to 90% of the genome size. They can be divided into minisatellite, microsatellite and satellite sequences. Satellite DNA sequences are considered to be a fast-evolving component of eukaryotic genomes, comprising tandemly-arrayed, highly-repetitive and highly-conserved monomer sequences. The monomer unit of satellite DNA is 150-400 base pairs (bp) in length. Repetitive sequences may be species- or genus-specific, and may be centromeric or subtelomeric in nature. They exhibit cohesive and concerted evolution caused by molecular drive, leading to high sequence homogeneity. Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as "tuning knobs" in the evolution. Therefore, knowledge of repetitive sequences assists our understanding of the organization, evolution and behavior of eukaryotic genomes. Repetitive sequences have cytoplasmic, cellular and developmental effects and play a role in chromosomal recombination. In the post-genomics era, with the introduction of next-generation sequencing technology, it is possible to evaluate complex genomes for analyzing repetitive sequences and deciphering the yet unknown functional potential of repetitive sequences. Copyright © 2014 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Aperture size, materiality of the secondary room, and listener location: Impact on the simulated impulse response of a coupled-volume concert hall

NASA Astrophysics Data System (ADS)

Ermann, Michael; Johnson, Marty E.; Harrison, Byron W.

2002-11-01

By adding a second room to a concert hall, and designing doors to control the sonic transparency between the two rooms, designers can create a new, coupled acoustic. Concert halls use coupling to achieve a variable, longer, and distinct reverberant quality for their musicians and listeners. For this study, a coupled-volume concert hall based on an existing performing arts center is conceived and computer modeled. It has a fixed geometric volume, form, and primary-room sound absorption. Ray-tracing software simulates impulse responses, varying both aperture size and secondary-room sound-absorption level, across a grid of receiver (listener) locations. The results are compared with statistical analysis that suggests a highly sensitive relationship between the double-sloped condition and the architecture of the space. This line of study aims to quantitatively and spatially correlate the double-sloped condition with (1) aperture size exposing the chamber, (2) sound absorptance in the coupled volume, and (3) listener location.

Aperture size, materiality of the secondary room and listener location: Impact on the simulated impulse response of a coupled-volume concert hall

NASA Astrophysics Data System (ADS)

Ermann, Michael; Johnson, Marty E.; Harrison, Byron W.

2003-04-01

By adding a second room to a concert hall, and designing doors to control the sonic transparency between the two rooms, designers can create a new, coupled acoustic. Concert halls use coupling to achieve a variable, longer and distinct reverberant quality for their musicians and listeners. For this study, a coupled-volume concert hall based on an existing performing arts center is conceived and computer-modeled. It has a fixed geometric volume, form and primary-room sound absorption. Ray-tracing software simulates impulse responses, varying both aperture size and secondary-room sound absorption level, across a grid of receiver (listener) locations. The results are compared with statistical analysis that suggests a highly sensitive relationship between the double-sloped condition and the architecture of the space. This line of study aims to quantitatively and spatially correlate the double-sloped condition with (1) aperture size exposing the chamber, (2) sound absorptance in the coupled volume, and (3) listener location.

Collective Motion of Humans in Mosh and Circle Pits at Heavy Metal Concerts

NASA Astrophysics Data System (ADS)

Silverberg, Jesse L.; Bierbaum, Matthew; Sethna, James P.; Cohen, Itai

2013-05-01

Human collective behavior can vary from calm to panicked depending on social context. Using videos publicly available online, we study the highly energized collective motion of attendees at heavy metal concerts. We find these extreme social gatherings generate similarly extreme behaviors: a disordered gaslike state called a mosh pit and an ordered vortexlike state called a circle pit. Both phenomena are reproduced in flocking simulations demonstrating that human collective behavior is consistent with the predictions of simplified models.

Sound Pressure Levels Measured in a University Concert Band: A Risk of Noise-Induced Hearing Loss?

ERIC Educational Resources Information Center

Holland, Nicholas V., III

2008-01-01

Researchers have reported public school band directors as experiencing noise-induced hearing loss. Little research has focused on collegiate band directors and university student musicians. The present study measures the sound pressure levels generated within a university concert band and compares sound levels with the criteria set by the…

Identifying Cis-Regulatory Changes Involved in the Evolution of Aerobic Fermentation in Yeasts

PubMed Central

Lin, Zhenguo; Wang, Tzi-Yuan; Tsai, Bing-Shi; Wu, Fang-Ting; Yu, Fu-Jung; Tseng, Yu-Jung; Sung, Huang-Mo; Li, Wen-Hsiung

2013-01-01

Gene regulation change has long been recognized as an important mechanism for phenotypic evolution. We used the evolution of yeast aerobic fermentation as a model to explore how gene regulation has evolved and how this process has contributed to phenotypic evolution and adaptation. Most eukaryotes fully oxidize glucose to CO2 and H2O in mitochondria to maximize energy yield, whereas some yeasts, such as Saccharomyces cerevisiae and its relatives, predominantly ferment glucose into ethanol even in the presence of oxygen, a phenomenon known as aerobic fermentation. We examined the genome-wide gene expression levels among 12 different yeasts and found that a group of genes involved in the mitochondrial respiration process showed the largest reduction in gene expression level during the evolution of aerobic fermentation. Our analysis revealed that the downregulation of these genes was significantly associated with massive loss of binding motifs of Cbf1p in the fermentative yeasts. Our experimental assays confirmed the binding of Cbf1p to the predicted motif and the activator role of Cbf1p. In summary, our study laid a foundation to unravel the long-time mystery about the genetic basis of evolution of aerobic fermentation, providing new insights into understanding the role of cis-regulatory changes in phenotypic evolution. PMID:23650209

Concerted Dynamic Motions of an FABP4 Model and Its Ligands Revealed by Microsecond Molecular Dynamics Simulations

PubMed Central

2015-01-01

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4–ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level. PMID:25231537

Concerted dynamic motions of an FABP4 model and its ligands revealed by microsecond molecular dynamics simulations.

PubMed

Li, Yan; Li, Xiang; Dong, Zigang

2014-10-14

In this work, we investigate the dynamic motions of fatty acid binding protein 4 (FABP4) in the absence and presence of a ligand by explicitly solvated all-atom molecular dynamics simulations. The dynamics of one ligand-free FABP4 and four ligand-bound FABP4s is compared via multiple 1.2 μs simulations. In our simulations, the protein interconverts between the open and closed states. Ligand-free FABP4 prefers the closed state, whereas ligand binding induces a conformational transition to the open state. Coupled with opening and closing of FABP4, the ligand adopts distinct binding modes, which are identified and compared with crystal structures. The concerted dynamics of protein and ligand suggests that there may exist multiple FABP4-ligand binding conformations. Thus, this work provides details about how ligand binding affects the conformational preference of FABP4 and how ligand binding is coupled with a conformational change of FABP4 at an atomic level.

Evolution of homeobox genes.

PubMed

Holland, Peter W H

2013-01-01

Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

Evolution of NASA's Earth Science Digital Object Identifier Registration System

NASA Technical Reports Server (NTRS)

Wanchoo, Lalit; James, Nathan

2017-01-01

NASA's Earth Science Data and Information System (ESDIS) Project has implemented a fully automated system for assigning Digital Object Identifiers (DOIs) to Earth Science data products being managed by its network of 12 distributed active archive centers (DAACs). A key factor in the successful evolution of the DOI registration system over last 7 years has been the incorporation of community input from three focus groups under the NASA's Earth Science Data System Working Group (ESDSWG). These groups were largely composed of DOI submitters and data curators from the 12 data centers serving the user communities of various science disciplines. The suggestions from these groups were formulated into recommendations for ESDIS consideration and implementation. The ESDIS DOI registration system has evolved to be fully functional with over 5,000 publicly accessible DOIs and over 200 DOIs being held in reserve status until the information required for registration is obtained. The goal is to assign DOIs to the entire 8000+ data collections under ESDIS management via its network of discipline-oriented data centers. DOIs make it easier for researchers to discover and use earth science data and they enable users to provide valid citations for the data they use in research. Also for the researcher wishing to reproduce the results presented in science publications, the DOI can be used to locate the exact data or data products being cited.

Auralization of concert hall acoustics using finite difference time domain methods and wave field synthesis

NASA Astrophysics Data System (ADS)

Hochgraf, Kelsey

Auralization methods have been used for a long time to simulate the acoustics of a concert hall for different seat positions. The goal of this thesis was to apply the concept of auralization to a larger audience area that the listener could walk through to compare differences in acoustics for a wide range of seat positions. For this purpose, the acoustics of Rensselaer's Experimental Media and Performing Arts Center (EMPAC) Concert Hall were simulated to create signals for a 136 channel wave field synthesis (WFS) system located at Rensselaer's Collaborative Research Augmented Immersive Virtual Environment (CRAIVE) Laboratory. By allowing multiple people to dynamically experience the concert hall's acoustics at the same time, this research gained perspective on what is important for achieving objective accuracy and subjective plausibility in an auralization. A finite difference time domain (FDTD) simulation on a three-dimensional face-centered cubic grid, combined at a crossover frequency of 800 Hz with a CATT-Acoustic(TM) simulation, was found to have a reverberation time, direct to reverberant sound energy ratio, and early reflection pattern that more closely matched measured data from the hall compared to a CATT-Acoustic(TM) simulation and other hybrid simulations. In the CRAIVE lab, nine experienced listeners found all hybrid auralizations (with varying source location, grid resolution, crossover frequency, and number of loudspeakers) to be more perceptually plausible than the CATT-Acoustic(TM) auralization. The FDTD simulation required two days to compute, while the CATT-Acoustic(TM) simulation required three separate TUCT(TM) computations, each taking four hours, to accommodate the large number of receivers. Given the perceptual advantages realized with WFS for auralization of a large, inhomogeneous sound field, it is recommended that hybrid simulations be used in the future to achieve more accurate and plausible auralizations. Predictions are made for a

A Preliminary Appraisal of Concerted Services in Training and Education in Rural Areas. Occasional Paper No. 1.

ERIC Educational Resources Information Center

Coster, John K.

In order to gather information on which to base decisions regarding the continuation of the Concerted Services in Training and Education in Rural Areas, a preliminary appraisal was made of three pilot projects located in Arkansas, New Mexico, and Minnesota. Overall impressions and reactions to attainment of objectives were made, and some major…

List identifies threatened ecosystems

NASA Astrophysics Data System (ADS)

Showstack, Randy

2012-09-01

The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications.

PubMed

Kan, Xian-Zhao; Wang, Shan-Shan; Ding, Xin; Wang, Xiao-Quan

2007-08-01

Nuclear ribosomal DNA (nrDNA) has been considered as an important tool for inferring phylogenetic relationships at many taxonomic levels. In comparison with its fast concerted evolution in angiosperms, nrDNA is symbolized by slow concerted evolution and substantial ITS region length variation in gymnosperms, particularly in Pinaceae. Here we studied structure characteristics, including subrepeat composition, size, GC content and secondary structure, of nrDNA ITS regions of all Pinaceae genera. The results showed that the ITS regions of all taxa studied contained subrepeat units, ranging from 2 to 9 in number, and these units could be divided into two types, longer subrepeat (LSR) without the motif (5'-GGCCACCCTAGTC) and shorter subrepeat (SSR) with the motif. Phylogenetic analyses indicate that the homology of some SSRs still can be recognized, providing important informations for the evolutionary history of nrDNA ITS and phylogeny of Pinaceae. In particular, the adjacent tandem SSRs are not more closely related to one another than they are to remote SSRs in some genera, which may imply that multiple structure variations such as recombination have occurred in the ITS1 region of these groups. This study also found that GC content in the ITS1 region is relevant to its sequence length and subrepeat number, and could provide some phylogenetic information, especially supporting the close relationships among Picea, Pinus, and Cathaya. Moreover, several characteristics of the secondary structure of Pinaceae ITS1 were found as follows: (1) the structure is dominated by several extended hairpins; (2) the configuration complexity is positively correlated with subrepeat number; (3) paired subrepeats often partially overlap at the conserved motif (5'-GGCCACCCTAGTC), and form a long stem, while other subrepeats fold onto itself, leaving part of the conserved motif exposed in hairpin loops.

Luminous Infrared Sources in the Local Group: Identifying the Missing Links in Massive Star Evolution

NASA Astrophysics Data System (ADS)

Britavskiy, N.; Bonanos, A. Z.; Mehner, A.

2015-01-01

We present the first systematic survey of dusty massive stars (RSGs, LBVs, sgB[e]) in nearby galaxies, with the goal of understanding their importance in massive star evolution. Using the fact that these stars are bright in mid-infrared colors due to dust, we provide a technique for selecting and identifying dusty evolved stars based on the results of Bonanos et al. (2009, 2010), Britavskiy et al. (2014), and archival Spitzer/IRAC photometry. We present the results of our spectroscopic follow-up of luminous infrared sources in the Local Group dwarf irregular galaxies: Pegasus, Phoenix, Sextans A and WLM. The survey aims to complete the census of dusty massive stars in the Local Group.

The first vineyard concert hall in North America

NASA Astrophysics Data System (ADS)

Jaffe, Christopher; Rivera, Carlos

2002-11-01

The first vineyard or surround concert hall designed and built in the Western Hemisphere is the Sala Nezahualcoyotl in Mexico City. The Hall was completed in 1976 and is part of the Cultural Center at the Universidad Nacional Autonoma de Mexico. The hall was named after a Toltec poet, architect, and musician who lived in the 15th century and was the Renaissance man of his day. In order to provide the familiar traditional sound of the rectangular (shoebox) European Hall, the acoustic designers set the criteria for reverberation times through the frequency spectrum and the Initial Time Delay Gap at every seat in the house to match the measurements taken at the Grosser Musik vereinssaal in Vienna and Boston Symphony Hall. In this paper we discuss the techniques used to create the traditional sound in a vineyard hall and the reaction of musicians and audiences to the completed facility. The Sala was the model for Suntory Hall in Japan which in turn spawned a number of vineyard halls in Japan. Most recently, the vineyard style seems to be appealing to more and more symphonic organizations in Europe and North America.

Outreach for Families and Girls- Astronomy at Outdoor Concerts and at Super Bowl or Halloween Star Parties

NASA Astrophysics Data System (ADS)

Lubowich, Donald A.

2011-05-01

Bring telescope to where the people are! Music and Astronomy Under the Stars (MAUS) is a NASA-funded as astronomy outreach program at community parks and music festivals (1000 - 25,000 people/event). While there have been many astronomy outreach activities and telescope observations at sidewalks and parks, this program targets a different audience - music lovers who are attending concerts in community parks or festivals. These music lovers who may not have visited science museums, planetariums, or star parties are exposed to telescope observations and astronomy information with no additional travel costs. MAUS includes solar observing, telescope observations including a live imaging system, an astronomical video, astronomy banners/posters, and hands-on activities. MAUS increased awareness, engagement, and interest in astronomy at classical, pop, rock, and ethnic music concerts. Since 2009 over 50,000 people have participated in these outreach activities including a significant number of families and young girls. In addition to concerts in local Long Island parks, there were MUAS events at Tanglewood (summer home of the Boston Symphony Orchestra), Jazz in Central Park, and Astronomy Night on the National Mall (co-sponsored by the White House Office of Science and Technology Policy). In 2011 MUAS will be expanded to include Ravinia (summer home of the Chicago Symphony Orchestra), the Newport Folk Festival, and the Bethel Woods Center for the Arts (site of the 1969 Woodstock festival). According to our survey results, music lovers became more informed about astronomy. Expanding Hofstra University's successful outreach programs, I propose the creation of a National Halloween Stars event targeting children and a National Super Bowl Star Party targeting girls, women, and the 2/3 of Americans who do not watch the Super Bowl. This can be combined with astronomers or amateur astronomers bringing telescopes to Super Bowl parties for football fans to stargaze during

Warm-Up Activities of Middle and High School Band Directors Participating in State-Level Concert Band Assessments

ERIC Educational Resources Information Center

Ward, Justin P.; Hancock, Carl B.

2016-01-01

The purpose of this study was to examine the warm-ups chosen by concert band directors participating in state-level performance assessments. We observed 29 middle and high school bands and coded the frequency and duration of warm-up activities and behaviors. Results indicated that most bands rehearsed music and played scales, long tones, and…

Switching of the positive feedback for RAS activation by a concerted function of SOS membrane association domains.

PubMed

Nakamura, Yuki; Hibino, Kayo; Yanagida, Toshio; Sako, Yasushi

2016-01-01

Son of sevenless (SOS) is a guanine nucleotide exchange factor that regulates cell behavior by activating the small GTPase RAS. Recent in vitro studies have suggested that an interaction between SOS and the GTP-bound active form of RAS generates a positive feedback loop that propagates RAS activation. However, it remains unclear how the multiple domains of SOS contribute to the regulation of the feedback loop in living cells. Here, we observed single molecules of SOS in living cells to analyze the kinetics and dynamics of SOS behavior. The results indicate that the histone fold and Grb2-binding domains of SOS concertedly produce an intermediate state of SOS on the cell surface. The fraction of the intermediated state was reduced in positive feedback mutants, suggesting that the feedback loop functions during the intermediate state. Translocation of RAF, recognizing the active form of RAS, to the cell surface was almost abolished in the positive feedback mutants. Thus, the concerted functions of multiple membrane-associating domains of SOS governed the positive feedback loop, which is crucial for cell fate decision regulated by RAS.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.

PubMed

Melters, Daniël P; Bradnam, Keith R; Young, Hugh A; Telis, Natalie; May, Michael R; Ruby, J Graham; Sebra, Robert; Peluso, Paul; Eid, John; Rank, David; Garcia, José Fernando; DeRisi, Joseph L; Smith, Timothy; Tobias, Christian; Ross-Ibarra, Jeffrey; Korf, Ian; Chan, Simon W L

2013-01-30

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

PubMed Central

2013-01-01

Background Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. Results Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution. Conclusions While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes. PMID:23363705

A Coordinated Emergency Response: A Color Dust Explosion at a 2015 Concert in Taiwan

PubMed Central

Yang, Chih-Ching

2016-01-01

In June 2015, nearly 500 concert attendees suffered injuries from smoke inhalation and severe burns following a color-dust explosion at a waterpark in Taiwan. We report on the progressions of the incident and government responses, share cross-departmental mobilization and case management lessons, and reflect on clinical and complex policy issues emerged. The timely and coordinated emergency responses, a high-quality universal health care system, and dedicated clinicians voluntarily working overtime resulted in an unprecedented 2.4% mortality rate (international statistics predicted 26.8%). PMID:27459446

Evidence for the Concerted Evolution between Short Linear Protein Motifs and Their Flanking Regions

PubMed Central

Chica, Claudia; Diella, Francesca; Gibson, Toby J.

2009-01-01

Background Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein–protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur inside flexible regions that are accessible for interaction. Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids. Results The evolution of regions flanking 116 functional linear motif instances was studied. The conservation of the amino acid sequence and order/disorder tendency of those regions was related to presence/absence of the instance. For the majority of the analysed instances, the pairs of sequences conserving the linear motif were also observed to maintain a similar local structural tendency and/or to have higher local sequence conservation when compared to pairs of sequences where one is missing the linear motif. Furthermore, those instances have a higher chance to co–evolve with the neighbouring residues in comparison to the distant ones. Those findings are supported by examples where the regulation of the linear motif–mediated interaction has been shown to depend on the modifications (e.g. phosphorylation) at neighbouring positions or is thought to benefit from the binding versatility of disordered regions. Conclusion The results suggest that flanking regions are relevant for linear motif–mediated interactions, both at the structural and sequence level. More interestingly, they indicate that the prediction of linear motif instances can be enriched with contextual information by performing a sequence analysis similar to the one presented here. This can facilitate the understanding of the role of these predicted instances in determining the protein function inside the broader context of the cellular network where they arise

Gain-of-function mutations in beet DODA2 identify key residues for betalain pigment evolution.

PubMed

Bean, Alexander; Sunnadeniya, Rasika; Akhavan, Neda; Campbell, Annabelle; Brown, Matthew; Lloyd, Alan

2018-05-13

The key enzymatic step in betalain biosynthesis involves conversion of l-3,4-dihydroxyphenylalanine (l-DOPA) to betalamic acid. One class of enzymes capable of this is 3,4-dihydroxyphenylalanine 4,5-dioxygenase (DODA). In betalain-producing species, multiple paralogs of this gene are maintained. This study demonstrates which paralogs function in the betalain pathway and determines the residue changes required to evolve a betalain-nonfunctional DODA into a betalain-functional DODA. Functionalities of two pairs of DODAs were tested by expression in beets, Arabidopsis and yeast, and gene silencing was performed by virus-induced gene silencing. Site-directed mutagenesis identified amino acid residues essential for betalamic acid production. Beta vulgaris and Mirabilis jalapa both possess a DODA1 lineage that functions in the betalain pathway and at least one other lineage, DODA2, that does not. Site-directed mutagenesis resulted in betalain biosynthesis by a previously nonfunctional DODA, revealing key residues required for evolution of the betalain pathway. Divergent functionality of DODA paralogs, one clade involved in betalain biosynthesis but others not, is present in various Caryophyllales species. A minimum of seven amino acid residue changes conferred betalain enzymatic activity to a betalain-nonfunctional DODA paralog, providing insight into the evolution of the betalain pigment pathway in plants. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

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

Liao, D.; Weiner, A.M.

1995-12-10

The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to studymore » the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.« less

The organization and evolution of the Responder satellite in species of the Drosophila melanogaster group: dynamic evolution of a target of meiotic drive.

PubMed

Larracuente, Amanda M

2014-11-25

Satellite DNA can make up a substantial fraction of eukaryotic genomes and has roles in genome structure and chromosome segregation. The rapid evolution of satellite DNA can contribute to genomic instability and genetic incompatibilities between species. Despite its ubiquity and its contribution to genome evolution, we currently know little about the dynamics of satellite DNA evolution. The Responder (Rsp) satellite DNA family is found in the pericentric heterochromatin of chromosome 2 of Drosophila melanogaster. Rsp is well-known for being the target of Segregation Distorter (SD)- an autosomal meiotic drive system in D. melanogaster. I present an evolutionary genetic analysis of the Rsp family of repeats in D. melanogaster and its closely-related species in the melanogaster group (D. simulans, D. sechellia, D. mauritiana, D. erecta, and D. yakuba) using a combination of available BAC sequences, whole genome shotgun Sanger reads, Illumina short read deep sequencing, and fluorescence in situ hybridization. I show that Rsp repeats have euchromatic locations throughout the D. melanogaster genome, that Rsp arrays show evidence for concerted evolution, and that Rsp repeats exist outside of D. melanogaster, in the melanogaster group. The repeats in these species are considerably diverged at the sequence level compared to D. melanogaster, and have a strikingly different genomic distribution, even between closely-related sister taxa. The genomic organization of the Rsp repeat in the D. melanogaster genome is complex-it exists of large blocks of tandem repeats in the heterochromatin and small blocks of tandem repeats in the euchromatin. My discovery of heterochromatic Rsp-like sequences outside of D. melanogaster suggests that SD evolved after its target satellite and that the evolution of the Rsp satellite family is highly dynamic over a short evolutionary time scale (<240,000 years).

A key ecological trait drove the evolution of biparental care and monogamy in an amphibian.

PubMed

Brown, Jason L; Morales, Victor; Summers, Kyle

2010-04-01

Linking specific ecological factors to the evolution of parental care pattern and mating system is a difficult task of key importance. We provide evidence from comparative analyses that an ecological factor (breeding pool size) is associated with the evolution of parental care across all frogs. We further show that the most intensive form of parental care (trophic egg feeding) evolved in concert with the use of small pools for tadpole deposition and that egg feeding was associated with the evolution of biparental care. Previous research on two Peruvian poison frogs (Ranitomeya imitator and Ranitomeya variabilis) revealed similar life histories, with the exception of breeding pool size. This key ecological difference led to divergence in parental care patterns and mating systems. We present ecological field experiments that demonstrate that biparental care is essential to tadpole survival in small (but not large) pools. Field observations demonstrate social monogamy in R. imitator, the species that uses small pools. Molecular analyses demonstrate genetic monogamy in R. imitator, the first example of genetic monogamy in an amphibian. In total, this evidence constitutes the most complete documentation to date that a single ecological factor drove the evolution of biparental care and genetic and social monogamy in an animal.

"Posh Music Should Equal Posh Dress": An Investigation into the Concert Dress and Physical Appearance of Female Soloists

ERIC Educational Resources Information Center

Griffiths, Noola K.

2010-01-01

This study investigates the effects of concert dress and physical appearance on perceptions of female classical soloists' musical abilities over a range of genres. Four female violinists were recorded playing three pieces, in four styles of dress of varying formality. Each combination of performer, piece and dress was recorded twice, once as the…

Bringing Astronomy Directly to New Audiences (50,000 People) at Outdoor Concerts and Music Festivals

NASA Astrophysics Data System (ADS)

Lubowich, D.

2014-07-01

My NASA-funded Music and Astronomy Under the Stars (MAUS) has brought astronomy to 50,000 music lovers at the National Mall (co-sponsor OSTP); Central Park Jazz, Newport Folk, Ravinia, or Tanglewood music festivals; and classical, folk, pop/rock, opera, Caribbean, or county-western concerts in parks assisted by astronomy clubs (55 events since 2009). Yo-Yo-Ma, the Chicago and Boston Symphony Orchestras, Ravi Coltrane, Esperanza Spalding, Phish, Blood Sweat and Tears, Deep Purple, Tony Orlando, and Wilco performed at these events. MAUS combines solar, optical, and radio telescope observations; large posters/banners (From the Earth to the Universe; Visions of the Universe); videos; hands-on activities (Night Sky Network; Harvard-Smithsonian CfA); imaging with a cell phone mount; and hand-outs (info on science museums, astronomy clubs, and citizen science) before and after the concerts or at intermission. MAUS reached underserved groups and attracted large enthusiastic crowds. Many young children participated in this family learning experience-often the first time they looked through a telescope. Outcomes: While < 50% of the participants took part in a science museum or activity in the past year (survey result), they found MAUS enjoyable and understandable; learned about astronomy; wanted to learn more; and increased their interest in science (ave. rating 3.6/4). Taking science directly to people is effective in promoting science education!

Concerted In Vitro Trimming of Viral HLA-B27-Restricted Ligands by Human ERAP1 and ERAP2 Aminopeptidases

PubMed Central

Lorente, Elena; Barriga, Alejandro; Johnstone, Carolina; Mir, Carmen; Jiménez, Mercedes; López, Daniel

2013-01-01

In the classical human leukocyte antigen (HLA) class I antigen processing and presentation pathway, the antigenic peptides are generated from viral proteins by multiple proteolytic cleavages of the proteasome (and in some cases other cytosolic proteases) and transported to the endoplasmic reticulum (ER) lumen where they are exposed to aminopeptidase activity. In human cells, two different ER-resident enzymes, ERAP1 and ERAP2, can trim the N-terminally extended residues of peptide precursors. In this study, the possible cooperative effect of generating five naturally processed HLA-B27 ligands by both proteases was analyzed. We identified differences in the products obtained with increased detection of natural HLA-B27 ligands by comparing double versus single enzyme digestions by mass spectrometry analysis. These in vitro data suggest that each enzyme can use the degradation products of the other as a substrate for new N-terminal trimming, indicating concerted aminoproteolytic activity of ERAP 1 and ERAP2. PMID:24223975

Concerted in vitro trimming of viral HLA-B27-restricted ligands by human ERAP1 and ERAP2 aminopeptidases.

PubMed

Lorente, Elena; Barriga, Alejandro; Johnstone, Carolina; Mir, Carmen; Jiménez, Mercedes; López, Daniel

2013-01-01

In the classical human leukocyte antigen (HLA) class I antigen processing and presentation pathway, the antigenic peptides are generated from viral proteins by multiple proteolytic cleavages of the proteasome (and in some cases other cytosolic proteases) and transported to the endoplasmic reticulum (ER) lumen where they are exposed to aminopeptidase activity. In human cells, two different ER-resident enzymes, ERAP1 and ERAP2, can trim the N-terminally extended residues of peptide precursors. In this study, the possible cooperative effect of generating five naturally processed HLA-B27 ligands by both proteases was analyzed. We identified differences in the products obtained with increased detection of natural HLA-B27 ligands by comparing double versus single enzyme digestions by mass spectrometry analysis. These in vitro data suggest that each enzyme can use the degradation products of the other as a substrate for new N-terminal trimming, indicating concerted aminoproteolytic activity of ERAP 1 and ERAP2.

Switching of the positive feedback for RAS activation by a concerted function of SOS membrane association domains

PubMed Central

Nakamura, Yuki; Hibino, Kayo; Yanagida, Toshio; Sako, Yasushi

2016-01-01

Son of sevenless (SOS) is a guanine nucleotide exchange factor that regulates cell behavior by activating the small GTPase RAS. Recent in vitro studies have suggested that an interaction between SOS and the GTP-bound active form of RAS generates a positive feedback loop that propagates RAS activation. However, it remains unclear how the multiple domains of SOS contribute to the regulation of the feedback loop in living cells. Here, we observed single molecules of SOS in living cells to analyze the kinetics and dynamics of SOS behavior. The results indicate that the histone fold and Grb2-binding domains of SOS concertedly produce an intermediate state of SOS on the cell surface. The fraction of the intermediated state was reduced in positive feedback mutants, suggesting that the feedback loop functions during the intermediate state. Translocation of RAF, recognizing the active form of RAS, to the cell surface was almost abolished in the positive feedback mutants. Thus, the concerted functions of multiple membrane-associating domains of SOS governed the positive feedback loop, which is crucial for cell fate decision regulated by RAS. PMID:27924253

Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies

PubMed Central

Daane, Jacob M.; Rohner, Nicolas; Konstantinidis, Peter; Djuranovic, Sergej; Harris, Matthew P.

2016-01-01

The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new comparative genomic approach that can be applied to a broad taxonomic sampling of nonmodel species to investigate the genetic basis of evolutionary change. Using our analysis pipeline, we show that duplication and divergence of fgfr1a is correlated with the reduction of scales within fishes of the genus Phoxinellus. As a parallel genetic mechanism is observed in scale-reduction within independent lineages of cypriniforms, our finding exposes significant developmental constraint guiding morphological evolution. In addition, we identified fixed variation in fgf20a within Phoxinellus and demonstrated that combinatorial loss-of-function of fgfr1a and fgf20a within zebrafish phenocopies the evolved scalation pattern. Together, these findings reveal epistatic interactions between fgfr1a and fgf20a as a developmental mechanism regulating skeletal variation among fishes. PMID:26452532

Organic chemical evolution

NASA Technical Reports Server (NTRS)

Chang, S.

1981-01-01

The course of organic chemical evolution preceding the emergence of life on earth is discussed based on evidence of processes occurring in interstellar space, the solar system and the primitive earth. Following a brief review of the equilibrium condensation model for the origin and evolution of the solar system, consideration is given to the nature and organic chemistry of interstellar clouds, comets, Jupiter, meteorites, Venus and Mars, and the prebiotic earth. Major issues to be resolved in the study of organic chemical evolution on earth are identified regarding condensation and accretion in the solar nebula, early geological evolution, the origin and evolution of the atmosphere, organic production rates, organic-inorganic interactions, environmental fluctuations, phase separation and molecular selectivity.

The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

PubMed Central

Koelle, Katia; Rasmussen, David A

2015-01-01

Recent phylogenetic analyses indicate that RNA virus populations carry a significant deleterious mutation load. This mutation load has the potential to shape patterns of adaptive evolution via genetic linkage to beneficial mutations. Here, we examine the effect of deleterious mutations on patterns of influenza A subtype H3N2's antigenic evolution in humans. By first analyzing simple models of influenza that incorporate a mutation load, we show that deleterious mutations, as expected, act to slow the virus's rate of antigenic evolution, while making it more punctuated in nature. These models further predict three distinct molecular pathways by which antigenic cluster transitions occur, and we find phylogenetic patterns consistent with each of these pathways in influenza virus sequences. Simulations of a more complex phylodynamic model further indicate that antigenic mutations act in concert with deleterious mutations to reproduce influenza's spindly hemagglutinin phylogeny, co-circulation of antigenic variants, and high annual attack rates. DOI: http://dx.doi.org/10.7554/eLife.07361.001 PMID:26371556

Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution

PubMed Central

Kumar, Narender; Mariappan, Vanitha; Baddam, Ramani; Lankapalli, Aditya K.; Shaik, Sabiha; Goh, Khean-Lee; Loke, Mun Fai; Perkins, Tim; Benghezal, Mohammed; Hasnain, Seyed E.; Vadivelu, Jamuna; Marshall, Barry J.; Ahmed, Niyaz

2015-01-01

The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host–pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner. PMID:25452339

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

PubMed

Gini, Beatrice; Mischel, Paul S

2014-08-01

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

Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid

PubMed Central

2011-01-01

Background Paphiopedilum is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence In Situ Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within Paphiopedilum. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity. Results 5S and 25S rDNA loci among Paphiopedilum species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity. Conclusions Paphiopedilum species display many chromosomal rearrangements - for example, duplications, translocations, and inversions - but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus

Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid.

PubMed

Lan, Tianying; Albert, Victor A

2011-09-12

Paphiopedilum is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence In Situ Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within Paphiopedilum. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity. 5S and 25S rDNA loci among Paphiopedilum species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity. Paphiopedilum species display many chromosomal rearrangements--for example, duplications, translocations, and inversions--but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus a model system for the study of

The Evolution of Musicality: What Can Be Learned from Language Evolution Research?

PubMed Central

Ravignani, Andrea; Thompson, Bill; Filippi, Piera

2018-01-01

Language and music share many commonalities, both as natural phenomena and as subjects of intellectual inquiry. Rather than exhaustively reviewing these connections, we focus on potential cross-pollination of methodological inquiries and attitudes. We highlight areas in which scholarship on the evolution of language may inform the evolution of music. We focus on the value of coupled empirical and formal methodologies, and on the futility of mysterianism, the declining view that the nature, origins and evolution of language cannot be addressed empirically. We identify key areas in which the evolution of language as a discipline has flourished historically, and suggest ways in which these advances can be integrated into the study of the evolution of music. PMID:29467601

The Evolution of Musicality: What Can Be Learned from Language Evolution Research?

PubMed

Ravignani, Andrea; Thompson, Bill; Filippi, Piera

2018-01-01

Language and music share many commonalities, both as natural phenomena and as subjects of intellectual inquiry. Rather than exhaustively reviewing these connections, we focus on potential cross-pollination of methodological inquiries and attitudes. We highlight areas in which scholarship on the evolution of language may inform the evolution of music. We focus on the value of coupled empirical and formal methodologies, and on the futility of mysterianism , the declining view that the nature, origins and evolution of language cannot be addressed empirically. We identify key areas in which the evolution of language as a discipline has flourished historically, and suggest ways in which these advances can be integrated into the study of the evolution of music.

Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution.

PubMed

Kumar, Narender; Mariappan, Vanitha; Baddam, Ramani; Lankapalli, Aditya K; Shaik, Sabiha; Goh, Khean-Lee; Loke, Mun Fai; Perkins, Tim; Benghezal, Mohammed; Hasnain, Seyed E; Vadivelu, Jamuna; Marshall, Barry J; Ahmed, Niyaz

2015-01-01

The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host-pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

[A concertation experience: prevention of WMSDs in workmanship of Parmigiano-Reggiano].

PubMed

Zecchi, G

2012-01-01

The dairy industry of Parmigiano-Reggiano represents in Emilia a resource and an important source of employment. A Protected Designation of Origin (DOP) regulates all stages of processing of milk into cheese "forms" in excess of 40 kg weight, favouring a "traditional" working which involves various manual steps tiring and stressful. From 2002 to 2008 the Service in charge of the Azienda USL of Reggio Emilia has developed a plan focused on musculoskeletal risks in this sector. The need for comparison on the conservation "craftsmanship" of the complex manufacturing process maintaining high attention to health and safety brought the AUSL of Reggio E. and later the AUSL of Modena and Parma, to choose the path of concertation with the social partners, aiming at substantial and non-formal application of the law. It is thus obtained the adoption of preventive measures in a sector so peculiar, complex and constantly changing. Conciliation remains privileged tool in relations between social partners and AUSL of Reggio E. in dairies.

Constraints in cancer evolution.

PubMed

Venkatesan, Subramanian; Birkbak, Nicolai J; Swanton, Charles

2017-02-08

Next-generation deep genome sequencing has only recently allowed us to quantitatively dissect the extent of heterogeneity within a tumour, resolving patterns of cancer evolution. Intratumour heterogeneity and natural selection contribute to resistance to anticancer therapies in the advanced setting. Recent evidence has also revealed that cancer evolution might be constrained. In this review, we discuss the origins of intratumour heterogeneity and subsequently focus on constraints imposed upon cancer evolution. The presence of (1) parallel evolution, (2) convergent evolution and (3) the biological impact of acquiring mutations in specific orders suggest that cancer evolution may be exploitable. These constraints on cancer evolution may help us identify cancer evolutionary rule books, which could eventually inform both diagnostic and therapeutic approaches to improve survival outcomes. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Conditioning Methodologies for DanceSport: Lessons from Gymnastics, Figure Skating, and Concert Dance Research.

PubMed

Outevsky, David; Martin, Blake Cw

2015-12-01

Dancesport, the competitive branch of ballroom dancing, places high physiological and psychological demands on its practitioners, but pedagogical resources in these areas for this dance form are limited. Dancesport competitors could benefit from strategies used in other aesthetic sports. In this review, we identify conditioning methodologies from gymnastics, figure skating, and contemporary, modern, and ballet dance forms that could have relevance and suitability for dancesport training, and propose several strategies for inclusion in the current dancesport curriculum. We reviewed articles derived from Google Scholar, PubMed, ScienceDirect, Taylor & Francis Online, and Web of Science search engines and databases, with publication dates from 1979 to 2013. The keywords included MeSH terms: dancing, gymnastics, physiology, energy metabolism, physical endurance, and range of motion. Out of 47 papers examined, 41 papers met the inclusion criteria (validity of scientific methods, topic relevance, transferability to dancesport, publication date). Quality and validity of the data were assessed by examining the methodologies in each study and comparing studies on similar populations as well as across time using the PRISMA 2009 checklist and flowchart. The relevant research suggests that macro-cycle periodization planning, aerobic and anaerobic conditioning, range of motion and muscular endurance training, and performance psychology methods have potential for adaptation for dancesport training. Dancesport coaches may help their students fulfill their ambitions as competitive athletes and dance artists by adapting the relevant performance enhancement strategies from gymnastics, figure skating, and concert dance forms presented in this paper.

Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell.

PubMed

Holthaus, Karin Brigit; Strasser, Bettina; Sipos, Wolfgang; Schmidt, Heiko A; Mlitz, Veronika; Sukseree, Supawadee; Weissenbacher, Anton; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

2016-03-01

The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The 5S rDNA in two Abracris grasshoppers (Ommatolampidinae: Acrididae): molecular and chromosomal organization.

PubMed

Bueno, Danilo; Palacios-Gimenez, Octavio Manuel; Martí, Dardo Andrea; Mariguela, Tatiane Casagrande; Cabral-de-Mello, Diogo Cavalcanti

2016-08-01

The 5S ribosomal DNA (rDNA) sequences are subject of dynamic evolution at chromosomal and molecular levels, evolving through concerted and/or birth-and-death fashion. Among grasshoppers, the chromosomal location for this sequence was established for some species, but little molecular information was obtained to infer evolutionary patterns. Here, we integrated data from chromosomal and nucleotide sequence analysis for 5S rDNA in two Abracris species aiming to identify evolutionary dynamics. For both species, two arrays were identified, a larger sequence (named type-I) that consisted of the entire 5S rDNA gene plus NTS (non-transcribed spacer) and a smaller (named type-II) with truncated 5S rDNA gene plus short NTS that was considered a pseudogene. For type-I sequences, the gene corresponding region contained the internal control region and poly-T motif and the NTS presented partial transposable elements. Between the species, nucleotide differences for type-I were noticed, while type-II was identical, suggesting pseudogenization in a common ancestor. At chromosomal point to view, the type-II was placed in one bivalent, while type-I occurred in multiple copies in distinct chromosomes. In Abracris, the evolution of 5S rDNA was apparently influenced by the chromosomal distribution of clusters (single or multiple location), resulting in a mixed mechanism integrating concerted and birth-and-death evolution depending on the unit.

Concerted vs. Sequential. Two Activation Patterns of Vast Arrays of Intracellular Ca2+ Channels in Muscle

PubMed Central

Zhou, Jinsong; Brum, Gustavo; González, Adom; Launikonis, Bradley S.; Stern, Michael D.; Ríos, Eduardo

2005-01-01

To signal cell responses, Ca2+ is released from storage through intracellular Ca2+ channels. Unlike most plasmalemmal channels, these are clustered in quasi-crystalline arrays, which should endow them with unique properties. Two distinct patterns of local activation of Ca2+ release were revealed in images of Ca2+ sparks in permeabilized cells of amphibian muscle. In the presence of sulfate, an anion that enters the SR and precipitates Ca2+, sparks became wider than in the conventional, glutamate-based solution. Some of these were “protoplatykurtic” (had a flat top from early on), suggesting an extensive array of channels that activate simultaneously. Under these conditions the rate of production of signal mass was roughly constant during the rise time of the spark and could be as high as 5 μm3 ms−1, consistent with a release current >50 pA since the beginning of the event. This pattern, called “concerted activation,” was observed also in rat muscle fibers. When sulfate was combined with a reduced cytosolic [Ca2+] (50 nM) these sparks coexisted (and interfered) with a sequential progression of channel opening, probably mediated by Ca2+-induced Ca2+ release (CICR). Sequential propagation, observed only in frogs, may require parajunctional channels, of RyR isoform β, which are absent in the rat. Concerted opening instead appears to be a property of RyR α in the amphibian and the homologous isoform 1 in the mammal. PMID:16186560

Evolution of the bovine lysozyme gene family: changes in gene expression and reversion of function.

PubMed

Irwin, D M

1995-09-01

Recruitment of lysozyme to a digestive function in ruminant artiodactyls is associated with amplification of the gene. At least four of the approximately ten genes are expressed in the stomach, and several are expressed in nonstomach tissues. Characterization of additional lysozymelike sequences in the bovine genome has identified most, if not all, of the members of this gene family. There are at least six stomachlike lysozyme genes, two of which are pseudogenes. The stomach lysozyme pseudogenes show a pattern of concerted evolution similar to that of the functional stomach genes. At least four nonstomach lysozyme genes exist. The nonstomach lysozyme genes are not monophyletic. A gene encoding a tracheal lysozyme was isolated, and the stomach lysozyme of advanced ruminants was found to be more closely related to the tracheal lysozyme than to the stomach lysozyme of the camel or other nonstomach lysozyme genes of ruminants. The tracheal lysozyme shares with stomach lysozymes of advanced ruminants the deletion of amino acid 103, and several other adaptive sequence characteristics of stomach lysozymes. I suggest here that tracheal lysozyme has reverted from a functional stomach lysozyme. Tracheal lysozyme then represents a second instance of a change in lysozyme gene expression and function within ruminants.

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants

DOE PAGES

Hraber, Peter; Korber, Bette; Wagh, Kshitij; ...

2015-10-21

Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations ofmore » mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. Here, with well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Finally, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.« less

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations.

PubMed

Lenski, Richard E

2017-10-01

Evolution is an on-going process, and it can be studied experimentally in organisms with rapid generations. My team has maintained 12 populations of Escherichia coli in a simple laboratory environment for >25 years and 60 000 generations. We have quantified the dynamics of adaptation by natural selection, seen some of the populations diverge into stably coexisting ecotypes, described changes in the bacteria's mutation rate, observed the new ability to exploit a previously untapped carbon source, characterized the dynamics of genome evolution and used parallel evolution to identify the genetic targets of selection. I discuss what the future might hold for this particular experiment, briefly highlight some other microbial evolution experiments and suggest how the fields of experimental evolution and microbial ecology might intersect going forward.

Prothrombin Activation by Platelet-associated Prothrombinase Proceeds through the Prethrombin-2 Pathway via a Concerted Mechanism*

PubMed Central

Haynes, Laura M.; Bouchard, Beth A.; Tracy, Paula B.; Mann, Kenneth G.

2012-01-01

The protease α-thrombin is a key enzyme of the coagulation process as it is at the cross-roads of both the pro- and anti-coagulant pathways. The main source of α-thrombin in vivo is the activation of prothrombin by the prothrombinase complex assembled on either an activated cell membrane or cell fragment, the most relevant of which is the activated platelet surface. When prothrombinase is assembled on synthetic phospholipid vesicles, prothrombin activation proceeds with an initial cleavage at Arg-320 yielding the catalytically active, yet effectively anticoagulant intermediate meizothrombin, which is released from the enzyme complex ∼30–40% of the time. Prothrombinase assembled on the surface of activated platelets has been shown to proceed through the inactive intermediate prethrombin-2 via an initial cleavage at Arg-271 followed by cleavage at Arg-320. The current work tests whether or not platelet-associated prothrombinase proceeds via a concerted mechanism through a study of prothrombinase assembly and function on collagen-adhered, thrombin-activated, washed human platelets in a flow chamber. Prothrombinase assembly was demonstrated through visualization of bound factor Xa by confocal microscopy using a fluorophore-labeled anti-factor Xa antibody, which demonstrated the presence of distinct platelet subpopulations capable of binding factor Xa. When prothrombin activation was monitored at a typical venous shear rate over preassembled platelet-associated prothrombinase neither potential intermediate, meizothrombin or prethrombin-2, was observed in the effluent. Collectively, these findings suggest that platelet-associated prothrombinase activates prothrombin via an efficient concerted mechanism in which neither intermediate is released. PMID:22989889

Evolution of trees and mycorrhizal fungi intensifies silicate mineral weathering

PubMed Central

Quirk, Joe; Beerling, David J.; Banwart, Steve A.; Kakonyi, Gabriella; Romero-Gonzalez, Maria E.; Leake, Jonathan R.

2012-01-01

Forested ecosystems diversified more than 350 Ma to become major engines of continental silicate weathering, regulating the Earth's atmospheric carbon dioxide concentration by driving calcium export into ocean carbonates. Our field experiments with mature trees demonstrate intensification of this weathering engine as tree lineages diversified in concert with their symbiotic mycorrhizal fungi. Preferential hyphal colonization of the calcium silicate-bearing rock, basalt, progressively increased with advancement from arbuscular mycorrhizal (AM) to later, independently evolved ectomycorrhizal (EM) fungi, and from gymnosperm to angiosperm hosts with both fungal groups. This led to ‘trenching’ of silicate mineral surfaces by AM and EM fungi, with EM gymnosperms and angiosperms releasing calcium from basalt at twice the rate of AM gymnosperms. Our findings indicate mycorrhiza-driven weathering may have originated hundreds of millions of years earlier than previously recognized and subsequently intensified with the evolution of trees and mycorrhizas to affect the Earth's long-term CO2 and climate history. PMID:22859556

Evolution of trees and mycorrhizal fungi intensifies silicate mineral weathering.

PubMed

Quirk, Joe; Beerling, David J; Banwart, Steve A; Kakonyi, Gabriella; Romero-Gonzalez, Maria E; Leake, Jonathan R

2012-12-23

Forested ecosystems diversified more than 350 Ma to become major engines of continental silicate weathering, regulating the Earth's atmospheric carbon dioxide concentration by driving calcium export into ocean carbonates. Our field experiments with mature trees demonstrate intensification of this weathering engine as tree lineages diversified in concert with their symbiotic mycorrhizal fungi. Preferential hyphal colonization of the calcium silicate-bearing rock, basalt, progressively increased with advancement from arbuscular mycorrhizal (AM) to later, independently evolved ectomycorrhizal (EM) fungi, and from gymnosperm to angiosperm hosts with both fungal groups. This led to 'trenching' of silicate mineral surfaces by AM and EM fungi, with EM gymnosperms and angiosperms releasing calcium from basalt at twice the rate of AM gymnosperms. Our findings indicate mycorrhiza-driven weathering may have originated hundreds of millions of years earlier than previously recognized and subsequently intensified with the evolution of trees and mycorrhizas to affect the Earth's long-term CO(2) and climate history.

Music Audiences 3.0: Concert-Goers' Psychological Motivations at the Dawn of Virtual Reality.

PubMed

Charron, Jean-Philippe

2017-01-01

Reviewing consumers' motivations to attend performances in a continuously evolving social and technological context is essential because live concerts generate an important and growing share of revenues for the music industry. Evolving fans' preferences and technological innovations constantly alter the way music is distributed and consumed. In a marketing 3.0 era, what consumers do with music is becoming more significant than simply owning or listening to a song. These changes are not only blurring the lines between production and consumption (i.e., co-creation), but also distorting the concept of live attendance altogether. Although mediated performances typically lack presence and authenticity, recent advances in immersive technologies, such as spherical videos and virtual reality goggles, could represent a new form of experiencing live music.

Music Audiences 3.0: Concert-Goers’ Psychological Motivations at the Dawn of Virtual Reality

PubMed Central

Charron, Jean-Philippe

2017-01-01

Reviewing consumers’ motivations to attend performances in a continuously evolving social and technological context is essential because live concerts generate an important and growing share of revenues for the music industry. Evolving fans’ preferences and technological innovations constantly alter the way music is distributed and consumed. In a marketing 3.0 era, what consumers do with music is becoming more significant than simply owning or listening to a song. These changes are not only blurring the lines between production and consumption (i.e., co-creation), but also distorting the concept of live attendance altogether. Although mediated performances typically lack presence and authenticity, recent advances in immersive technologies, such as spherical videos and virtual reality goggles, could represent a new form of experiencing live music. PMID:28588528

Identifying Protoclusters in the High Redshift Universe and Mapping Their Evolution

NASA Astrophysics Data System (ADS)

Franck, Jay Robert

2018-01-01

To investigate the growth and evolution of the earliest structures in the Universe, we identify more than 200 galaxy overdensities in the Candidate Cluster and Protocluster Catalog (CCPC). This compilation is produced by mining open astronomy data sets for over-densities of high redshift galaxies that are spectroscopically confirmed. At these redshifts, the Universe is only a few billion years old. This data mining approach yields a nearly 10 fold increase in the number of known protoclusters in the literature. The CCPC also includes the highest redshift, spectroscopically confirmed protocluster at z=6.56. For nearly 1500 galaxies contained in the CCPC between redshifts of 2.02, the brightest galaxies are older and more massive than anticipated by the model.

Parametrization in models of subcritical glass fracture: Activation offset and concerted activation

NASA Astrophysics Data System (ADS)

Rodrigues, Bruno Poletto; Hühn, Carolin; Erlebach, Andreas; Mey, Dorothea; Sierka, Marek; Wondraczek, Lothar

2017-08-01

There are two established but fundamentally different empirical approaches to parametrize the rate of subcritical fracture in brittle materials. While both are relying on a thermally activated reaction of bond rupture, the difference lies in the way as to how the externally applied stresses affect the local energy landscape. In the consideration of inorganic glasses, the strain energy is typically taken as an off-set on the activation barrier. As an alternative interpretation, the system’s volumetric strain-energy is added to its thermal energy. Such an interpretation is consistent with the democratic fiber bundle model. Here, we test this approach of concerted activation against macroscopic data of bond cleavage activation energy, and also against ab initio quantum chemical simulation of the energy barrier for cracking in silica. The fact that both models are able to reproduce experimental observation to a remarkable degree highlights the importance of a holistic consideration towards non-empirical understanding.

An analysis of concert saxophone vibrato through the examination of recordings by eight prominent soloists

NASA Astrophysics Data System (ADS)

Zinninger, Thomas

This study examines concert saxophone vibrato through the analysis of several recordings of standard repertoire by prominent soloists. The vibrato of Vincent Abato, Arno Bornkamp, Claude Delangle, Jean-Marie Londeix, Marcel Mule, Otis Murphy, Sigurd Rascher, and Eugene Rousseau is analyzed with regards to rate, extent, shape, and discretionary use. Examination of these parameters was conducted through both general observation and precise measurements with the aid of a spectrogram. Statistical analyses of the results provide tendencies for overall vibrato use, as well as the effects of certain musical attributes (note length, tempo, dynamic, range) on vibrato. The results of this analysis are also compared among each soloist and against pre-existing theories or findings in vibrato research.

Sound quality (SQ) of concert halls: Physical and subjective attributes

NASA Astrophysics Data System (ADS)

Beranek, Leo L.

2003-10-01

Each new concert hall has the following stated goal: ``Acoustics equal to the best in the world.'' The owner can specify the number of seats, areas of public spaces, lighting intensities, etc. But, the attributes of acoustical quality cannot as yet be specified. Most acoustical consultants seem to feel that a ``seat of the pants'' experience is the only possible specification. But the architect's goal is a monument to himself and he believes the acoustical consultant should achieve the ``best in the world'' goal without visible means. Numbers for specifications are needed. In this paper 40 years of pertinent research are described: What are the critical physical attributes of good acoustics, how do we measure them, and how can they be translated into architectural specifications? Four steps have been involved: (1) interviews of conductors and music critics to determine (a) their acoustical rank orderings of a large number of halls and (b) which acoustical characteristics do they believe are important, viz., reverberance, strength of sound, etc.; (2) a determination of which physical measures correlate with their beliefs plus others that are physiologically important; (3) measurements of those physical quantities in the rank-ordered halls; and (5) the correlation of the measured values with the subjective quality ratings.

Identifying and Modeling Dynamic Preference Evolution in Multipurpose Water Resources Systems

NASA Astrophysics Data System (ADS)

Mason, E.; Giuliani, M.; Castelletti, A.; Amigoni, F.

2018-04-01

Multipurpose water systems are usually operated on a tradeoff of conflicting operating objectives. Under steady state climatic and socioeconomic conditions, such tradeoff is supposed to represent a fair and/or efficient preference. Extreme variability in external forcing might affect water operators' risk aversion and force a change in her/his preference. Properly accounting for these shifts is key to any rigorous retrospective assessment of the operator's behaviors, and to build descriptive models for projecting the future system evolution. In this study, we explore how the selection of different preferences is linked to variations in the external forcing. We argue that preference selection evolves according to recent, extreme variations in system performance: underperforming in one of the objectives pushes the preference toward the harmed objective. To test this assumption, we developed a rational procedure to simulate the operator's preference selection. We map this selection onto a multilateral negotiation, where multiple virtual agents independently optimize different objectives. The agents periodically negotiate a compromise policy for the operation of the system. Agents' attitudes in each negotiation step are determined by the recent system performance measured by the specific objective they maximize. We then propose a numerical model of preference dynamics that implements a concept from cognitive psychology, the availability bias. We test our modeling framework on a synthetic lake operated for flood control and water supply. Results show that our model successfully captures the operator's preference selection and dynamic evolution driven by extreme wet and dry situations.

Evolution of biological complexity

PubMed Central

Adami, Christoph; Ofria, Charles; Collier, Travis C.

2000-01-01

To make a case for or against a trend in the evolution of complexity in biological evolution, complexity needs to be both rigorously defined and measurable. A recent information-theoretic (but intuitively evident) definition identifies genomic complexity with the amount of information a sequence stores about its environment. We investigate the evolution of genomic complexity in populations of digital organisms and monitor in detail the evolutionary transitions that increase complexity. We show that, because natural selection forces genomes to behave as a natural “Maxwell Demon,” within a fixed environment, genomic complexity is forced to increase. PMID:10781045

Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell

PubMed Central

Holthaus, Karin Brigit; Strasser, Bettina; Sipos, Wolfgang; Schmidt, Heiko A.; Mlitz, Veronika; Sukseree, Supawadee; Weissenbacher, Anton; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold

2016-01-01

The evolution of reptiles, birds, and mammals was associated with the origin of unique integumentary structures. Studies on lizards, chicken, and humans have suggested that the evolution of major structural proteins of the outermost, cornified layers of the epidermis was driven by the diversification of a gene cluster called Epidermal Differentiation Complex (EDC). Turtles have evolved unique defense mechanisms that depend on mechanically resilient modifications of the epidermis. To investigate whether the evolution of the integument in these reptiles was associated with specific adaptations of the sequences and expression patterns of EDC-related genes, we utilized newly available genome sequences to determine the epidermal differentiation gene complement of turtles. The EDC of the western painted turtle (Chrysemys picta bellii) comprises more than 100 genes, including at least 48 genes that encode proteins referred to as beta-keratins or corneous beta-proteins. Several EDC proteins have evolved cysteine/proline contents beyond 50% of total amino acid residues. Comparative genomics suggests that distinct subfamilies of EDC genes have been expanded and partly translocated to loci outside of the EDC in turtles. Gene expression analysis in the European pond turtle (Emys orbicularis) showed that EDC genes are differentially expressed in the skin of the various body sites and that a subset of beta-keratin genes within the EDC as well as those located outside of the EDC are expressed predominantly in the shell. Our findings give strong support to the hypothesis that the evolutionary innovation of the turtle shell involved specific molecular adaptations of epidermal differentiation. PMID:26601937

Evidence for concerted ring opening and C-Br bond breaking in UV-excited bromocyclopropane.

PubMed

Pandit, Shubhrangshu; Preston, Thomas J; King, Simon J; Vallance, Claire; Orr-Ewing, Andrew J

2016-06-28

Photodissociation of gaseous bromocyclopropane via its A-band continuum has been studied at excitation wavelengths ranging from 230 nm to 267 nm. Velocity-map images of ground-state bromine atoms (Br), spin-orbit excited bromine atoms (Br(∗)), and C3H5 hydrocarbon radicals reveal the kinetic energies of these various photofragments. Both Br and Br(∗) atoms are predominantly generated via repulsive excited electronic states in a prompt photodissociation process in which the hydrocarbon co-fragment is a cyclopropyl radical. However, the images obtained at the mass of the hydrocarbon radical fragment identify a channel with total kinetic energy greater than that deduced from the Br and Br(∗) images, and with a kinetic energy distribution that exceeds the energetic limit for Br + cyclopropyl radical products. The velocity-map images of these C3H5 fragments have lower angular anisotropies than measured for Br and Br(∗), indicating molecular restructuring during dissociation. The high kinetic energy C3H5 signals are assigned to allyl radicals generated by a minor photochemical pathway which involves concerted C-Br bond dissociation and cyclopropyl ring-opening following single ultraviolet (UV)-photon absorption. Slow photofragments also contribute to the velocity map images obtained at the C3H5 radical mass, but the corresponding slow Br atoms are not observed. These features in the images are attributed to C3H5 (+) from the photodissociation of the C3H5Br(+) molecular cation following two-photon ionization of the parent compound. This assignment is confirmed by 118-nm vacuum ultraviolet ionization studies that prepare the molecular cation in its ground electronic state prior to UV photodissociation.

Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics

PubMed Central

Romo, Tod D.; Grossfield, Alan; Pitman, Michael C.

2010-01-01

Abstract The recently solved crystallographic structures for the A2A adenosine receptor and the β1 and β2 adrenergic receptors have shown important differences between members of the class-A G-protein-coupled receptors and their archetypal model, rhodopsin, such as the apparent breaking of the ionic lock that stabilizes the inactive structure. Here, we characterize a 1.02 μs all-atom simulation of an apo-β2 adrenergic receptor that is missing the third intracellular loop to better understand the inactive structure. Although we find that the structure is remarkably rigid, there is a rapid influx of water into the core of the protein, as well as a slight expansion of the molecule relative to the crystal structure. In contrast to the x-ray crystal structures, the ionic lock rapidly reforms, although we see an activation-precursor-like event wherein the ionic lock opens for ∼200 ns, accompanied by movements in the transmembrane helices associated with activation. When the lock reforms, we see the structure return to its inactive conformation. We also find that the ionic lock exists in three states: closed (or locked), semi-open with a bridging water molecule, and open. The interconversion of these states involves the concerted motion of the entire protein. We characterize these states and the concerted motion underlying their interconversion. These findings may help elucidate the connection between key local events and the associated global structural changes during activation. PMID:20074514

Concerted evolution of body mass and cell size: similar patterns among species of birds (Galliformes) and mammals (Rodentia)

PubMed Central

Dragosz-Kluska, Dominika; Pis, Tomasz; Pawlik, Katarzyna; Kapustka, Filip; Kilarski, Wincenty M.; Kozłowski, Jan

2018-01-01

ABSTRACT Cell size plays a role in body size evolution and environmental adaptations. Addressing these roles, we studied body mass and cell size in Galliformes birds and Rodentia mammals, and collected published data on their genome sizes. In birds, we measured erythrocyte nuclei and basal metabolic rates (BMRs). In birds and mammals, larger species consistently evolved larger cells for five cell types (erythrocytes, enterocytes, chondrocytes, skin epithelial cells, and kidney proximal tubule cells) and evolved smaller hepatocytes. We found no evidence that cell size differences originated through genome size changes. We conclude that the organism-wide coordination of cell size changes might be an evolutionarily conservative characteristic, and the convergent evolutionary body size and cell size changes in Galliformes and Rodentia suggest the adaptive significance of cell size. Recent theory predicts that species evolving larger cells waste less energy on tissue maintenance but have reduced capacities to deliver oxygen to mitochondria and metabolize resources. Indeed, birds with larger size of the abovementioned cell types and smaller hepatocytes have evolved lower mass-specific BMRs. We propose that the inconsistent pattern in hepatocytes derives from the efficient delivery system to hepatocytes, combined with their intense involvement in supracellular function and anabolic activity. PMID:29540429

How Create an Astronomy Outreach Program to Bring Astronomy to Thousands of People at Outdoor Concerts Astronomy Festivals, or Tourist Sites

NASA Astrophysics Data System (ADS)

Lubowich, Donald

2015-08-01

I describe how to create an astronomy program for thousands of people at outdoor concerts based on my $308,000 NASA-funded Music and Astronomy Under the Stars (MAUS) program (60 events 2009 - 2013), and the Astronomy Festival on the National Mall (AFNM, 10,000 people/yr).MAUS reached 50,000 music lovers at local parks and at the Central Park Jazz, Newport Folk, Ravinia, or Tanglewood Music Festivals with classical, folk, pop/rock, opera, Caribbean, or county-western concerts assisted by astronomy clubs. Yo-Yo-Ma, the Chicago and Boston Symphony Orchestras, Ravi Coltrane, Esperanza Spalding, Phish, Blood Sweat and Tears, Deep Purple, Tony Orlando, and Wilco performed at these events. AFNM was started in 2010 with co-sponsorship by the White House Office of Science and Technology Policy. MAUS and AFMN combine solar, optical, and radio telescope observations; large posters/banners; hands-on activities, imaging with a cell phone mount; citizen science activities; hand-outs; and teacher info packet. Representatives from scientific institutions participated. Tyco Brahe, Johannes Kepler, and Caroline Herschel made guest appearances.MAUS reached underserved groups and attracted large crowds. Young kids participated in this family learning experience-often the first time they looked through a telescope. While < 50% of the participants took part in a science activity in the past year, they found MAUS enjoyable and understandable; learned about astronomy; wanted to learn more; and increased their interest in science (ave. rating 3.6/4). MAUS is effective in promoting science education!Lessons learned: plan early; create partnerships with parks, concert organizers, and astronomy clubs; test equipment; have backup equipment; create professional displays; select the best location to obtain a largest number of participants; use social media/www sites to promote the events; use many telescopes for multiple targets; project a live image or video; select equipment that is easy to

Cofactors involved in light-driven charge separation in photosystem I identified by subpicosecond infrared spectroscopy.

PubMed

Di Donato, Mariangela; Stahl, Andreas D; van Stokkum, Ivo H M; van Grondelle, Rienk; Groot, Marie-Louise

2011-02-01

Photosystem I is one of the key players in the conversion of solar energy into chemical energy. While the chlorophyll dimer P(700) has long been identified as the primary electron donor, the components involved in the primary charge separation process in PSI remain undetermined. Here, we have studied the charge separation dynamics in Photosystem I trimers from Synechococcus elongatus by femtosecond vis-pump/mid-infrared-probe spectroscopy upon excitation at 700, 710, and 715 nm. Because of the high specificity of the infrared region for the redox state and small differences in the molecular structure of pigments, we were able to clearly identify specific marker bands indicating chlorophyll (Chl) oxidation. Magnitudes of chlorophyll cation signals are observed to increase faster than the time resolution of the experiment (~0.2 ps) upon both excitation conditions: 700 nm and selective red excitation. Two models, involving either ultrafast charge separation or charge transfer character of the red pigments in PSI, are discussed to explain this observation. A further increase in the magnitudes of cation signals on a subpicosecond time scale (0.8-1 ps) indicates the formation of the primary radical pair. Evolution in the cation region with time constants of 7 and 40 ps reveals the formation of the secondary radical pair, involving a secondary electron donor. Modeling of the data allows us to extract the spectra of the two radical pairs, which have IR signatures consistent with A+A₀- and P₇₀₀+A₁-. We conclude that the cofactor chlorophyll A acts as the primary donor in PSI. The existence of an equilibrium between the two radical pairs we interpret as concerted hole/electron transfer between the pairs of electron donors and acceptors, until after 40 ps, relaxation leads to a full population of the P₇₀₀+A₁. radical pair.

Stepwise vs concerted excited state tautomerization of 2-hydroxypyridine: Ammonia dimer wire mediated hydrogen/proton transfer

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

Esboui, Mounir, E-mail: mounir.esboui@fst.rnu.tn; Technical and Vocational Training Corporation, Hail College of Technology, P.O. Box 1960, Hail 81441

The stepwise and concerted excited state intermolecular proton transfer (PT) and hydrogen transfer (HT) reactions in 2-hydroxypyridine-(NH{sub 3}){sub 2} complex in the gas phase under Cs symmetry constraint and without any symmetry constraints were performed using quantum chemical calculations. It shows that upon excitation, the hydrogen bonded in 2HP-(NH{sub 3}){sub 2} cluster facilitates the releasing of both hydrogen and proton transfer reactions along ammonia wire leading to the formation of the 2-pyridone tautomer. For the stepwise mechanism, it has been found that the proton and the hydrogen may transfer consecutively. These processes are distinguished from each other through charge translocationmore » analysis and the coupling between the motion of the proton and the electron density distribution along ammonia wire. For the complex under Cs symmetry, the excited state HT occurs on the A″({sup 1}πσ{sup ∗}) and A′({sup 1}nσ{sup ∗}) states over two accessible energy barriers along reaction coordinates, and excited state PT proceeds mainly through the A′({sup 1}ππ{sup ∗}) and A″({sup 1}nπ{sup ∗}) potential energy surfaces. For the unconstrained complex, potential energy profiles show two {sup 1}ππ{sup ∗}-{sup 1}πσ{sup ∗} conical intersections along enol → keto reaction path indicating that proton and H atom are localized, respectively, on the first and second ammonia of the wire. Moreover, the concerted excited state PT is competitive to take place with the stepwise process, because it proceeds over low barriers of 0.14 eV and 0.11 eV with respect to the Franck-Condon excitation of enol tautomer, respectively, under Cs symmetry and without any symmetry constraints. These barriers can be probably overcome through tunneling effect.« less

Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated.

PubMed

Ivanov, Sergei D; Grant, Ian M; Marx, Dominik

2015-09-28

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

Computational evolution: taking liberties.

PubMed

Correia, Luís

2010-09-01

Evolution has, for a long time, inspired computer scientists to produce computer models mimicking its behavior. Evolutionary algorithm (EA) is one of the areas where this approach has flourished. EAs have been used to model and study evolution, but they have been especially developed for their aptitude as optimization tools for engineering. Developed models are quite simple in comparison with their natural sources of inspiration. However, since EAs run on computers, we have the freedom, especially in optimization models, to test approaches both realistic and outright speculative, from the biological point of view. In this article, we discuss different common evolutionary algorithm models, and then present some alternatives of interest. These include biologically inspired models, such as co-evolution and, in particular, symbiogenetics and outright artificial operators and representations. In each case, the advantages of the modifications to the standard model are identified. The other area of computational evolution, which has allowed us to study basic principles of evolution and ecology dynamics, is the development of artificial life platforms for open-ended evolution of artificial organisms. With these platforms, biologists can test theories by directly manipulating individuals and operators, observing the resulting effects in a realistic way. An overview of the most prominent of such environments is also presented. If instead of artificial platforms we use the real world for evolving artificial life, then we are dealing with evolutionary robotics (ERs). A brief description of this area is presented, analyzing its relations to biology. Finally, we present the conclusions and identify future research avenues in the frontier of computation and biology. Hopefully, this will help to draw the attention of more biologists and computer scientists to the benefits of such interdisciplinary research.

The Evolution of Ribosomal DNA: Divergent Paralogues and Phylogenetic Implications

PubMed Central

Buckler-IV, E. S.; Ippolito, A.; Holtsford, T. P.

1997-01-01

Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies. PMID:9055091

Mainstreaming Caenorhabditis elegans in experimental evolution.

PubMed

Gray, Jeremy C; Cutter, Asher D

2014-03-07

Experimental evolution provides a powerful manipulative tool for probing evolutionary process and mechanism. As this approach to hypothesis testing has taken purchase in biology, so too has the number of experimental systems that use it, each with its own unique strengths and weaknesses. The depth of biological knowledge about Caenorhabditis nematodes, combined with their laboratory tractability, positions them well for exploiting experimental evolution in animal systems to understand deep questions in evolution and ecology, as well as in molecular genetics and systems biology. To date, Caenorhabditis elegans and related species have proved themselves in experimental evolution studies of the process of mutation, host-pathogen coevolution, mating system evolution and life-history theory. Yet these organisms are not broadly recognized for their utility for evolution experiments and remain underexploited. Here, we outline this experimental evolution work undertaken so far in Caenorhabditis, detail simple methodological tricks that can be exploited and identify research areas that are ripe for future discovery.

Large-scale evolution of the central-east Greenland margin: New insights to the North Atlantic glaciation history

NASA Astrophysics Data System (ADS)

Pérez, Lara F.; Nielsen, Tove; Knutz, Paul C.; Kuijpers, Antoon; Damm, Volkmar

2018-04-01

The continental shelf of central-east Greenland is shaped by several glacially carved transverse troughs that form the oceanward extension of the major fjord systems. The evolution of these troughs through time, and their relation with the large-scale glaciation of the Northern Hemisphere, is poorly understood. In this study seismostratigraphic analyses have been carried out to determine the morphological and structural development of this important sector of the East Greenland glaciated margin. The age of major stratigraphic discontinuities has been constrained by a direct tie to ODP site 987 drilled in the Greenland Sea basin plain off Scoresby Sund fan system. The areal distribution and internal facies of the identified seismic units reveal the large-scale depositional pattern formed by ice-streams draining a major part of the central-east Greenland ice sheet. Initial sedimentation along the margin was, however, mainly controlled by tectonic processes related to the margin construction, continental uplift, and fluvial processes. From late Miocene to present, progradational and erosional patterns point to repeated glacial advances across the shelf. The evolution of depo-centres suggests that ice sheet advances over the continental shelf have occurred since late Miocene, about 2 Myr earlier than previously assumed. This cross-shelf glaciation is more pronounced during late Miocene and early Pliocene along Blosseville Kyst and around the Pliocene/Pleistocene boundary off Scoresby Sund; indicating a northward migration of the glacial advance. The two main periods of glaciation were separated by a major retreat of the ice sheet to an inland position during middle Pliocene. Mounded-wavy deposits interpreted as current-related deposits suggest the presence of changing along-slope current dynamics in concert with the development of the modern North Atlantic oceanographic pattern.

Epigenetic silencing of BTB and CNC homology 2 and concerted promoter CpG methylation in gastric cancer.

PubMed

Haam, Keeok; Kim, Hee-Jin; Lee, Kyung-Tae; Kim, Jeong-Hwan; Kim, Mirang; Kim, Seon-Young; Noh, Seung-Moo; Song, Kyu-Sang; Kim, Yong Sung

2014-09-01

BTB and CNC homology 2 (BACH2) is a lymphoid-specific transcription factor with a prominent role in B-cell development. Genetic polymorphisms within a single locus encoding BACH2 are associated with various autoimmune diseases and allergies. In this study, restriction landmark genomic scanning revealed methylation at a NotI site in a CpG island covering the BACH2 promoter in gastric cancer cell lines and primary gastric tumors. Increased methylation of the BACH2 promoter was observed in 52% (43/83) of primary gastric tumors, and BACH2 hypermethylation was significantly associated with decreased gene expression. Treatment with 5-aza-2'-deoxycytidine and/or trichostatin. A restored BACH2 expression in BACH2-silenced gastric cancer cell lines, and knockdown of BACH2 using short hairpin RNA (i.e. RNA interference) increased cell proliferation in gastric cancer cells. Clinicopathologic data showed that decreased BACH2 expression occurred significantly more frequently in intestinal-type (27/44, 61%) compared with diffuse-type (13/50, 26%) gastric cancers (P<0.001). Furthermore, BACH2 promoter methylation paralleled that of previously identified targets, such as LRRC3B, LIMS2, PRKD1 and POPDC3, in a given set of gastric tumors. We propose that concerted methylation in many promoters plays a role in accelerating gastric tumor formation and that methylated promoter loci may be targets for therapeutic treatment, such as the recently introduced technique of epigenetic editing. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Potential drivers of virulence evolution in aquaculture

USGS Publications Warehouse

Kennedy, David A.; Kurath, Gael; Brito, Ilana L.; Purcell, Maureen K.; Read, Andrew F.; Winton, James R.; Wargo, Andrew R.

2016-01-01

Infectious diseases are economically detrimental to aquaculture, and with continued expansion and intensification of aquaculture, the importance of managing infectious diseases will likely increase in the future. Here, we use evolution of virulence theory, along with examples, to identify aquaculture practices that might lead to the evolution of increased pathogen virulence. We identify eight practices common in aquaculture that theory predicts may favor evolution toward higher pathogen virulence. Four are related to intensive aquaculture operations, and four others are related specifically to infectious disease control. Our intention is to make aquaculture managers aware of these risks, such that with increased vigilance, they might be able to detect and prevent the emergence and spread of increasingly troublesome pathogen strains in the future.

Radical Abstraction Reactions with Concerted Fragmentation in the Chain Decay of Nitroalkanes

NASA Astrophysics Data System (ADS)

Denisov, E. T.; Shestakov, A. F.

2018-05-01

Reactions of the type X• + HCR2CH2NO2 → XH + R2C=CH2 + N•O2 are exothermic, due to the breaking of weak C-N bonds and the formation of energy-intensive C=C bonds. Quantum chemistry calculations of the transition state using the reactions of Et• and EtO• with 2-nitrobutane shows that such reactions can be categorized as one-step, due to the extreme instability of the intermediate nitrobutyl radical toward decay with the formation of N•O2. Kinetic parameters that allow us to calculate the energy of activation and rate constant of such a reaction from its enthalpy are estimated using a model of intersecting parabolas. Enthalpies, energies of activation, and rate constants are calculated for a series of reactions with the participation of Et•, EtO•, RO•2, N•O2 radicals on the one hand and a series of nitroalkanes on the other. A new kinetic scheme of the chain decay of nitroalkanes with the participation of abstraction reactions with concerted fragmentation is proposed on the basis of the obtained data.

Student Teachers' Approaches to Teaching Biological Evolution

NASA Astrophysics Data System (ADS)

Borgerding, Lisa A.; Klein, Vanessa A.; Ghosh, Rajlakshmi; Eibel, Albert

2015-06-01

Evolution is fundamental to biology and scientific literacy, but teaching high school evolution is often difficult. Evolution teachers face several challenges including limited content knowledge, personal conflicts with evolution, expectations of resistance, concerns about students' conflicts with religion, and curricular constraints. Evolution teaching can be particularly challenging for student teachers who are just beginning to gain pedagogical knowledge and pedagogical content knowledge related to evolution teaching and who seek approval from university supervisors and cooperating teachers. Science teacher educators need to know how to best support student teachers as they broach the sometimes daunting task of teaching evolution within student teaching placements. This multiple case study report documents how three student teachers approached evolution instruction and what influenced their approaches. Data sources included student teacher interviews, field note observations for 4-5 days of evolution instruction, and evolution instructional artifacts. Data were analyzed using grounded theory approaches to develop individual cases and a cross-case analysis. Seven influences (state exams and standards, cooperating teacher, ideas about teaching and learning, concerns about evolution controversy, personal commitment to evolution, knowledge and preparation for teaching evolution, and own evolution learning experiences) were identified and compared across cases. Implications for science teacher preparation and future research are provided.

First steps in experimental cancer evolution

PubMed Central

Taylor, Tiffany B; Johnson, Louise J; Jackson, Robert W; Brockhurst, Michael A; Dash, Philip R

2013-01-01

Evolutionary processes play a central role in the development, progression and response to treatment of cancers. The current challenge facing researchers is to harness evolutionary theory to further our understanding of the clinical progression of cancers. Central to this endeavour will be the development of experimental systems and approaches by which theories of cancer evolution can be effectively tested. We argue here that the experimental evolution approach – whereby evolution is observed in real time and which has typically employed microorganisms – can be usefully applied to cancer. This approach allows us to disentangle the ecological causes of natural selection, identify the genetic basis of evolutionary changes and determine their repeatability. Cell cultures used in cancer research share many of the desirable traits that make microorganisms ideal for studying evolution. As such, experimental cancer evolution is feasible and likely to give great insight into the selective pressures driving the evolution of clinically destructive cancer traits. We highlight three areas of evolutionary theory with importance to cancer biology that are amenable to experimental evolution: drug resistance, social evolution and resource competition. Understanding the diversity, persistence and evolution of cancers is vital for treatment and drug development, and an experimental evolution approach could provide strategic directions and focus for future research. PMID:23745144

Evolution and Flow.

ERIC Educational Resources Information Center

Csikszentmihalyi, Mihaly

1997-01-01

Presents flow theory in the context of evolution. Defines the elements of "flow" and contends that flow results in an optimal state of inner harmony which improves one's chance for survival. Identifies consequences of flow for creativity, peak performance, talent development, productivity, self-esteem, and stress reduction. Examines the…

Evolution of the cerebellar cortex: the selective expansion of prefrontal-projecting cerebellar lobules.

PubMed

Balsters, J H; Cussans, E; Diedrichsen, J; Phillips, K A; Preuss, T M; Rilling, J K; Ramnani, N

2010-02-01

It has been suggested that interconnected brain areas evolve in tandem because evolutionary pressures act on complete functional systems rather than on individual brain areas. The cerebellar cortex has reciprocal connections with both the prefrontal cortex and motor cortex, forming independent loops with each. Specifically, in capuchin monkeys cerebellar cortical lobules Crus I and Crus II connect with prefrontal cortex, whereas the primary motor cortex connects with cerebellar lobules V, VI, VIIb, and VIIIa. Comparisons of extant primate species suggest that the prefrontal cortex has expanded more than cortical motor areas in human evolution. Given the enlargement of the prefrontal cortex relative to motor cortex in humans, our hypothesis would predict corresponding volumetric increases in the parts of the cerebellum connected to the prefrontal cortex, relative to cerebellar lobules connected to the motor cortex. We tested the hypothesis by comparing the volumes of cerebellar lobules in structural MRI scans in capuchins, chimpanzees and humans. The fractions of cerebellar volume occupied by Crus I and Crus II were significantly larger in humans compared to chimpanzees and capuchins. Our results therefore support the hypothesis that in the cortico-cerebellar system, functionally related structures evolve in concert with each other. The evolutionary expansion of these prefrontal-projecting cerebellar territories might contribute to the evolution of the higher cognitive functions of humans. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Student Acquisition of Biological Evolution-Related Misconceptions: The Role of Public High School Introductory Biology Teachers

ERIC Educational Resources Information Center

Yates, Tony Brett

2011-01-01

In order to eliminate student misconceptions concerning biological evolution, it is important to identify their sources. The purposes of this study were to: (a) identify biological evolution-related misconceptions held by Oklahoma public high school Biology I teachers; (b) identify biological evolution-related misconceptions held by Oklahoma…

Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked Evolution of Human Antibody Repertoires to Fusion and Attachment Glycoproteins

PubMed Central

Fuentes, Sandra; Coyle, Elizabeth M.; Beeler, Judy; Golding, Hana; Khurana, Surender

2016-01-01

Respiratory Syncytial Virus (RSV) is the major cause of pneumonia among infants. Here we elucidated the antibody repertoire following primary RSV infection and traced its evolution through adolescence and adulthood. Whole genome-fragment phage display libraries (GFPDL) expressing linear and conformational epitopes in the RSV fusion protein (F) and attachment protein (G) were used for unbiased epitope profiling of infant sera prior to and following RSV infection. F-GFPDL analyses demonstrated modest changes in the anti-F epitope repertoires post-RSV infection, while G-GFPDL analyses revealed 100-fold increase in number of bound phages. The G-reactive epitopes spanned the N- and C-terminus of the G ectodomain, along with increased reactivity to the central conserved domain (CCD). Panels of F and G antigenic sites were synthesized to evaluate sera from young children (<2 yr), adolescents (14–18 yr) and adults (30–45 yr) in SPR real-time kinetics assays. A steady increase in RSV-F epitope repertoires from young children to adults was observed using peptides and F proteins. Importantly, several novel epitopes were identified in pre-fusion F and an immunodominant epitope in the F-p27. In all age groups, antibody binding to pre-fusion F was 2–3 folds higher than to post-fusion form. For RSV-G, antibody responses were high following early RSV infection in children, but declined significantly in adults, using either G proteins or peptides. This study identified unlinked evolution of anti-F and anti G responses and supportive evidence for immune pressure driven evolution of RSV-G. These findings could help development of effective countermeasures including vaccines. PMID:27100289

Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin

PubMed Central

Hauck, Nastasja C.; Kirpach, Josiane; Kiefer, Christina; Farinelle, Sophie; Morris, Stephen A.; Muller, Claude P.; Lu, I-Na

2018-01-01

To overcome yearly efforts and costs for the production of seasonal influenza vaccines, new approaches for the induction of broadly protective and long-lasting immune responses have been developed in the past decade. To warrant safety and efficacy of the emerging crossreactive vaccine candidates, it is critical to understand the evolution of influenza viruses in response to these new immune pressures. Here we applied unique molecular identifiers in next generation sequencing to analyze the evolution of influenza quasispecies under in vivo antibody pressure targeting the hemagglutinin (HA) long alpha helix (LAH). Our vaccine targeting LAH of hemagglutinin elicited significant seroconversion and protection against homologous and heterologous influenza virus strains in mice. The vaccine not only significantly reduced lung viral titers, but also induced a well-known bottleneck effect by decreasing virus diversity. In contrast to the classical bottleneck effect, here we showed a significant increase in the frequency of viruses with amino acid sequences identical to that of vaccine targeting LAH domain. No escape mutant emerged after vaccination. These results not only support the potential of a universal influenza vaccine targeting the conserved LAH domains, but also clearly demonstrate that the well-established bottleneck effect on viral quasispecies evolution does not necessarily generate escape mutants. PMID:29587397

Identifying Ca2+-Binding Sites in Proteins by Liquid Chromatography-Mass Spectrometry Using Ca2+-Directed Dissociations

PubMed Central

Jamalian, Azadeh; Sneekes, Evert-Jan; Wienk, Hans; Dekker, Lennard J. M.; Ruttink, Paul J. A.; Ursem, Mario; Luider, Theo M.; Burgers, Peter C.

2014-01-01

Here we describe a new method to identify calcium-binding sites in proteins using high-resolution liquid chromatography-mass spectrometry in concert with calcium-directed collision-induced dissociations. Our method does not require any modifications to the liquid chromatography-mass spectrometry apparatus, uses standard digestion protocols, and can be applied to existing high-resolution MS data files. In contrast to NMR, our method is applicable to very small amounts of complex protein mixtures (femtomole level). Calcium-bound peptides can be identified using three criteria: (1) the calculated exact mass of the calcium containing peptide; (2) specific dissociations of the calcium-containing peptide from threonine and serine residues; and (3) the very similar retention times of the calcium-containing peptide and the free peptide. PMID:25023127

On the Theory of Evolution Versus the Concept of Evolution: Three Observations

PubMed Central

Paz-y-Miño C., Guillermo

2016-01-01

Here we address three misconceptions stated by Rice et al. in their observations of our article Paz-y-Miño and Espinosa (Evo Edu Outreach 2:655-675, 2009), published in this journal. The five authors titled their note “The Theory of Evolution is Not an Explanation for the Origin of Life.” First, we argue that it is fallacious to believe that because the formulation of the theory of evolution, as conceived in the 1800s, did not include an explanation for the origin of life, nor of the universe, the concept of evolution would not allow us to hypothesize the possible beginnings of life and its connections to the cosmos. Not only Stanley Miller's experiments of 1953 led scientists to envision a continuum from the inorganic world to the origin and diversification of life, but also Darwin's own writings of 1871. Second, to dismiss the notion of Rice et al. that evolution does not provide explanations concerning the universe or the cosmos, we identify compelling scientific discussions on the topics: Zaikowski et al. (Evo Edu Outreach 1:65–73, 2008), Krauss (Evo Edu Outreach 3:193–197, 2010), Peretó et al. (Orig Life Evol Biosph 39:395–406, 2009) and Follmann and Brownson (Naturwissenschaften 96:1265-1292, 2009). Third, although we acknowledge that the term Darwinism may not be inclusive of all new discoveries in evolution, and also that creationists and Intelligent Designers hijack the term to portray evolution as ideology, we demonstrate that there is no statistical evidence suggesting that the word Darwinism interferes with public acceptance of evolution, nor does the inclusion of the origin of life or the universe within the concept of evolution. We examine the epistemological and empirical distinction between the theory of evolution and the concept of evolution and conclude that, although the distinction is important, it should not compromise scientific logic. PMID:26949441

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life.

PubMed

Wissler, Lothar; Codoñer, Francisco M; Gu, Jenny; Reusch, Thorsten B H; Olsen, Jeanine L; Procaccini, Gabriele; Bornberg-Bauer, Erich

2011-01-12

Seagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs) of two wide-spread and ecologically important seagrass species, the Mediterranean seagrass Posidonia oceanica (L.) Delile and the eelgrass Zostera marina L., which have independently evolved from aquatic ancestors. This replicated, yet independent evolutionary history facilitates the identification of traits that may have evolved in parallel and are possible instrumental candidates for adaptation to a marine habitat. In our study, we provide the first quantitative perspective on molecular adaptations in two seagrass species. By constructing orthologous gene clusters shared between two seagrasses (Z. marina and P. oceanica) and eight distantly related terrestrial angiosperm species, 51 genes could be identified with detection of positive selection along the seagrass branches of the phylogenetic tree. Characterization of these positively selected genes using KEGG pathways and the Gene Ontology uncovered that these genes are mostly involved in translation, metabolism, and photosynthesis. These results provide first insights into which seagrass genes have diverged from their terrestrial counterparts via an initial aquatic stage characteristic of the order and to the derived fully-marine stage characteristic of seagrasses. We discuss how adaptive changes in these processes may have contributed to the evolution towards an aquatic and marine existence.

Time-dependent permeability evolution in compacting volcanic fracture systems and implications for gas overpressure

NASA Astrophysics Data System (ADS)

Farquharson, Jamie I.; Wadsworth, Fabian B.; Heap, Michael J.; Baud, Patrick

2017-06-01

Volcanic eruptions are driven by the ascent of volatile-laden magma. The capacity of a volcano system to outgas these volatiles-its permeability-controls the explosive potential, and fractures at volcanic conduit margins play a crucial role in tempering eruption explosivity by acting as outgassing pathways. However, these fractures are often filled with hot volcanic debris that welds and compacts over time, meaning that these permeable pathways have a finite lifetime. While numerous studies emphasize that permeability evolution is important for regulating pressure in shallow volcanic systems, how and when this occurs remains an outstanding question in volcanology. In this contribution, we show that different pressure evolution regimes can be expected across a range of silicic systems as a function of the width and distribution of fractures in the system, the timescales over which they can outgas (a function of depth and temperature), and the permeability of the host material. We define outgassing, diffusive relaxation, and pressure increase regimes, which are distinguished by comparing the characteristic timescales over which they operate. Moreover, we define a critical permeability threshold, which determines (in concert with characteristic timescales of diffusive mass exchange between the pore and melt phases) whether systems fracture and outgas efficiently, or if a volcano will be prone to pressure increases, incomplete healing, and explosive failure.

Cognition and the evolution of camouflage.

PubMed

Skelhorn, John; Rowe, Candy

2016-02-24

Camouflage is one of the most widespread forms of anti-predator defence and prevents prey individuals from being detected or correctly recognized by would-be predators. Over the past decade, there has been a resurgence of interest in both the evolution of prey camouflage patterns, and in understanding animal cognition in a more ecological context. However, these fields rarely collide, and the role of cognition in the evolution of camouflage is poorly understood. Here, we review what we currently know about the role of both predator and prey cognition in the evolution of prey camouflage, outline why cognition may be an important selective pressure driving the evolution of camouflage and consider how studying the cognitive processes of animals may prove to be a useful tool to study the evolution of camouflage, and vice versa. In doing so, we highlight that we still have a lot to learn about the role of cognition in the evolution of camouflage and identify a number of avenues for future research. © 2016 The Author(s).

Cognition and the evolution of camouflage

PubMed Central

2016-01-01

Camouflage is one of the most widespread forms of anti-predator defence and prevents prey individuals from being detected or correctly recognized by would-be predators. Over the past decade, there has been a resurgence of interest in both the evolution of prey camouflage patterns, and in understanding animal cognition in a more ecological context. However, these fields rarely collide, and the role of cognition in the evolution of camouflage is poorly understood. Here, we review what we currently know about the role of both predator and prey cognition in the evolution of prey camouflage, outline why cognition may be an important selective pressure driving the evolution of camouflage and consider how studying the cognitive processes of animals may prove to be a useful tool to study the evolution of camouflage, and vice versa. In doing so, we highlight that we still have a lot to learn about the role of cognition in the evolution of camouflage and identify a number of avenues for future research. PMID:26911959

Prey-capture Strategies of Fish-hunting Cone Snails: Behavior, Neurobiology and Evolution

PubMed Central

Olivera, Baldomero M.; Seger, Jon; Horvath, Martin P.; Fedosov, Alexander

2015-01-01

The venomous fish-hunting cone snails (Conus) comprise eight distinct lineages evolved from ancestors that preyed on worms. In this article we attempt to reconstruct events resulting in this shift in food resource by closely examining patterns of behavior, biochemical agents (toxins) that facilitate prey capture, and the combinations of toxins present in extant species. The first sections introduce three different hunting behaviors associated with piscivory: “taser and tether”, “net engulfment”, and “strike and stalk”. The first two fish-hunting behaviors are clearly associated with distinct groups of venom components, called cabals, which act in concert to modify the behavior of prey in a specific manner. Derived fish-hunting behavior clearly also correlates with physical features of the radular tooth, the device that injects these biochemical components. Mapping behavior, biochemical components, and radular tooth features onto phylogenetic trees shows that fish-hunting behavior emerged at lease twice during evolution. The system presented here may be one of the best examples where diversity in structure, physiology and molecular features was initially driven by particular pathways selected through behavior. PMID:26397110

Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.

PubMed

Christen, Victor; Hartung, Michael; Groß, Anika

2015-01-01

A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications. Here we present REX (Region Evolution eXplorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an analysis platform for currently about 1,000 versions of 16 well-known life science ontologies. Interactive workflows allow an explorative analysis of changing ontology regions and can be used to study evolution trends for long-term periods. REX is a web application providing an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies. It is available at http://www.izbi.de/rex.

Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

PubMed

Clarke, Thomas H; Garb, Jessica E; Hayashi, Cheryl Y; Arensburger, Peter; Ayoub, Nadia A

2015-06-08

The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Concerted Uranium Research in Europe (CURE): toward a collaborative project integrating dosimetry, epidemiology and radiobiology to study the effects of occupational uranium exposure.

PubMed

Laurent, Olivier; Gomolka, Maria; Haylock, Richard; Blanchardon, Eric; Giussani, Augusto; Atkinson, Will; Baatout, Sarah; Bingham, Derek; Cardis, Elisabeth; Hall, Janet; Tomasek, Ladislav; Ancelet, Sophie; Badie, Christophe; Bethel, Gary; Bertho, Jean-Marc; Bouet, Ségolène; Bull, Richard; Challeton-de Vathaire, Cécile; Cockerill, Rupert; Davesne, Estelle; Ebrahimian, Teni; Engels, Hilde; Gillies, Michael; Grellier, James; Grison, Stephane; Gueguen, Yann; Hornhardt, Sabine; Ibanez, Chrystelle; Kabacik, Sylwia; Kotik, Lukas; Kreuzer, Michaela; Lebacq, Anne Laure; Marsh, James; Nosske, Dietmar; O'Hagan, Jackie; Pernot, Eileen; Puncher, Matthew; Rage, Estelle; Riddell, Tony; Roy, Laurence; Samson, Eric; Souidi, Maamar; Turner, Michelle C; Zhivin, Sergey; Laurier, Dominique

2016-06-01

The potential health impacts of chronic exposures to uranium, as they occur in occupational settings, are not well characterized. Most epidemiological studies have been limited by small sample sizes, and a lack of harmonization of methods used to quantify radiation doses resulting from uranium exposure. Experimental studies have shown that uranium has biological effects, but their implications for human health are not clear. New studies that would combine the strengths of large, well-designed epidemiological datasets with those of state-of-the-art biological methods would help improve the characterization of the biological and health effects of occupational uranium exposure. The aim of the European Commission concerted action CURE (Concerted Uranium Research in Europe) was to develop protocols for such a future collaborative research project, in which dosimetry, epidemiology and biology would be integrated to better characterize the effects of occupational uranium exposure. These protocols were developed from existing European cohorts of workers exposed to uranium together with expertise in epidemiology, biology and dosimetry of CURE partner institutions. The preparatory work of CURE should allow a large scale collaborative project to be launched, in order to better characterize the effects of uranium exposure and more generally of alpha particles and low doses of ionizing radiation.

Pulsed photoacoustic detection of flash-induced oxygen evolution from intact leaves and its oscillations

PubMed Central

Canaani, Ora; Malkin, Shmuel; Mauzerall, David

1988-01-01

Photoacoustic signals from intact leaves, produced upon excitation with single-turnover flashes, were shown to be dependent on their position in the flash sequence. Compared to the signal obtained from the first flash, all the others were time-shifted and had increased amplitudes. The signal from the third flash had the largest deviation, whereas that from the second flash deviated only minimally. The amplitude difference of the signals relative to that from the first flash was measured at a convenient time point (5 ms) and showed oscillations of period 4, similar to the O2-evolution pattern from algae. These oscillations were strongly damped, tending to a steady state from about the seventh flash on. The extra photoacoustic signal (relative to the first flash) was shown to be inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea, heat treatment, or water infiltration. Its change with flash number, its saturation with increasing flash energy, and the above inhibition criteria indicate that it originates in pulsed O2 evolution. The sound wave produced by the first flash, however, arose by a photothermal mechanism only, as shown by its linear dependence on the flash intensity and insensitivity to the above treatments. The above flash pattern demonstrates that the photocycle of the S states (i.e., positive charge accumulation before two water molecules can be oxidized in a concerted way to produce molecular oxygen) occurs in intact leaves. It proves the applicability of the photoacoustic method for mechanistic studies of O2 evolution in leaves under physiological conditions. Water content of leaves is readily measured by this method. Images PMID:16593952

Emerging principles of regulatory evolution.

PubMed

Prud'homme, Benjamin; Gompel, Nicolas; Carroll, Sean B

2007-05-15

Understanding the genetic and molecular mechanisms governing the evolution of morphology is a major challenge in biology. Because most animals share a conserved repertoire of body-building and -patterning genes, morphological diversity appears to evolve primarily through changes in the deployment of these genes during development. The complex expression patterns of developmentally regulated genes are typically controlled by numerous independent cis-regulatory elements (CREs). It has been proposed that morphological evolution relies predominantly on changes in the architecture of gene regulatory networks and in particular on functional changes within CREs. Here, we discuss recent experimental studies that support this hypothesis and reveal some unanticipated features of how regulatory evolution occurs. From this growing body of evidence, we identify three key operating principles underlying regulatory evolution, that is, how regulatory evolution: (i) uses available genetic components in the form of preexisting and active transcription factors and CREs to generate novelty; (ii) minimizes the penalty to overall fitness by introducing discrete changes in gene expression; and (iii) allows interactions to arise among any transcription factor and downstream CRE. These principles endow regulatory evolution with a vast creative potential that accounts for both relatively modest morphological differences among closely related species and more profound anatomical divergences among groups at higher taxonomical levels.

The Evolution of Darwinism.

ERIC Educational Resources Information Center

Stebbins, G. Ledyard; Ayala, Francisco J.

1985-01-01

Recent developments in molecular biology and new interpretations of the fossil record are gradually altering and adding to Charles Darwin's theory, which has been the standard view of the process of evolution for 40 years. Several of these developments and interpretations are identified and discussed. (JN)

The Evolution of Empathy

ERIC Educational Resources Information Center

Hackney, Harold

1978-01-01

Therapeutic empathy has been an often-used construct by counseling professionals. Through that usage, the term has evolved in meaning and significance from its original presentation by Carl Rogers. This article traces that evolution by identifying its users and contributors over the past 20 years. (Author)

Evolution Acceptance and Epistemological Beliefs of College Biology Students

ERIC Educational Resources Information Center

Borgerding, Lisa A.; Deniz, Hasan; Anderson, Elizabeth Shevock

2017-01-01

Evolutionary theory is central to biology, and scientifically accurate evolution instruction is promoted within national and state standards documents. Previous literature has identified students' epistemological beliefs as potential predictors of evolution acceptance. The present work seeks to explore more directly how student views of evolution…

Mapping the evolution of scientific fields.

PubMed

Herrera, Mark; Roberts, David C; Gulbahce, Natali

2010-05-04

Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society Physics and Astronomy Classification Scheme (PACS) numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using a community finding algorithm, and describe the time evolution of these fields over the course of 1985-2006. The communities we identify map to known scientific fields, and their age depends on their size and activity. We expect our approach to quantifying the evolution of ideas to be relevant for making predictions about the future of science and thus help to guide its development.

Biomarkers for Uranium Risk Assessment for the Development of the CURE (Concerted Uranium Research in Europe) Molecular Epidemiological Protocol.

PubMed

Guéguen, Yann; Roy, Laurence; Hornhardt, Sabine; Badie, Christophe; Hall, Janet; Baatout, Sarah; Pernot, Eileen; Tomasek, Ladislav; Laurent, Olivier; Ebrahimian, Teni; Ibanez, Chrystelle; Grison, Stephane; Kabacik, Sylwia; Laurier, Dominique; Gomolka, Maria

2017-01-01

Despite substantial experimental and epidemiological research, there is limited knowledge of the uranium-induce health effects after chronic low-dose exposures in humans. Biological markers can objectively characterize pathological processes or environmental responses to uranium and confounding agents. The integration of such biological markers into a molecular epidemiological study would be a useful approach to improve and refine estimations of uranium-induced health risks. To initiate such a study, Concerted Uranium Research in Europe (CURE) was established, and involves biologists, epidemiologists and dosimetrists. The aims of the biological work package of CURE were: 1. To identify biomarkers and biological specimens relevant to uranium exposure; 2. To define standard operating procedures (SOPs); and 3. To set up a common protocol (logistic, questionnaire, ethical aspects) to perform a large-scale molecular epidemiologic study in uranium-exposed cohorts. An intensive literature review was performed and led to the identification of biomarkers related to: 1. retention organs (lungs, kidneys and bone); 2. other systems/organs with suspected effects (cardiovascular system, central nervous system and lympho-hematopoietic system); 3. target molecules (DNA damage, genomic instability); and 4. high-throughput methods for the identification of new biomarkers. To obtain high-quality biological materials, SOPs were established for the sampling and storage of different biospecimens. A questionnaire was developed to assess potential confounding factors. The proposed strategy can be adapted to other internal exposures and should improve the characterization of the biological and health effects that are relevant for risk assessment.

The Search for 'Evolution-Proof' Antibiotics.

PubMed

Bell, Graham; MacLean, Craig

2018-06-01

The effectiveness of antibiotics has been widely compromised by the evolution of resistance among pathogenic bacteria. It would be restored by the development of antibiotics to which bacteria cannot evolve resistance. We first discuss two kinds of 'evolution-proof' antibiotic. The first comprises literally evolution-proof antibiotics to which bacteria cannot become resistant by mutation or horizontal gene transfer. The second category comprises agents to which resistance may arise, but so rarely that it does not become epidemic. The likelihood that resistance to a novel agent will spread is evaluated here by a simple model that includes biological and therapeutic parameters governing the evolution of resistance within hosts and the transmission of resistant strains between hosts. This model leads to the conclusion that epidemic spread is unlikely if the frequency of mutations that confer resistance falls below a defined minimum value, and it identifies potential targets for intervention to prevent the evolution of resistance. Whether or not evolution-proof antibiotics are ever found, searching for them is likely to improve the deployment of new and existing agents by advancing our understanding of how resistance evolves. Copyright © 2017. Published by Elsevier Ltd.

Phenotypic convergence in bacterial adaptive evolution to ethanol stress.

PubMed

Horinouchi, Takaaki; Suzuki, Shingo; Hirasawa, Takashi; Ono, Naoaki; Yomo, Tetsuya; Shimizu, Hiroshi; Furusawa, Chikara

2015-09-03

Bacterial cells have a remarkable ability to adapt to environmental changes, a phenomenon known as adaptive evolution. During adaptive evolution, phenotype and genotype dynamically changes; however, the relationship between these changes and associated constraints is yet to be fully elucidated. In this study, we analyzed phenotypic and genotypic changes in Escherichia coli cells during adaptive evolution to ethanol stress. Phenotypic changes were quantified by transcriptome and metabolome analyses and were similar among independently evolved ethanol tolerant populations, which indicate the existence of evolutionary constraints in the dynamics of adaptive evolution. Furthermore, the contribution of identified mutations in one of the tolerant strains was evaluated using site-directed mutagenesis. The result demonstrated that the introduction of all identified mutations cannot fully explain the observed tolerance in the tolerant strain. The results demonstrated that the convergence of adaptive phenotypic changes and diverse genotypic changes, which suggested that the phenotype-genotype mapping is complex. The integration of transcriptome and genome data provides a quantitative understanding of evolutionary constraints.

Living in the danger zone: Exposure to predators and the evolution of spines and body armor in mammals.

PubMed

Stankowich, Theodore; Campbell, Lisa A

2016-07-01

Mammals have independently evolved a wide variety of morphological adaptations for use in avoiding death by predation, including spines, quills, dermal plates, and noxious sprays. Although these traits appear to protect their bearer from predatory attack, it is less obvious why some species evolved them and others have not. We investigated the ecological correlates favoring the evolution of specialized defenses in mammals, focusing on conspicuousness to predators due to body size and openness of habitat. We scored species for the degree to which they are protected by spines, quills, dermal plating, and sprays and used phylogenetic comparative analyses to study the morphological and ecological factors that may favor their evolution. We show that medium-sized insectivorous mammals (∼800 g to 9 kg) that live in open habitats are more likely to possess one of these defensive traits to reduce predation. Smaller species (<200 g) and those in closed habitats can typically rely on crypsis to avoid predators, and larger species (>10 kg) are less susceptible to predation by most small- to medium-sized predators. We discuss how diet, metabolic rate, and defensive strategy evolve in concert to allow species to exploit this ecomorphological "danger zone" niche. © 2016 The Author(s).

The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla

PubMed Central

Fontanillas, Eric; Welch, John J; Thomas, Jessica A; Bromham, Lindell

2007-01-01

Background Molecular clock dates, which place the origin of animal phyla deep in the Precambrian, have been used to reject the hypothesis of a rapid evolutionary radiation of animal phyla supported by the fossil record. One possible explanation of the discrepancy is the potential for fast substitution rates early in the metazoan radiation. However, concerted rate variation, occurring simultaneously in multiple lineages, cannot be detected by "clock tests", and so another way to explore such variation is to look for correlated changes between rates and other biological factors. Here we investigate two possible causes of fast early rates: change in average body size or diversification rate of deep metazoan lineages. Results For nine genes for phylogenetically independent comparisons between 50 metazoan phyla, orders, and classes, we find a significant correlation between average body size and rate of molecular evolution of mitochondrial genes. The data also indicate that diversification rate may have a positive effect on rates of mitochondrial molecular evolution. Conclusion If average body sizes were significantly smaller in the early history of the Metazoa, and if rates of diversification were much higher, then it is possible that mitochondrial genes have undergone a slow-down in evolutionary rate, which could affect date estimates made from these genes. PMID:17592650

Visiting the cinema, concerts, museums or art exhibitions as determinant of survival: a Swedish fourteen-year cohort follow-up.

PubMed

Konlaan, B B; Bygren, L O; Johansson, S E

2000-09-01

The aim of this study was to ascertain the possible influence of attending various kinds of cultural events or visiting cultural institutions as a determinant of survival. A cohort of individuals aged 25-74 years from a random sample were interviewed by trained non-medical interviewers in 1982 and 1983. The interviews covered standard-of-living variables. Our independent variables covered visiting cultural institutions and attendance at cultural events, reading books or periodicals, and music making. The non-response rate was about 25%. The cohort was followed with respect to survival for 14 years up to 31st December 1996. The background covariates that were used for control purposes were age, sex, cash buffer, educational standard, long-term disease, smoking, and physical exercise. Our setting was the Swedish survey of living conditions among the adult Swedish population aged 25-74 years. About 10,609 individuals were interviewed in 1982 and 1983. The outcome measure was survival until 31st December 1996. In all, 916 men and 600 women died during this period. We found a higher mortality risk for those people who rarely visited the cinema, concerts, museums, or art exhibitions compared with those visiting them most often. The significant relative risks ranging between RR 1.14 (95% CI. 1.01-1.31) of attending art exhibitions, and RR 1.42 (CI. 1.25-1.60) of attending museums, when adjusting for the nine other variables. Visits to the cinema and concerts gave significant RR in between. We could not discern any beneficial effect of attending the theatre, church service or sports event as a spectator or any effect of reading or music making. Our conclusion is that attendance at certain kinds of cultural events may have a beneficial effect on longevity.

Mapping the Evolution of Scientific Fields

PubMed Central

Herrera, Mark; Roberts, David C.; Gulbahce, Natali

2010-01-01

Despite the apparent cross-disciplinary interactions among scientific fields, a formal description of their evolution is lacking. Here we describe a novel approach to study the dynamics and evolution of scientific fields using a network-based analysis. We build an idea network consisting of American Physical Society Physics and Astronomy Classification Scheme (PACS) numbers as nodes representing scientific concepts. Two PACS numbers are linked if there exist publications that reference them simultaneously. We locate scientific fields using a community finding algorithm, and describe the time evolution of these fields over the course of 1985–2006. The communities we identify map to known scientific fields, and their age depends on their size and activity. We expect our approach to quantifying the evolution of ideas to be relevant for making predictions about the future of science and thus help to guide its development. PMID:20463949

Proton-Coupled Electron Transfer in a Strongly Coupled Photosystem II-Inspired Chromophore–Imidazole–Phenol Complex: Stepwise Oxidation and Concerted Reduction

DOE PAGES

Manbeck, Gerald F.; Fujita, Etsuko; Concepcion, Javier J.

2016-08-18

Proton-coupled electron-transfer (PCET) reactions were studied in acetonitrile for a Photosystem II (PSII) inspired [Ru(bpy) 2(phen-imidazole-Ph(OH)( tBu) 2)] 2+, in which Ru(III) generated by a flash-quench sequence oxidizes the appended phenol and the proton is transferred to the hydrogen bonded imidazole base. In contrast to related systems, the donor and acceptor are strongly coupled, as indicated by the shift in the Ru III/IIcouple upon phenol oxidation, and intramolecular oxidation of the phenol by Ru(III) is energetically favorable by both stepwise or concerted pathways. The phenol oxidation occurs via a stepwise ET-PT mechanism with k ET = 2.7 × 10 7more » s ₋1 and a kinetic isotope effect (KIE) of 0.99 ± 0.03. The electron transfer reaction was characterized as adiabatic with λ DA = 1.16 eV and 280 < H DA < 540 cm ₋1 consistent with strong electronic coupling and slow solvent dynamics. Reduction of the phenoxyl radical by the quencher radical was examined as the analogue of the redox reaction between the PSII tyrosyl radical and the oxygen evolving complex (OEC). In our PSII-inspired complex, the recombination reaction activation energy is < 2 kcal mol ₋1. In conclusion, the reaction is nonadiabatic (V PCET ~ 22 cm ₋1 (H) and 49 cm ₋1 (D)), concerted, and exhibits an unexpected inverse KIE of 0.55 that is attributed to greater overlap of the reactant vibronic ground state with the OD vibronic states of the proton acceptor due to the smaller quantum spacing of the deuterium vibrational levels.« less

Hamiltonian identifiability assisted by single-probe measurement

NASA Astrophysics Data System (ADS)

Sone, Akira; Cappellaro, Paola; Quantum Engineering Group Team

2017-04-01

We study the Hamiltonian identifiability of a many-body spin- 1 / 2 system assisted by the measurement on a single quantum probe based on the eigensystem realization algorithm (ERA) approach employed in. We demonstrate a potential application of Gröbner basis to the identifiability test of the Hamiltonian, and provide the necessary experimental resources, such as the lower bound in the number of the required sampling points, the upper bound in total required evolution time, and thus the total measurement time. Focusing on the examples of the identifiability in the spin chain model with nearest-neighbor interaction, we classify the spin-chain Hamiltonian based on its identifiability, and provide the control protocols to engineer the non-identifiable Hamiltonian to be an identifiable Hamiltonian.

POEM: Identifying Joint Additive Effects on Regulatory Circuits.

PubMed

Botzman, Maya; Nachshon, Aharon; Brodt, Avital; Gat-Viks, Irit

2016-01-01

Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress toward a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such "modularization" approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects. Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs. The software described in this article is available at csgi.tau.ac.il/POEM/.

Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

PubMed

Shem-Ad, Tzilhav; Irit, Orr; Yifrach, Ofer

2013-01-01

The tight electro-mechanical coupling between the voltage-sensing and pore domains of Kv channels lies at the heart of their fundamental roles in electrical signaling. Structural data have identified two voltage sensor pore inter-domain interaction surfaces, thus providing a framework to explain the molecular basis for the tight coupling of these domains. While the contribution of the intra-subunit lower domain interface to the electro-mechanical coupling that underlies channel opening is relatively well understood, the contribution of the inter-subunit upper interface to channel gating is not yet clear. Relying on energy perturbation and thermodynamic coupling analyses of tandem-dimeric Shaker Kv channels, we show that mutation of upper interface residues from both sides of the voltage sensor-pore domain interface stabilizes the closed channel state. These mutations, however, do not affect slow inactivation gating. We, moreover, find that upper interface residues form a network of state-dependent interactions that stabilize the open channel state. Finally, we note that the observed residue interaction network does not change during slow inactivation gating. The upper voltage sensing-pore interaction surface thus only undergoes conformational rearrangements during channel activation gating. We suggest that inter-subunit interactions across the upper domain interface mediate allosteric communication between channel subunits that contributes to the concerted nature of the late pore opening transition of Kv channels.

Concerted action of two dlx paralogs in sensory placode formation.

PubMed

Solomon, Keely S; Fritz, Andreas

2002-07-01

Sensory placodes are ectodermal thickenings that give rise to elements of the vertebrate cranial sensory nervous system, including the inner ear and nose. Although mutations have been described in humans, mice and zebrafish that perturb ear and nose development, no mutation is known to prevent sensory placode formation. Thus, it has been postulated that a functional redundancy exists in the genetic mechanisms that govern sensory placode development. We describe a zebrafish deletion mutation, b380, which results in a lack of both otic and olfactory placodes. The b380 deletion removes several known genes and expressed sequence tags, including dlx3 and dlx7, two transcription factors that share a homoeobox domain similar in sequence to the Drosophila Distal-less gene. dlx3 and dlx7 are expressed in an overlapping pattern in the regions that produce the otic and olfactory placodes in zebrafish. We present evidence suggesting that it is specifically the removal of these two genes that leads to the otic and olfactory phenotype of b380 mutants. Using morpholinos, antisense oligonucleotides that effectively block translation of target genes, we find that functional reduction of both dlx genes contributes to placode loss. Expression patterns of the otic marker pax2.1, olfactory marker anxV and eya1, a marker of both placodes, in morpholino-injected embryos recapitulate the reduced expression of these genes seen in b380 mutants. We also examine expression of dlx3 and dlx7 in the morpholino-injected embryos and present evidence for existence of auto- and cross-regulatory control of expression among these genes. We demonstrate that dlx3 is necessary and sufficient for proper otic and olfactory placode development. However, our results indicate that dlx3 and dlx7 act in concert and their importance in placode formation is only revealed by inactivating both paralogs.

Restless 5S: the re-arrangement(s) and evolution of the nuclear ribosomal DNA in land plants.

PubMed

Wicke, Susann; Costa, Andrea; Muñoz, Jesùs; Quandt, Dietmar

2011-11-01

Among eukaryotes two types of nuclear ribosomal DNA (nrDNA) organization have been observed. Either all components, i.e. the small ribosomal subunit, 5.8S, large ribosomal subunit, and 5S occur tandemly arranged or the 5S rDNA forms a separate cluster of its own. Generalizations based on data derived from just a few model organisms have led to a superimposition of structural and evolutionary traits to the entire plant kingdom asserting that plants generally possess separate arrays. This study reveals that plant nrDNA organization into separate arrays is not a distinctive feature, but rather assignable almost solely to seed plants. We show that early diverging land plants and presumably streptophyte algae share a co-localization of all rRNA genes within one repeat unit. This raises the possibility that the state of rDNA gene co-localization had occurred in their common ancestor. Separate rDNA arrays were identified for all basal seed plants and water ferns, implying at least two independent 5S rDNA transposition events during land plant evolution. Screening for 5S derived Cassandra transposable elements which might have played a role during the transposition events, indicated that this retrotransposon is absent in early diverging vascular plants including early fern lineages. Thus, Cassandra can be rejected as a primary mechanism for 5S rDNA transposition in water ferns. However, the evolution of Cassandra and other eukaryotic 5S derived elements might have been a side effect of the 5S rDNA cluster formation. Structural analysis of the intergenic spacers of the ribosomal clusters revealed that transposition events partially affect spacer regions and suggests a slightly different transcription regulation of 5S rDNA in early land plants. 5S rDNA upstream regulatory elements are highly divergent or absent from the LSU-5S spacers of most early divergent land plant lineages. Several putative scenarios and mechanisms involved in the concerted relocation of hundreds of 5S

Closed-Loop Control Better than Open-Loop Control of Profofol TCI Guided by BIS: A Randomized, Controlled, Multicenter Clinical Trial to Evaluate the CONCERT-CL Closed-Loop System

PubMed Central

Zhang, Xuena; Wu, Anshi; Yao, Shanglong; Xue, Zhanggang; Yue, Yun

2015-01-01

Background The CONCERT-CL closed-loop infusion system designed by VERYARK Technology Co., Ltd. (Guangxi, China) is an innovation using TCI combined with closed-loop controlled intravenous anesthesia under the guide of BIS. In this study we performed a randomized, controlled, multicenter study to compare closed-loop control and open-loop control of propofol by using the CONCERT-CL closed-loop infusion system. Methods 180 surgical patients from three medical centers undergone TCI intravenous anesthesia with propofol and remifentanil were randomly assigned to propofol closed-loop group and propofol opened-loop groups. Primary outcome was global score (GS, GS = (MDAPE+Wobble)/% of time of bispectral index (BIS) 40-60). Secondary outcomes were doses of the anesthetics and emergence time from anesthesia, such as, time to tracheal extubation. Results There were 89 and 86 patients in the closed-loop and opened-loop groups, respectively. GS in the closed-loop groups (22.21±8.50) were lower than that in the opened-loop group (27.19±15.26) (p=0.009). The higher proportion of time of BIS between 40 and 60 was also observed in the closed-loop group (84.11±9.50%), while that was 79.92±13.17% in the opened-loop group, (p=0.016). No significant differences in propofol dose and time of tracheal extubation were observed. The frequency of propofol regulation in the closed-loop group (31.55±9.46 times/hr) was obverse higher than that in the opened-loop group (6.84±6.21 times/hr) (p=0.000). Conclusion The CONCERT-CL closed-loop infusion system can automatically regulate the TCI of propofol, maintain the BIS value in an adequate range and reduce the workload of anesthesiologists better than open-loop system. Trial Registration ChiCTR ChiCTR-OOR-14005551 PMID:25886041

Evolution of the “Drivers” of Translational Cancer Epidemiology: Analysis of Funded Grants and the Literature

PubMed Central

Lam, Tram Kim; Chang, Christine Q.; Rogers, Scott D.; Khoury, Muin J.; Schully, Sheri D.

2015-01-01

Concurrently with a workshop sponsored by the National Cancer Institute, we identified key “drivers” for accelerating cancer epidemiology across the translational research continuum in the 21st century: emerging technologies, a multilevel approach, knowledge integration, and team science. To map the evolution of these “drivers” and translational phases (T0–T4) in the past decade, we analyzed cancer epidemiology grants funded by the National Cancer Institute and published literature for 2000, 2005, and 2010. For each year, we evaluated the aims of all new/competing grants and abstracts of randomly selected PubMed articles. Compared with grants based on a single institution, consortium-based grants were more likely to incorporate contemporary technologies (P = 0.012), engage in multilevel analyses (P = 0.010), and incorporate elements of knowledge integration (P = 0.036). Approximately 74% of analyzed grants and publications involved discovery (T0) or characterization (T1) research, suggesting a need for more translational (T2–T4) research. Our evaluation indicated limited research in 1) a multilevel approach that incorporates molecular, individual, social, and environmental determinants and 2) knowledge integration that evaluates the robustness of scientific evidence. Cancer epidemiology is at the cusp of a paradigm shift, and the field will need to accelerate the pace of translating scientific discoveries in order to impart population health benefits. While multi-institutional and technology-driven collaboration is happening, concerted efforts to incorporate other key elements are warranted for the discipline to meet future challenges. PMID:25767265

Concerted electron-proton transfer in the optical excitation of hydrogen-bonded dyes.

PubMed

Westlake, Brittany C; Brennaman, M Kyle; Concepcion, Javier J; Paul, Jared J; Bettis, Stephanie E; Hampton, Shaun D; Miller, Stephen A; Lebedeva, Natalia V; Forbes, Malcolm D E; Moran, Andrew M; Meyer, Thomas J; Papanikolas, John M

2011-05-24

The simultaneous, concerted transfer of electrons and protons--electron-proton transfer (EPT)--is an important mechanism utilized in chemistry and biology to avoid high energy intermediates. There are many examples of thermally activated EPT in ground-state reactions and in excited states following photoexcitation and thermal relaxation. Here we report application of ultrafast excitation with absorption and Raman monitoring to detect a photochemically driven EPT process (photo-EPT). In this process, both electrons and protons are transferred during the absorption of a photon. Photo-EPT is induced by intramolecular charge-transfer (ICT) excitation of hydrogen-bonded-base adducts with either a coumarin dye or 4-nitro-4'-biphenylphenol. Femtosecond transient absorption spectral measurements following ICT excitation reveal the appearance of two spectroscopically distinct states having different dynamical signatures. One of these states corresponds to a conventional ICT excited state in which the transferring H(+) is initially associated with the proton donor. Proton transfer to the base (B) then occurs on the picosecond time scale. The other state is an ICT-EPT photoproduct. Upon excitation it forms initially in the nuclear configuration of the ground state by application of the Franck-Condon principle. However, due to the change in electronic configuration induced by the transition, excitation is accompanied by proton transfer with the protonated base formed with a highly elongated (+)H ─ B bond. Coherent Raman spectroscopy confirms the presence of a vibrational mode corresponding to the protonated base in the optically prepared state.

DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus.

PubMed

Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R; Stefanović, Saša; Dickinson, Timothy A

2015-04-28

DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication

DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus

PubMed Central

Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R.; Stefanović, Saša; Dickinson, Timothy A.

2015-01-01

DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication

Understanding and protecting the world's biodiversity: the role and legacy of the SCAR programme "Evolution and Biodiversity in the Antarctic".

PubMed

di Prisco, Guido; Convey, Peter; Gutt, Julian; Cowan, Don; Conlan, Kathleen; Verde, Cinzia

2012-12-01

Current global changes are prompting scientists and governments to consider the risk of extinction of species inhabiting environments influenced by ice. Concerted, multidisciplinary, international programmes aimed at understanding life processes, evolution and adaptations in the Polar Regions will help to counteract such an event by protecting polar life and ecosystems. There is a long tradition of international scientific cooperation in Antarctica that provides a strong foundation for such approaches. While basic understanding is emerging, we still largely lack predictive biological models, and need to achieve further integration amongst biological and non-biological disciplines. The ongoing SCAR Science Research Programme, "Evolution and Biodiversity in the Antarctic (EBA)" has successfully carried out its crucial role of providing an overarching umbrella for SCAR research in Life Sciences. Now is the time for aiming to progress beyond this important role, and the Antarctic biology community is proposing two programmes, focussed on distinct but complementary aspects of polar biology and working across marine, freshwater and terrestrial environments: "State of the Antarctic Ecosystem (AntEco)", and "Antarctic Thresholds--Ecosystem Resilience and Adaptation (AnT-ERA)". These programmes are the legacy of EBA, and they are key to understanding and protect Antarctic biodiversity. Copyright © 2012 Elsevier B.V. All rights reserved.

The skull roof tracks the brain during the evolution and development of reptiles including birds.

PubMed

Fabbri, Matteo; Mongiardino Koch, Nicolás; Pritchard, Adam C; Hanson, Michael; Hoffman, Eva; Bever, Gabriel S; Balanoff, Amy M; Morris, Zachary S; Field, Daniel J; Camacho, Jasmin; Rowe, Timothy B; Norell, Mark A; Smith, Roger M; Abzhanov, Arhat; Bhullar, Bhart-Anjan S

2017-10-01

Major transformations in brain size and proportions, such as the enlargement of the brain during the evolution of birds, are accompanied by profound modifications to the skull roof. However, the hypothesis of concerted evolution of shape between brain and skull roof over major phylogenetic transitions, and in particular of an ontogenetic relationship between specific regions of the brain and the skull roof, has never been formally tested. We performed 3D morphometric analyses to examine the deep history of brain and skull-roof morphology in Reptilia, focusing on changes during the well-documented transition from early reptiles through archosauromorphs, including nonavian dinosaurs, to birds. Non-avialan taxa cluster tightly together in morphospace, whereas Archaeopteryx and crown birds occupy a separate region. There is a one-to-one correspondence between the forebrain and frontal bone and the midbrain and parietal bone. Furthermore, the position of the forebrain-midbrain boundary correlates significantly with the position of the frontoparietal suture across the phylogenetic breadth of Reptilia and during the ontogeny of individual taxa. Conservation of position and identity in the skull roof is apparent, and there is no support for previous hypotheses that the avian parietal is a transformed postparietal. The correlation and apparent developmental link between regions of the brain and bony skull elements are likely to be ancestral to Tetrapoda and may be fundamental to all of Osteichthyes, coeval with the origin of the dermatocranium.

Concerted spatial-frequency and polarization-phase filtering of laser images of polycrystalline networks of blood plasma smears

NASA Astrophysics Data System (ADS)

Ushenko, Yu A.

2012-11-01

The complex technique of concerted polarization-phase and spatial-frequency filtering of blood plasma laser images is suggested. The possibility of obtaining the coordinate distributions of phases of linearly and circularly birefringent protein networks of blood plasma separately is presented. The statistical (moments of the first to fourth orders) and scale self-similar (logarithmic dependences of power spectra) structure of phase maps of different types of birefringence of blood plasma of two groups of patients-healthy people (donors) and those suffering from rectal cancer-is investigated. The diagnostically sensitive parameters of a pathological change of the birefringence of blood plasma polycrystalline networks are determined. The effectiveness of this technique for detecting change in birefringence in the smears of other biological fluids in diagnosing the appearance of cholelithiasis (bile), operative differentiation of the acute and gangrenous appendicitis (exudate), and differentiation of inflammatory diseases of joints (synovial fluid) is shown.

Phenotypic integration and the evolution of signal repertoires: A case study of treefrog acoustic communication.

PubMed

Reichert, Michael S; Höbel, Gerlinde

2018-03-01

Animal signals are inherently complex phenotypes with many interacting parts combining to elicit responses from receivers. The pattern of interrelationships between signal components reflects the extent to which each component is expressed, and responds to selection, either in concert with or independently of others. Furthermore, many species have complex repertoires consisting of multiple signal types used in different contexts, and common morphological and physiological constraints may result in interrelationships extending across the multiple signals in species' repertoires. The evolutionary significance of interrelationships between signal traits can be explored within the framework of phenotypic integration, which offers a suite of quantitative techniques to characterize complex phenotypes. In particular, these techniques allow for the assessment of modularity and integration, which describe, respectively, the extent to which sets of traits covary either independently or jointly. Although signal and repertoire complexity are thought to be major drivers of diversification and social evolution, few studies have explicitly measured the phenotypic integration of signals to investigate the evolution of diverse communication systems. We applied methods from phenotypic integration studies to quantify integration in the two primary vocalization types (advertisement and aggressive calls) in the treefrogs Hyla versicolor , Hyla cinerea, and Dendropsophus ebraccatus . We recorded male calls and calculated standardized phenotypic variance-covariance ( P ) matrices for characteristics within and across call types. We found significant integration across call types, but the strength of integration varied by species and corresponded with the acoustic similarity of the call types within each species. H. versicolor had the most modular advertisement and aggressive calls and the least acoustically similar call types. Additionally, P was robust to changing social competition

Maximal Predictability Approach for Identifying the Right Descriptors for Electrocatalytic Reactions.

PubMed

Krishnamurthy, Dilip; Sumaria, Vaidish; Viswanathan, Venkatasubramanian

2018-02-01

Density functional theory (DFT) calculations are being routinely used to identify new material candidates that approach activity near fundamental limits imposed by thermodynamics or scaling relations. DFT calculations are associated with inherent uncertainty, which limits the ability to delineate materials (distinguishability) that possess high activity. Development of error-estimation capabilities in DFT has enabled uncertainty propagation through activity-prediction models. In this work, we demonstrate an approach to propagating uncertainty through thermodynamic activity models leading to a probability distribution of the computed activity and thereby its expectation value. A new metric, prediction efficiency, is defined, which provides a quantitative measure of the ability to distinguish activity of materials and can be used to identify the optimal descriptor(s) ΔG opt . We demonstrate the framework for four important electrochemical reactions: hydrogen evolution, chlorine evolution, oxygen reduction and oxygen evolution. Future studies could utilize expected activity and prediction efficiency to significantly improve the prediction accuracy of highly active material candidates.

Mapping sound intensities by seating position in a university concert band: A risk of hearing loss, temporary threshold shifts, and comparisons with standards of OSHA and NIOSH

NASA Astrophysics Data System (ADS)

Holland, Nicholas Vedder, III

Exposure to loud sounds is one of the leading causes of hearing loss in the United States. The purpose of the current research was to measure the sound pressure levels generated within a university concert band and determine if those levels exceeded permissible sound limits for exposure according to criteria set by the Occupational Safety and Health Administration (OSHA) and the National Institute of Occupational Safety and Health (NIOSH). Time-weighted averages (TWA) were obtained via a dosimeter during six rehearsals for nine members of the ensemble (plus the conductor), who were seated in frontal proximity to "instruments of power" (trumpets, trombones, and percussion; (Backus, 1977). Subjects received audiometer tests prior to and after each rehearsal to determine any temporary threshold shifts (TTS). Single sample t tests were calculated to compare TWA means and the maximum sound intensity exposures set by OSHA and NIOSH. Correlations were calculated between TWAs and TTSs, as well as TTSs and the number of semesters subjects reported being seated in proximity to instruments of power. The TWA-OSHA mean of 90.2 dBA was not significantly greater than the specified OSHA maximum standard of 90.0 dBA (p > .05). The TWA-NIOSH mean of 93.1 dBA was, however, significantly greater than the NIOSH specified maximum standard of 85.0 dBA (p < .05). The correlation between TWAs and TTSs was considered weak (r = .21 for OSHA, r = .20 for NIOSH); the correlation between TTSs and semesters of proximity to instruments of power was also considered weak (r = .13). TWAs cumulatively exceeded both association's sound exposure limits at 11 specified locations (nine subjects and both ears of the conductor) throughout the concert band's rehearsals. In addition, hearing acuity, as determined by TTSs, was substantially affected negatively by the intensities produced in the concert band. The researcher concluded that conductors, as well as their performers, must be aware of possible

Concerted action of zinc and ProSAP/Shank in synaptogenesis and synapse maturation

PubMed Central

Grabrucker, Andreas M; Knight, Mary J; Proepper, Christian; Bockmann, Juergen; Joubert, Marisa; Rowan, Magali; Nienhaus, G UIrich; Garner, Craig C; Bowie, Jim U; Kreutz, Michael R; Gundelfinger, Eckart D; Boeckers, Tobias M

2011-01-01

Neuronal morphology and number of synapses is not static, but can change in response to a variety of factors, a process called synaptic plasticity. These structural and molecular changes are believed to represent the basis for learning and memory, thereby underling both the developmental and activity-dependent remodelling of excitatory synapses. Here, we report that Zn2+ ions, which are highly enriched within the postsynaptic density (PSD), are able to influence the recruitment of ProSAP/Shank proteins to PSDs in a family member-specific manner during the course of synaptogenesis and synapse maturation. Through selectively overexpressing each family member at excitatory postsynapses and comparing this to shRNA-mediated knockdown, we could demonstrate that only the overexpression of zinc-sensitive ProSAP1/Shank2 or ProSAP2/Shank3 leads to increased synapse density, although all of them cause a decrease upon knockdown. Furthermore, depletion of synaptic Zn2+ along with the knockdown of zinc-insensitive Shank1 causes the rapid disintegration of PSDs and the loss of several postsynaptic molecules including Homer1, PSD-95 and NMDA receptors. These findings lead to the model that the concerted action of ProSAP/Shank and Zn2+ is essential for the structural integrity of PSDs and moreover that it is an important element of synapse formation, maturation and structural plasticity. PMID:21217644

Isolation and characterization of major histocompatibility complex class II B genes in cranes.

PubMed

Kohyama, Tetsuo I; Akiyama, Takuya; Nishida, Chizuko; Takami, Kazutoshi; Onuma, Manabu; Momose, Kunikazu; Masuda, Ryuichi

2015-11-01

In this study, we isolated and characterized the major histocompatibility complex (MHC) class II B genes in cranes. Genomic sequences spanning exons 1 to 4 were amplified and determined in 13 crane species and three other species closely related to cranes. In all, 55 unique sequences were identified, and at least two polymorphic MHC class II B loci were found in most species. An analysis of sequence polymorphisms showed the signature of positive selection and recombination. A phylogenetic reconstruction based on exon 2 sequences indicated that trans-species polymorphism has persisted for at least 10 million years, whereas phylogenetic analyses of the sequences flanking exon 2 revealed a pattern of concerted evolution. These results suggest that both balancing selection and recombination play important roles in the crane MHC evolution.

Biological information systems: Evolution as cognition-based information management.

PubMed

Miller, William B

2018-05-01

An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses. Copyright © 2017 Elsevier Ltd. All rights reserved.

POEM: Identifying Joint Additive Effects on Regulatory Circuits

PubMed Central

Botzman, Maya; Nachshon, Aharon; Brodt, Avital; Gat-Viks, Irit

2016-01-01

Motivation: Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress toward a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such “modularization” approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects. Results: Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs. Availability: The software described in this article is available at csgi.tau.ac.il/POEM/. PMID:27148351

Empirical fitness landscapes and the predictability of evolution.

PubMed

de Visser, J Arjan G M; Krug, Joachim

2014-07-01

The genotype-fitness map (that is, the fitness landscape) is a key determinant of evolution, yet it has mostly been used as a superficial metaphor because we know little about its structure. This is now changing, as real fitness landscapes are being analysed by constructing genotypes with all possible combinations of small sets of mutations observed in phylogenies or in evolution experiments. In turn, these first glimpses of empirical fitness landscapes inspire theoretical analyses of the predictability of evolution. Here, we review these recent empirical and theoretical developments, identify methodological issues and organizing principles, and discuss possibilities to develop more realistic fitness landscape models.

Evolution of vertebrate mechanosensory hair cells and inner ears: toward identifying stimuli that select mutation driven altered morphologies

PubMed Central

Fritzsch, Bernd; Straka, Hans

2014-01-01

Among the major distance senses of vertebrates, the ear is unique in its complex morphological changes during evolution. Conceivably, these changes enable the ear to adapt toward sensing various physically well-characterized stimuli. This review develops a scenario that integrates sensory cell with organ evolution. We propose that molecular and cellular evolution of the vertebrate hair cells occurred prior to the formation of the vertebrate ear. We previously proposed that the genes driving hair cell differentiation, were aggregated in the otic region through developmental re-patterning that generated a unique vertebrate embryonic structure, the otic placode. In agreement with the presence of graviceptive receptors in many vertebrate outgroups, it is likely that the vertebrate ear originally functioned as a simple gravity-sensing organ. Based on the rare occurrence of angular acceleration receptors in vertebrate outgroups, we further propose that the canal system evolved with a more sophisticated ear morphogenesis. This evolving morphogenesis obviously turned the initial otocyst into a complex set of canals and recesses, harboring multiple sensory epithelia each adapted to the acquisition of a specific aspect of a given physical stimulus. As support for this evolutionary progression, we provide several details of the molecular basis of ear development. PMID:24281353

The Effects of Predator Evolution and Genetic Variation on Predator-Prey Population-Level Dynamics.

PubMed

Cortez, Michael H; Patel, Swati

2017-07-01

This paper explores how predator evolution and the magnitude of predator genetic variation alter the population-level dynamics of predator-prey systems. We do this by analyzing a general eco-evolutionary predator-prey model using four methods: Method 1 identifies how eco-evolutionary feedbacks alter system stability in the fast and slow evolution limits; Method 2 identifies how the amount of standing predator genetic variation alters system stability; Method 3 identifies how the phase lags in predator-prey cycles depend on the amount of genetic variation; and Method 4 determines conditions for different cycle shapes in the fast and slow evolution limits using geometric singular perturbation theory. With these four methods, we identify the conditions under which predator evolution alters system stability and shapes of predator-prey cycles, and how those effect depend on the amount of genetic variation in the predator population. We discuss the advantages and disadvantages of each method and the relations between the four methods. This work shows how the four methods can be used in tandem to make general predictions about eco-evolutionary dynamics and feedbacks.

Robotic technology evolution and transfer

NASA Technical Reports Server (NTRS)

Marzwell, Neville I.

1992-01-01

A report concerning technology transfer in the area of robotics is presented in vugraph form. The following topics are discussed: definition of technology innovation and tech-transfer; concepts relevant for understanding tech-transfer; models advanced to portray tech-transfer process; factors identified as promoting tech-transfer; factors identified as impeding tech-transfer; what important roles do individuals fulfill in tech-transfer; federal infrastructure for promoting tech-transfer; federal infrastructure for promoting tech-transfer; robotic technology evolution; robotic technology transferred; and recommendations for successful robotics tech-transfer.

Experimental evolution of protein–protein interaction networks

PubMed Central

Kaçar, Betül; Gaucher, Eric A.

2013-01-01

The modern synthesis of evolutionary theory and genetics has enabled us to discover underlying molecular mechanisms of organismal evolution. We know that in order to maximize an organism's fitness in a particular environment, individual interactions among components of protein and nucleic acid networks need to be optimized by natural selection, or sometimes through random processes, as the organism responds to changes and/or challenges in the environment. Despite the significant role of molecular networks in determining an organism's adaptation to its environment, we still do not know how such inter- and intra-molecular interactions within networks change over time and contribute to an organism's evolvability while maintaining overall network functions. One way to address this challenge is to identify connections between molecular networks and their host organisms, to manipulate these connections, and then attempt to understand how such perturbations influence molecular dynamics of the network and thus influence evolutionary paths and organismal fitness. In the present review, we discuss how integrating evolutionary history with experimental systems that combine tools drawn from molecular evolution, synthetic biology and biochemistry allow us to identify the underlying mechanisms of organismal evolution, particularly from the perspective of protein interaction networks. PMID:23849056

Evolution of ionospheric convection and ULFs during the 27 March 2017 storm: ERG-SuperDARN campaign

NASA Astrophysics Data System (ADS)

Hori, T.; Nishitani, N.; Shepherd, S. G.; Ruohoniemi, J. M.; Connors, M. G.; Teramoto, M.; Nakano, S.; Seki, K.; Takahashi, N.; Kasahara, S.; Yokota, S.; Mitani, T.; Takashima, T.; Higashio, N.; Matsuoka, A.; Asamura, K.; Kazama, Y.; Wang, S. Y.; Tam, S. W. Y.; Miyoshi, Y.; Shinohara, I.

2017-12-01

The Exploration of energization and Radiation in Geospace (ERG) satellite, which was nicknamed "Arase" after its launch on late December, 2016, has successfully started regular observations recently. In concert with in situ measurement made by Arase in the inner magnetosphere, campaign observations with SuperDARN radars have been conducted with a special scan mode "interleaved_normalscan" since March, 2017. Some of the radars being operated in the special mode observed the dynamic evolution of ionospheric convection including superimposed ULF-like convection fluctuations with frequencies of mHz over the North American sector during a moderate magnetic storm on March 27, 2017. The large-scale evolution provided by the radar observations in the early morning sector shows that the ionospheric convection changed direction between westward and eastward several times in the course of the storm main phase. Some meso-scale patchy structures seen on 2-D profiles of the line-of-sight (LOS) velocity propagated both westward and eastward just after a major substorm intensification. Interestingly, the velocity fluctuations were accompanied by a drifting energetic electron population as observed by particle instruments onboard Arase. A simulation of the inner magnetosphere coupled with a global MHD simulation for this event reproduces intense particle injections in the premidnight sector, consistent with the energy dispersion of the observed drifting population. A detailed interpretation of the observations including those captured by Arase is discussed and compared with the simulation results.

Concerted growth and ordering of cobalt nanorod arrays as revealed by tandem in situ SAXS-XAS studies

DOE PAGES

Cormary, Benoit; Li, Tao; Liakakos, Nikos; ...

2016-06-14

The molecular and ensemble dynamics for the growth of hierarchical supercrystals of cobalt nanorods have been studied by in situ tandem X-ray Absorption Spectroscopy – Small Angle X-ray Scattering (XAS - SAXS). The super-crystals were obtained by reducing a Co(II) precursor under H 2 in the presence of a long chain amine and a long chain carboxylic acid. Complementary time-dependent ex situ TEM studies were also performed. The experimental data provide critical insights into the nanorod growth mechanism, and unequivocal evidence for a concerted growth-organization process. Nanorod formation involves cobalt nucleation, a fast atom by atom anisotropic growth and amore » slower oriented attach-ment process that continues well after cobalt reduction is complete. As a result, smectic-like ordering of the nanorods appears very early in the process, as soon as nanoparticle elongation appears, and nanorod growth takes place inside organized super-lattices, which can be regarded as mesocrystals.« less

Concerted electron-proton transfer in the optical excitation of hydrogen-bonded dyes

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

Westlake, Brittany C.; Brennaman, Kyle M.; Concepcion, Javier J.

2011-05-24

The simultaneous, concerted transfer of electrons and protons—electron-proton transfer (EPT)—is an important mechanism utilized in chemistry and biology to avoid high energy intermediates. There are many examples of thermally activated EPT in ground-state reactions and in excited states following photoexcitation and thermal relaxation. Here we report application of ultrafast excitation with absorption and Raman monitoring to detect a photochemically driven EPT process (photo-EPT). In this process, both electrons and protons are transferred during the absorption of a photon. Photo-EPT is induced by intramolecular charge-transfer (ICT) excitation of hydrogen-bonded-base adducts with either a coumarin dye or 4-nitro-4'-biphenylphenol. Femtosecond transient absorption spectralmore » measurements following ICT excitation reveal the appearance of two spectroscopically distinct states having different dynamical signatures. One of these states corresponds to a conventional ICT excited state in which the transferring H⁺ is initially associated with the proton donor. Proton transfer to the base (B) then occurs on the picosecond time scale. The other state is an ICT-EPT photoproduct. Upon excitation it forms initially in the nuclear configuration of the ground state by application of the Franck–Condon principle. However, due to the change in electronic configuration induced by the transition, excitation is accompanied by proton transfer with the protonated base formed with a highly elongated ⁺H–B bond. Coherent Raman spectroscopy confirms the presence of a vibrational mode corresponding to the protonated base in the optically prepared state.« less

Dynamic Convergent Evolution Drives the Passage Adaptation across 48 Years' History of H3N2 Influenza Evolution.

PubMed

Chen, Hui; Deng, Qiang; Ng, Sock Hoon; Lee, Raphael Tze Chuen; Maurer-Stroh, Sebastian; Zhai, Weiwei

2016-12-01

Influenza viruses are often propagated in a diverse set of culturing media and additional substitutions known as passage adaptation can cause extra evolution in the target strain, leading to ineffective vaccines. Using 25,482 H3N2 HA1 sequences curated from Global Initiative on Sharing All Influenza Data and National Center for Biotechnology Information databases, we found that passage adaptation is a very dynamic process that changes over time and evolves in a seesaw like pattern. After crossing the species boundary from bird to human in 1968, the influenza H3N2 virus evolves to be better adapted to the human environment and passaging them in embryonated eggs (i.e., an avian environment) leads to increasingly stronger positive selection. On the contrary, passage adaptation to the mammalian cell lines changes from positive selection to negative selection. Using two statistical tests, we identified 19 codon positions around the receptor binding domain strongly contributing to passage adaptation in the embryonated egg. These sites show strong convergent evolution and overlap extensively with positively selected sites identified in humans, suggesting that passage adaptation can confound many of the earlier studies on influenza evolution. Interestingly, passage adaptation in recent years seems to target a few codon positions in antigenic surface epitopes, which makes it difficult to produce antigenically unaltered vaccines using embryonic eggs. Our study outlines another interesting scenario whereby both convergent and adaptive evolution are working in synchrony driving viral adaptation. Future studies from sequence analysis to vaccine production need to take careful consideration of passage adaptation. © 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.

Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

PubMed Central

Clarke, Thomas H.; Garb, Jessica E.; Hayashi, Cheryl Y.; Arensburger, Peter; Ayoub, Nadia A.

2015-01-01

The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). PMID:26058392

Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis

PubMed Central

Garrett, Wendy S.; Gallini, Carey A.; Yatsunenko, Tanya; Michaud, Monia; DuBois, Andrea; Delaney, Mary L.; Punit, Shivesh; Karlsson, Maria; Bry, Lynn; Glickman, Jonathan N.; Gordon, Jeffrey I.; Onderdonk, Andrew B.; Glimcher, Laurie H.

2010-01-01

SUMMARY In inflammatory bowel disease, the relationship between a host and gut microbial community goes awry. We have characterized the fecal microbial communities in a mouse IBD model driven by T-bet deficiency in the innate immune system. 16S rRNA-based analysis of T-bet−/− × Rag2−/− and Rag2−/− mice revealed distinctive communities that correlate with host genotype. Culture-based surveys, invasion assays, antibiotic treatment, and TNF-α blockade disclosed that the presence of Klebsiella pneumoniae and Proteus mirabilis correlates with colitis in T-bet−/− × Rag2−/− animals, and that T-bet−/− × Rag2−/− derived strains can elicit colitis in Rag2−/− and wild-type adults. Cross-fostering experiments provided evidence for the role of these organisms in maternal transmission of disease. This model provides a foundation for defining how gut microbial communities work in concert with specific culturable colitogenic agents to cause IBD, and a foundation for conducting proof-of-concept tests of new preventative or therapeutic measures directed at components of the gut microbiota and/or host. PMID:20833380

Rapid birth-and-death evolution of the xenobiotic metabolizing NAT gene family in vertebrates with evidence of adaptive selection

PubMed Central

2013-01-01

Background The arylamine N-acetyltransferases (NATs) are a unique family of enzymes widely distributed in nature that play a crucial role in the detoxification of aromatic amine xenobiotics. Considering the temporal changes in the levels and toxicity of environmentally available chemicals, the metabolic function of NATs is likely to be under adaptive evolution to broaden or change substrate specificity over time, making NATs a promising subject for evolutionary analyses. In this study, we trace the molecular evolutionary history of the NAT gene family during the last ~450 million years of vertebrate evolution and define the likely role of gene duplication, gene conversion and positive selection in the evolutionary dynamics of this family. Results A phylogenetic analysis of 77 NAT sequences from 38 vertebrate species retrieved from public genomic databases shows that NATs are phylogenetically unstable genes, characterized by frequent gene duplications and losses even among closely related species, and that concerted evolution only played a minor role in the patterns of sequence divergence. Local signals of positive selection are detected in several lineages, probably reflecting response to changes in xenobiotic exposure. We then put a special emphasis on the study of the last ~85 million years of primate NAT evolution by determining the NAT homologous sequences in 13 additional primate species. Our phylogenetic analysis supports the view that the three human NAT genes emerged from a first duplication event in the common ancestor of Simiiformes, yielding NAT1 and an ancestral NAT gene which in turn, duplicated in the common ancestor of Catarrhini, giving rise to NAT2 and the NATP pseudogene. Our analysis suggests a main role of purifying selection in NAT1 protein evolution, whereas NAT2 was predicted to mostly evolve under positive selection to change its amino acid sequence over time. These findings are consistent with a differential role of the two human isoenzymes

Leveraging contemporary species introductions to test phylogenetic hypotheses of trait evolution.

PubMed

Lu-Irving, Patricia; Marx, Hannah E; Dlugosch, Katrina M

2018-05-10

Plant trait evolution is a topic of interest across disciplines and scales. Phylogenetic studies are powerful for generating hypotheses about the mechanisms that have shaped plant traits and their evolution. Introduced plants are a rich source of data on contemporary trait evolution. Introductions could provide especially useful tests of a variety of evolutionary hypotheses because the environments selecting on evolving traits are still present. We review phylogenetic and contemporary studies of trait evolution and identify areas of overlap and areas for further integration. Emerging tools which can promote integration include broadly focused repositories of trait data, and comparative models of trait evolution that consider both intra and interspecific variation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Carbonate landscapes evolution: Insights from 36Cl

NASA Astrophysics Data System (ADS)

Godard, Vincent; Thomas, Franck; Ollivier, Vincent; Bellier, Olivier; Shabanian, Esmaeil; Miramont, Cécile; Fleury, Jules; Benedetti, Lucilla; Guillou, Valéry; Aster Team

2017-04-01

Carbonate landscapes cover a significant fraction of the Earth surface, but their long-term dynamics is still poorly understood. When comparing with the situation in areas underlain by quartz-rich lithologies, where the routine use of 10Be-derived denudation rates has delivered fundamental insights on landscape evolution processes, this knowledge gap is particularly notable. Recent advances in the measurement of 36Cl and better understanding of its production pathways has opened the way to the development of a similar physically-based and quantitative analysis of landscape evolution in carbonate settings. However, beyond these methodological considerations, we still face fundamental geomorphological open questions, as for example the assessment of the importance of congruent carbonate dissolution in long-wavelength topographic evolution. Such unresolved problems concerning the relative importance of physical and chemical weathering processes lead to question the applicability of standard slope-dependent Geomorphic Transport Laws in carbonate settings. These issues have been addressed studying the geomorphological evolution of selected limestone ranges in Provence, SE France, where 36Cl concentration measurements in bedrock and stream sediment samples allow constraining denudation over 10 ka time-scale. We first identify a significant denudation contrast between the summit surface and the flanks of the ranges, pointing to a substantial contribution of gravity-driven processes to the landscape evolution, in addition to dissolution. Furthermore, a detailed analysis of the relationships between hillslope morphology and hilltop denudation allow to identify a fundamental transition between two regimes: (1) a dynamics where hillslope evolution is controlled by linear diffusive downslope regolith transport; and, (2) a domain where denudation is limited by the rate at which physical and chemical weathering processes can produce clasts and lower the hilltop. Such an abrupt

Determinants of the rate of protein sequence evolution

PubMed Central

Zhang, Jianzhi; Yang, Jian-Rong

2015-01-01

The rate and mechanism of protein sequence evolution have been central questions in evolutionary biology since the 1960s. Although the rate of protein sequence evolution depends primarily on the level of functional constraint, exactly what constitutes functional constraint has remained unclear. The increasing availability of genomic data has allowed for much needed empirical examinations on the nature of functional constraint. These studies found that the evolutionary rate of a protein is predominantly influenced by its expression level rather than functional importance. A combination of theoretical and empirical analyses have identified multiple mechanisms behind these observations and demonstrated a prominent role that selection against errors in molecular and cellular processes plays in protein evolution. PMID:26055156

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.

Concerted Mitigation of O···H and C(π)···H Interactions Prospects Sixfold Gain in Optical Nonlinearity of Ionic Stilbazolium Derivatives

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

Cole, Jacqueline M.; Lin, Tze-Chia; Edwards, Alison J.

2015-03-04

DAST (4-dimethylamino-N-methyl-4-stilbazolium tosylate) is the most commercially successful organic nonlinear optical (NLO) material for frequency-doubling, integrated optics, and THz wave applications. Its success is predicated on its high optical nonlinearity with concurrent sufficient thermal stability. Many chemical derivatives of DAST have therefore been developed to optimize their properties; yet, to date, none have surpassed the overall superiority of DAST for NLO photonic applications. This is perhaps because DAST is an ionic salt wherein its NLO-active cation is influenced by multiple types of subtle intermolecular forces that are hard to quantify, thus, making difficult the molecular engineering of better functioning DASTmore » derivatives. Here, we establish a model parameter, ηinter, that isolates the influence of intermolecular interactions on second-order optical nonlinearity in DAST and its derivatives, using second-harmonic generation (SHG) as a qualifier; by systematically mapping intercorrelations of all possible pairs of intermolecular interactions to ηinter, we uncover a relationship between concerted intermolecular interactions and SHG output. This correlation reveals that a sixfold gain in the intrinsic second-order NLO performance of DAST is possible, by eliminating the identified interactions. This prediction offers the first opportunity to systematically design next-generation DAST-based photonic device nanotechnology to realize such a prospect.« less

Defining a relationship between incident wave parameters and morphologic evolution of shoals on ebb tidal deltas using long term X-band radar observation from RIOS

NASA Astrophysics Data System (ADS)

Humberston, J. L.; McNinch, J.; Lippmann, T. C.

2016-12-01

The morphology of tidal inlet ebb-shoals varies dynamically over time, particularly in response to large wave events. Understanding which wave qualities most influence shoals' evolution would support advancements in sediment bypassing models as well as targeted maintenance dredging for hydrographic purposes. Unfortunately, shallow and rapidly changing bathymetry, turbid waters and ambiguous wave speeds resulting from multiple shoaling and de-shoaling areas limits many traditional surveying techniques from obtaining the spatial and temporal resolution necessary to effectively characterize shoal development. The Radar Inlet Observing System (RIOS) is a uniquely designed mobile X-band radar system that can be deployed to inlet environments and, using roof-mounted solar panels and an automatically triggered highly efficient diesel generator, run automated hourly collections and wirelessly stream data for up to several months at a time in nearly all weather and water conditions. During 2015 and early 2016, RIOS was deployed to St. Augustine Inlet, FL., New River Inlet, N.C., and Oregon Inlet, N.C. for periods of one to six months to allow for measureable shoal evolution. During deployments, ten minute collections (at 1 Hz) were conducted every hour and the data gridded to a 5m alongshore/cross-shore grid. Raw intensity returns were time-averaged and analyzed to define three metrics of shoal evolution: movement direction, movement velocity and inferred bathymetry. For each location and time period, wave frequencies, wave directions and significant wave heights were collected from the nearest wave-buoy. Time lapse videos of shoal positions were inspected and used in concert with cross-correlations values from each pair of shoal and wave parameters to determine the incident wave qualities most strongly relating to shoal evolution. Preliminary results suggest wave height, more than frequency, controls shoal movement. Wave direction and size collaboratively appear to direct

Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

PubMed Central

Ames, Ryan M.; Money, Daniel; Lovell, Simon C.

2014-01-01

The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes. PMID:24921666

Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae)

PubMed Central

2011-01-01

Background The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae) of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS) revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG) are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of LEAFY and the alcohol dehydrogenase gene (Adh) were selected to investigate their molecular evolution and phylogenetic utility. Results DNA sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some Adh homologs are putatively nonfunctional. A partial region of Adh1 was sequenced for 18 Pyrus species and three subparalogs representing Adh1-1 were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of LEAFY, multiple inparalogs were discovered for both LFY1int2 and LFY2int2. LFY1int2 is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of Pyrus using LFY2int2-N. Conclusions Our study represents the first phylogenetic analyses based on LCNGs in Pyrus

Evolution equation for quantum coherence

PubMed Central

Hu, Ming-Liang; Fan, Heng

2016-01-01

The estimation of the decoherence process of an open quantum system is of both theoretical significance and experimental appealing. Practically, the decoherence can be easily estimated if the coherence evolution satisfies some simple relations. We introduce a framework for studying evolution equation of coherence. Based on this framework, we prove a simple factorization relation (FR) for the l1 norm of coherence, and identified the sets of quantum channels for which this FR holds. By using this FR, we further determine condition on the transformation matrix of the quantum channel which can support permanently freezing of the l1 norm of coherence. We finally reveal the universality of this FR by showing that it holds for many other related coherence and quantum correlation measures. PMID:27382933

Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism.

PubMed

Holme, Petter; Huss, Mikael; Lee, Sang Hoon

2011-05-06

The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same physics that gives molecules their stability and affinity to react. These fundamental factors cannot be captured by standard null-models based on randomization. The unique property of organismal metabolism is that it is controlled, to some extent, by an enzymatic machinery that is subject to evolution. In this paper, we explore the possibility that reaction systems of planetary atmospheres can serve as a null-model against which we can define metabolic structure and trace the influence of evolution. We find that the two types of data can be distinguished by their respective degree distributions. This is especially clear when looking at the degree distribution of the reaction network (of reaction connected to each other if they involve the same molecular species). For the Earth's atmospheric network and the human metabolic network, we look into more detail for an underlying explanation of this deviation. However, we cannot pinpoint a single cause of the difference, rather there are several concurrent factors. By examining quantities relating to the modular-functional organization of the metabolism, we confirm that metabolic networks have a more complex modular organization than the atmospheric networks, but not much more. We interpret the more variegated modular arrangement of metabolism as a trace of evolved functionality. On the other hand, it is quite remarkable how similar the structures of these two types of networks are, which emphasizes that the constraints from the chemical properties of the molecules has a larger influence in shaping the reaction system than does natural selection.

The Concert of Europe and Great Power Governance Today: What Can the Order of 19th-Century Europe Teach Policymakers About International Order in the 21st Century

DTIC Science & Technology

2017-01-01

powers from the temptations of unilateral opportunism. The best-known and most-important success story here was the creation of the German...possibly mentally ill, the foreign minister committed suicide in the summer of 1822. His successor, George Canning, was a relative Concert skeptic... temptation . As discussed earlier, this was a process that might have started with the divide over liberal revolutions in the 1820s. In the prior

Moving Evolution Education Forward: A Systematic Analysis of Literature to Identify Gaps in Collective Knowledge for Teaching

ERIC Educational Resources Information Center

Ziadie, M. A.; Andrews, T. C.

2018-01-01

Evolution is a unifying theory in biology and is challenging for undergraduates to learn. An instructor's ability to help students learn is influenced by pedagogical content knowledge (PCK), which is topic-specific knowledge of teaching and learning. Instructors need PCK for every topic they teach, which is a tremendous body of knowledge to…

The Nature of the Arguments for Creationism, Intelligent Design, and Evolution

ERIC Educational Resources Information Center

Barnes, Ralph M.; Church, Rebecca A.; Draznin-Nagy, Samuel

2017-01-01

Seventy-two Internet documents promoting creationism, intelligent design (I.D.), or evolution were selected for analysis. The primary goal of each of the 72 documents was to present arguments for creationism, I.D., or evolution. We first identified all arguments in these documents. Each argument was then coded in terms of both argument type…

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

Formation and evolution of magma-poor margins, an example of the West Iberia margin

NASA Astrophysics Data System (ADS)

Perez-Gussinye, Marta; Andres-Martinez, Miguel; Morgan, Jason P.; Ranero, Cesar R.; Reston, Tim

2016-04-01

The West Iberia-Newfoundland (WIM-NF) conjugate margins have been geophysically and geologically surveyed for the last 30 years and have arguably become a paradigm for magma-poor extensional margins. Here we present a coherent picture of the WIM-NF rift to drift evolution that emerges from these observations and numerical modeling, and point out important differences that may exist with other magma-poor margins world-wide. The WIM-NF is characterized by a continental crust that thins asymmetrically and a wide and symmetric continent-ocean transition (COT) interpreted to consist of exhumed and serpentinised mantle with magmatic products increasing oceanward. The architectural evolution of these margins is mainly dominated by cooling under very slow extension velocities (<~6 mm/yr half-rate) and a lower crust that most probably was not extremely weak at the start of rifting. These conditions lead to a system where initially deformation is distributed over a broad area and the upper, lower crust and lithosphere are decoupled. As extension progresses upper, lower, crust and mantle become tightly coupled and deformation localizes due to strengthening and cooling during rifting. Coupling leads to asymmetric asthenospheric uplift and weakening of the hanginwall of the active fault, where a new fault forms. This continued process leads to the formation of an array of sequential faults that dip and become younger oceanward. Here we show that these processes acting in concert: 1) reproduce the margin asymmetry observed at the WIM-NF, 2) explain the fault geometry evolution from planar, to listric to detachment like by having one common Andersonian framework, 3) lead to the symmetric exhumation of mantle with little magmatism, and 4) explain the younging of the syn-rift towards the basin centre and imply that unconformities separating syn- and post-rift may be diachronous and younger towards the ocean. Finally, we show that different lower crustal rheologies lead to different

Molecular organization and phylogenetic analysis of 5S rDNA in crustaceans of the genus Pollicipes reveal birth-and-death evolution and strong purifying selection.

PubMed

Perina, Alejandra; Seoane, David; González-Tizón, Ana M; Rodríguez-Fariña, Fernanda; Martínez-Lage, Andrés

2011-10-17

The 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units that consist of a transcribing region (5S) and a variable nontranscribed spacer (NTS), in higher eukaryotes. Until recently the 5S rDNA was thought to be subject to concerted evolution, however, in several taxa, sequence divergence levels between the 5S and the NTS were found higher than expected under this model. So, many studies have shown that birth-and-death processes and selection can drive the evolution of 5S rDNA. In analyses of 5S rDNA evolution is found several 5S rDNA types in the genome, with low levels of nucleotide variation in the 5S and a spacer region highly divergent. Molecular organization and nucleotide sequence of the 5S ribosomal DNA multigene family (5S rDNA) were investigated in three Pollicipes species in an evolutionary context. The nucleotide sequence variation revealed that several 5S rDNA variants occur in Pollicipes genomes. They are clustered in up to seven different types based on differences in their nontranscribed spacers (NTS). Five different units of 5S rDNA were characterized in P. pollicipes and two different units in P. elegans and P. polymerus. Analysis of these sequences showed that identical types were shared among species and that two pseudogenes were present. We predicted the secondary structure and characterized the upstream and downstream conserved elements. Phylogenetic analysis showed an among-species clustering pattern of 5S rDNA types. These results suggest that the evolution of Pollicipes 5S rDNA is driven by birth-and-death processes with strong purifying selection.

Space Station Freedom extravehicular activity systems evolution study

NASA Technical Reports Server (NTRS)

Rouen, Michael

1990-01-01

Evaluation of Space Station Freedom (SSF) support of manned exploration is in progress to identify SSF extravehicular activity (EVA) system evolution requirements and capabilities. The output from these studies will provide data to support the preliminary design process to ensure that Space Station EVA system requirements for future missions (including the transportation node) are adequately considered and reflected in the baseline design. The study considers SSF support of future missions and the EVA system baseline to determine adequacy of EVA requirements and capabilities and to identify additional requirements, capabilities, and necessary technology upgrades. The EVA demands levied by formal requirements and indicated by evolutionary mission scenarios are high for the out-years of Space Station Freedom. An EVA system designed to meet the baseline requirements can easily evolve to meet evolution demands with few exceptions. Results to date indicate that upgrades or modifications to the EVA system may be necessary to meet the full range of EVA thermal environments associated with the transportation node. Work continues to quantify the EVA capability in this regard. Evolution mission scenarios with EVA and ground unshielded nuclear propulsion engines are inconsistent with anthropomorphic EVA capabilities.

Kinetic Studies on the Reaction of Chlorosulfonyl Isocyanate with Monofluoralkenes: Experimental Evidence for Both Stepwise and Concerted Mechanisms, and a Pre-equilibrium Complex on the Reaction Pathway

DTIC Science & Technology

2012-12-14

lactams that are readily reduced to β-lactams. Substitution of a vinyl hydrogen for a vinyl fluorine changes the dynamics for reaction with CSI so...hydrogen for a vinyl fluorine changes the dynamics for reaction with CSI so that a concerted pathway is favored. Rate constants were measured for...step pathway has not been demonstrated experimentally.3c In a recent paper, we found that substituting a hydrogen for a fluorine on the π-bond of an

Female genital schistosomiasis (FGS): from case reports to a call for concerted action against this neglected gynaecological disease.

PubMed

Christinet, Vanessa; Lazdins-Helds, Janis K; Stothard, J Russell; Reinhard-Rupp, Jutta

2016-06-01

In recent years, control of neglected tropical diseases has been increasingly gaining momentum and interventions against schistosomiasis are being progressively scaled-up through expansion of donated praziquantel and preventive chemotherapy campaigns. However, the public health importance of female genital schistosomiasis is not fully recognised nor its control is adequately addressed. Taking a clinical and anatomopathological perspective, we evaluated the available literature to highlight the importance of female genital schistosomiasis and its connections with two sexually transmitted infections of global importance, Human Immunodeficiency Virus (HIV) and Human Papilloma Virus. Outside the long list of clinical descriptive reports beginning in 1899, there is presently a shocking gap in epidemiological assessment and a significant underestimation of the burden of FGS remains. The scarcity of integrated approaches to address female genital schistosomiasis calls for more concerted action in its detection, treatment and prevention alongside other concomitant women's health issues, otherwise female genital schistosomiasis will remain a neglected gynaecological disease. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Evolution of IPv6 Internet topology with unusual sudden changes

NASA Astrophysics Data System (ADS)

Ai, Jun; Zhao, Hai; Kathleen, M. Carley; Su, Zhan; Li, Hui

2013-07-01

The evolution of Internet topology is not always smooth but sometimes with unusual sudden changes. Consequently, identifying patterns of unusual topology evolution is critical for Internet topology modeling and simulation. We analyze IPv6 Internet topology evolution in IP-level graph to demonstrate how it changes in uncommon ways to restructure the Internet. After evaluating the changes of average degree, average path length, and some other metrics over time, we find that in the case of a large-scale growing the Internet becomes more robust; whereas in a top—bottom connection enhancement the Internet maintains its efficiency with links largely decreased.

Teaching Evolution: A Heuristic Study of Personal and Cultural Dissonance

NASA Astrophysics Data System (ADS)

Grimes, Larry G.

Darwinian evolution is a robustly supported scientific theory. Yet creationists continue to challenge its teaching in American public schools. Biology teachers in all 50 states are responsible for teaching science content standards that include evolution. As products of their backgrounds and affiliations teachers bring personal attitudes and beliefs to their teaching. The purpose of this study was to explore how biology teachers perceive, describe, and value their teaching of evolution. This research question was explored through a heuristic qualitative methodology. Eight veteran California high school biology teachers were queried as to their beliefs, perceptions, experiences and practices of teaching evolution. Both personal and professional documents were collected. Data was presented in the form of biographical essays that highlight teachers' backgrounds, experiences, perspectives and practices of teaching evolution. Of special interest was how they describe pressure over teaching evolution during a decade of standards and No Child Left Behind high-stakes testing mandates. Five common themes emerged. Standards have increased the overall amount of evolution that is taught. High-stakes testing has decreased the depth at which evolution is taught. Teacher belief systems strongly influence how evolution is taught. Fear of creationist challenges effect evolution teaching strategies. And lastly, concern over the potential effects of teaching evolution on student worldviews was mixed. Three categories of teacher concern over the potential impact of evolution on student worldviews were identified: Concerned, Strategist, and Carefree. In the final analysis teacher beliefs and attitudes still appeared to he the most important factor influencing how evolution is taught.

Control of concerted two bond versus single bond dissociation in CH(3)Co(CO)(4) via an intermediate state using pump-dump laser pulses.

PubMed

Ambrosek, David; González, Leticia

2007-10-07

Wavepacket propagations on ab initio multiconfigurational two-dimensional potential energy surfaces for CH(3)Co(CO)(4) indicate that after irradiation to the lowest first and second electronic excited states, concerted dissociation of CH(3) and the axial CO ligand takes place. We employ a pump-dump sequence of pulses with appropriate frequencies and time delays to achieve the selective breakage of a single bond by controlling the dissociation angle. The pump and dump pulse sequence exploits the unbound surface where dissociation occurs in a counterintuitive fashion; stretching of one bond in an intermediate state enhances the single dissociation of the other bond.

Evolution of cranial telescoping in echolocating whales (Cetacea: Odontoceti).

PubMed

Churchill, Morgan; Geisler, Jonathan H; Beatty, Brian L; Goswami, Anjali

2018-05-01

Odontocete (echolocating whale) skulls exhibit extreme posterior displacement and overlapping of facial bones, here referred to as retrograde cranial telescoping. To examine retrograde cranial telescoping across 40 million years of whale evolution, we collected 3D scans of whale skulls spanning odontocete evolution. We used a sliding semilandmark morphometric approach with Procrustes superimposition and PCA to capture and describe the morphological variation present in the facial region, followed by Ancestral Character State Reconstruction (ACSR) and evolutionary model fitting on significant components to determine how retrograde cranial telescoping evolved. The first PC score explains the majority of variation associated with telescoping and reflects the posterior migration of the external nares and premaxilla alongside expansion of the maxilla and frontal. The earliest diverging fossil odontocetes were found to exhibit a lesser degree of cranial telescoping than later diverging but contemporary whale taxa. Major shifts in PC scores and centroid size are identified at the base of Odontoceti, and early burst and punctuated equilibrium models best fit the evolution of retrograde telescoping. This indicates that the Oligocene was a period of unusually high diversity and evolution in whale skull morphology, with little subsequent evolution in telescoping. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Factors Potentially Influencing Student Acceptance of Biological Evolution

NASA Astrophysics Data System (ADS)

Wiles, Jason R.

This investigation explored scientific, religious, and otherwise nonscientific factors that may influence student acceptance of biological evolution and related concepts, how students perceived these factors to have influenced their levels of acceptance of evolution and changes therein, and what patterns arose among students' articulations of how their levels of acceptance of evolution may have changed. This exploration also measured the extent to which students' levels of acceptance changed following a treatment designed to address factors identified as potentially affecting student acceptance of evolution. Acceptance of evolution was measured using the MATE instrument (Rutledge and Warden, 1999; Rutledge and Sadler, 2007) among participants enrolled in a secondary-level academic program during the summer prior to their final year of high school and as they transitioned to the post-secondary level. Student acceptance of evolution was measured to be significantly higher than pre-treatment levels both immediately following and slightly over one year after treatment. Qualitative data from informal questionnaires, from formal course evaluations, and from semi-structured interviews of students engaged in secondary level education and former students at various stages of post-secondary education confirmed that the suspected factors were perceived by participants to have influenced their levels of acceptance of evolution. Furthermore, participant reports provided insight regarding the relative effects they perceived these factors to have had on their evolution acceptance levels. Additionally, many participants reported that their science teachers in public schools had avoided, omitted, or denigrated evolution during instruction, and several of these students expressed frustration regarding what they perceived to have been a lack of education of an important scientific principle. Finally, no students expressed feelings of being offended by having been taught about

Hamiltonian identifiability assisted by a single-probe measurement

NASA Astrophysics Data System (ADS)

Sone, Akira; Cappellaro, Paola

2017-02-01

We study the Hamiltonian identifiability of a many-body spin-1 /2 system assisted by the measurement on a single quantum probe based on the eigensystem realization algorithm approach employed in Zhang and Sarovar, Phys. Rev. Lett. 113, 080401 (2014), 10.1103/PhysRevLett.113.080401. We demonstrate a potential application of Gröbner basis to the identifiability test of the Hamiltonian, and provide the necessary experimental resources, such as the lower bound in the number of the required sampling points, the upper bound in total required evolution time, and thus the total measurement time. Focusing on the examples of the identifiability in the spin-chain model with nearest-neighbor interaction, we classify the spin-chain Hamiltonian based on its identifiability, and provide the control protocols to engineer the nonidentifiable Hamiltonian to be an identifiable Hamiltonian.

Following the Social Media: Aspect Evolution of Online Discussion

NASA Astrophysics Data System (ADS)

Tang, Xuning; Yang, Christopher C.

Due to the advance of Internet and Web 2.0 technologies, it is easy to extract thousands of threads about a topic of interest from an online forum but it is nontrivial to capture the blueprint of different aspects (i.e., subtopic, or facet) associated with the topic. To better understand and analyze a forum discussion given topic, it is important to uncover the evolution relationships (temporal dependencies) between different topic aspects (i.e. how the discussion topic is evolving). Traditional Topic Detection and Tracking (TDT) techniques usually organize topics as a flat structure but it does not present the evolution relationships between topic aspects. In addition, the properties of short and sparse messages make the content-based TDT techniques difficult to perform well in identifying evolution relationships. The contributions in this paper are two-folded. We formally define a topic aspect evolution graph modeling framework and propose to utilize social network information, content similarity and temporal proximity to model evolution relationships between topic aspects. The experimental results showed that, by incorporating social network information, our technique significantly outperformed content-based technique in the task of extracting evolution relationships between topic aspects.

Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution.

PubMed

Ajmal, Wajya; Khan, Hiba; Abbasi, Amir Ali

2014-12-01

Understanding the genetic mechanisms underlying the organismal complexity and origin of novelties during vertebrate history is one of the central goals of evolutionary biology. Ohno (1970) was the first to postulate that whole genome duplications (WGD) have played a vital role in the evolution of new gene functions: permitting an increase in morphological, physiological and anatomical complexity during early vertebrate history. Here, we analyze the evolutionary history of human FGFR-bearing paralogon (human autosome 4/5/8/10) by the phylogenetic analysis of multigene families with triplicate and quadruplicate distribution on these chromosomes. Our results categorized the histories of 21 families into discrete co-duplicated groups. Genes of a particular co-duplicated group exhibit identical evolutionary history and have duplicated in concert with each other, whereas genes belonging to different groups have dissimilar histories and have not duplicated concurrently. Taken together with our previously published data, we submit that there is sufficient empirical evidence to disprove the 1R/2R hypothesis and to support the general prediction that vertebrate genome evolved by relatively small-scale, regional duplication events that spread across the history of life. Copyright © 2014 Elsevier Inc. All rights reserved.

The Evolution of the Multicoloured Face of Mandrills: Insights from the Perceptual Space of Colour Vision

PubMed Central

Renoult, Julien P.; Schaefer, H. Martin; Sallé, Bettina; Charpentier, Marie J. E.

2011-01-01

Multicomponent signals consist of several traits that are perceived as a whole. Although many animals rely on multicomponent signals to communicate, the selective pressures shaping these signals are still poorly understood. Previous work has mainly investigated the evolution of multicomponent signals by studying each trait individually, which may not accurately reflect the selective pressures exerted by the holistic perception of signal receivers. Here, we study the design of the multicoloured face of an Old World primate, the mandrill (Mandrillus sphinx), in relation to two aspects of signalling that are expected to be selected by receivers: conspicuousness and information. Using reflectance data on the blue and red colours of the faces of 34 males and a new method of hue vectorisation in a perceptual space of colour vision, we show that the blue hue maximises contrasts to both the red hue and the foliage background colouration, thereby increasing the conspicuousness of the whole display. We further show that although blue saturation, red saturation and the contrast between blue and red colours are all correlated with dominance, dominance is most accurately indicated by the blue-red contrast. Taken together our results suggest that the evolution of blue and red facial colours in male mandrills are not independent and are likely driven by the holistic perception of conspecifics. In this view, we propose that the multicoloured face of mandrills acts as a multicomponent signal. Last, we show that information accuracy increases with the conspicuousness of the whole display, indicating that both aspects of signalling can evolve in concert. PMID:22216180

Evolution of functional specialization and division of labor.

PubMed

Rueffler, Claus; Hermisson, Joachim; Wagner, Günter P

2012-02-07

Division of labor among functionally specialized modules occurs at all levels of biological organization in both animals and plants. Well-known examples include the evolution of specialized enzymes after gene duplication, the evolution of specialized cell types, limb diversification in arthropods, and the evolution of specialized colony members in many taxa of marine invertebrates and social insects. Here, we identify conditions favoring the evolution of division of labor by means of a general mathematical model. Our starting point is the assumption that modules contribute to two different biological tasks and that the potential of modules to contribute to these tasks is traded off. Our results are phrased in terms of properties of performance functions that map the phenotype of modules to measures of performance. We show that division of labor is favored by three factors: positional effects that predispose modules for one of the tasks, accelerating performance functions, and synergistic interactions between modules. If modules can be lost or damaged, selection for robustness can counteract selection for functional specialization. To illustrate our theory we apply it to the evolution of specialized enzymes coded by duplicated genes.

Arresting Evolution.

PubMed

Bull, James J; Barrick, Jeffrey E

2017-12-01

Evolution in the form of selective breeding has long been harnessed as a useful tool by humans. However, rapid evolution can also be a danger to our health and a stumbling block for biotechnology. Unwanted evolution can underlie the emergence of drug and pesticide resistance, cancer, and weeds. It makes live vaccines and engineered cells inherently unreliable and unpredictable, and therefore potentially unsafe. Yet, there are strategies that have been and can possibly be used to stop or slow many types of evolution. We review and classify existing population genetics-inspired methods for arresting evolution. Then, we discuss how genome editing techniques enable a radically new set of approaches to limit evolution. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

A Glimpse into the Satellite DNA Library in Characidae Fish (Teleostei, Characiformes)

PubMed Central

Utsunomia, Ricardo; Ruiz-Ruano, Francisco J.; Silva, Duílio M. Z. A.; Serrano, Érica A.; Rosa, Ivana F.; Scudeler, Patrícia E. S.; Hashimoto, Diogo T.; Oliveira, Claudio; Camacho, Juan Pedro M.; Foresti, Fausto

2017-01-01

Satellite DNA (satDNA) is an abundant fraction of repetitive DNA in eukaryotic genomes and plays an important role in genome organization and evolution. In general, satDNA sequences follow a concerted evolutionary pattern through the intragenomic homogenization of different repeat units. In addition, the satDNA library hypothesis predicts that related species share a series of satDNA variants descended from a common ancestor species, with differential amplification of different satDNA variants. The finding of a same satDNA family in species belonging to different genera within Characidae fish provided the opportunity to test both concerted evolution and library hypotheses. For this purpose, we analyzed here sequence variation and abundance of this satDNA family in ten species, by a combination of next generation sequencing (NGS), PCR and Sanger sequencing, and fluorescence in situ hybridization (FISH). We found extensive between-species variation for the number and size of pericentromeric FISH signals. At genomic level, the analysis of 1000s of DNA sequences obtained by Illumina sequencing and PCR amplification allowed defining 150 haplotypes which were linked in a common minimum spanning tree, where different patterns of concerted evolution were apparent. This also provided a glimpse into the satDNA library of this group of species. In consistency with the library hypothesis, different variants for this satDNA showed high differences in abundance between species, from highly abundant to simply relictual variants. PMID:28855916

The evolution of lethal intergroup violence.

PubMed

Kelly, Raymond C

2005-10-25

Recent findings and analyses in evolutionary biology, archaeology, and ethnology provide a favorable conjuncture for examining the evolution of lethal intergroup violence among hominids during the 2.9-million-year Paleolithic time span. Here, I seek to identify and investigate the main turning points in this evolutionary trajectory and to delineate the periodization that follows from this inquiry.

Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus.

PubMed

Yang, Liandong; Wang, Ying; Zhang, Zhaolei; He, Shunping

2014-12-26

Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Habitable Zone Evolution

NASA Astrophysics Data System (ADS)

Waltham, D.; Lota, J.

2012-12-01

The location of the habitable zone around a star depends upon stellar luminosity and upon the properties of a potentially habitable planet such as its mass and near-surface volatile inventory. Stellar luminosity generally increases as a star ages whilst planetary properties change through time as a consequence of biological and geological evolution. Hence, the location of the habitable zone changes through time as a result of both stellar evolution and planetary evolution. Using the Earth's Phanerozoic temperature history as a constraint, it is shown that changes in our own habitable zone over the last 540 My have been dominated by planetary evolution rather than solar evolution. Furthermore, sparse data from earlier times suggests that planetary evolution may have dominated habitable zone development throughout our biosphere's history. Hence, the existence of a continuously habitable zone depends upon accidents of complex bio-geochemical evolution more than it does upon relatively simple stellar-evolution. Evolution of the inner margin of the habitable zone through time using three different estimates for climate sensitivity. The dashed line shows a typical predicted evolution assuming this was driven simply by a steady increase in solar luminosity. Solar evolution does not account for the observations. Evolution of the outer margin of the habitable zone through time using three different estimates for climate sensitivity. The dashed line shows a typical predicted evolution assuming this was driven simply by a steady increase in solar luminosity. Solar evolution does not account for the observations.

Similar traits, different genes? Examining convergent evolution in related weedy rice populations.

PubMed

Thurber, Carrie S; Jia, Melissa H; Jia, Yulin; Caicedo, Ana L

2013-02-01

Convergent phenotypic evolution may or may not be associated with convergent genotypic evolution. Agricultural weeds have repeatedly been selected for weed-adaptive traits such as rapid growth, increased seed dispersal and dormancy, thus providing an ideal system for the study of convergent evolution. Here, we identify QTL underlying weedy traits and compare their genetic architecture to assess the potential for convergent genetic evolution in two distinct populations of weedy rice. F(2) offspring from crosses between an indica cultivar and two individuals from genetically differentiated U.S. weedy rice populations were used to map QTL for four quantitative (heading date, seed shattering, plant height and growth rate) and two qualitative traits. We identified QTL on nine of the twelve rice chromosomes, yet most QTL locations do not overlap between the two populations. Shared QTL among weed groups were only seen for heading date, a trait for which weedy groups have diverged from their cultivated ancestors and from each other. Sharing of some QTL with wild rice also suggests a possible role in weed evolution for genes under selection during domestication. The lack of overlapping QTL for the remaining traits suggests that, despite a close evolutionary relationship, weedy rice groups have adapted to the same agricultural environment through different genetic mechanisms. © 2012 Blackwell Publishing Ltd.

The Terebridae and teretoxins: Combining phylogeny and anatomy for concerted discovery of bioactive compounds.

PubMed

Puillandre, Nicolas; Holford, Mandë

2010-09-17

The Conoidea superfamily, comprised of cone snails, terebrids, and turrids, is an exceptionally promising group for the discovery of natural peptide toxins. The potential of conoidean toxins has been realized with the distribution of the first Conus (cone snail) drug, Prialt (ziconotide), an analgesic used to alleviate chronic pain in HIV and cancer patients. Cone snail toxins (conotoxins) are highly variable, a consequence of a high mutation rate associated to duplication events and positive selection. As Conus and terebrids diverged in the early Paleocene, the toxins from terebrids (teretoxins) may demonstrate highly divergent and unique functionalities. Recent analyses of the Terebridae, a largely distributed family with more than 300 described species, indicate they have evolutionary and pharmacological potential. Based on a three gene (COI, 12S and 16S) molecular phylogeny, including ~50 species from the West-Pacific, five main terebrid lineages were discriminated: two of these lineages independently lost their venom apparatus, and one venomous lineage was previously unknown. Knowing the phylogenetic relationships within the Terebridae aids in effectively targeting divergent lineages with novel peptide toxins. Preliminary results indicate that teretoxins are similar in structure and composition to conotoxins, suggesting teretoxins are an attractive line of research to discover and develop new therapeutics that target ion channels and receptors. Using conotoxins as a guideline, and innovative natural products discovery strategies, such as the Concerted Discovery Strategy, the potential of the Terebridae and their toxins are explored as a pioneering pharmacological resource.

Kinetoplastid phylogenetics, with special reference to the evolution of parasitic trypanosomes.

PubMed

Stevens, J R

2008-09-01

To fully understand the evolutionary history of parasitic kinetoplastids and to understand the context within which the evolution of each parasite group has developed, an understanding not just of the parasites, but of all kinetoplastids is required. Accordingly, this paper provides an overview of kinetoplastid evolution and systematics, including coverage of the proposal by Moreira et al. (2004) to divide kinetoplasts into Prokinetoplastina (Ichthyobodo and Perkinsiella) and Metakinetoplastina (other bodonids and trypanosomatids). The implications of such a revision, with regard to correctly identifying outgroup taxa for studies of evolution within taxa of medical importance, are addressed, together with a more detailed review of the evolution and origins of the trypanosomes in the light of new phylogenies, new approaches and revisions in kinetoplastid systematics.

Parallel Electrochemical Treatment System and Application for Identifying Acid-Stable Oxygen Evolution Electrocatalysts

DOE PAGES

Jones, Ryan J. R.; Shinde, Aniketa; Guevarra, Dan; ...

2015-01-05

There are many energy technologies require electrochemical stability or preactivation of functional materials. Due to the long experiment duration required for either electrochemical preactivation or evaluation of operational stability, parallel screening is required to enable high throughput experimentation. We found that imposing operational electrochemical conditions to a library of materials in parallel creates several opportunities for experimental artifacts. We discuss the electrochemical engineering principles and operational parameters that mitigate artifacts int he parallel electrochemical treatment system. We also demonstrate the effects of resistive losses within the planar working electrode through a combination of finite element modeling and illustrative experiments. Operationmore » of the parallel-plate, membrane-separated electrochemical treatment system is demonstrated by exposing a composition library of mixed metal oxides to oxygen evolution conditions in 1M sulfuric acid for 2h. This application is particularly important because the electrolysis and photoelectrolysis of water are promising future energy technologies inhibited by the lack of highly active, acid-stable catalysts containing only earth abundant elements.« less

The evolution of lethal intergroup violence

PubMed Central

Kelly, Raymond C.

2005-01-01

Recent findings and analyses in evolutionary biology, archaeology, and ethnology provide a favorable conjuncture for examining the evolution of lethal intergroup violence among hominids during the 2.9-million-year Paleolithic time span. Here, I seek to identify and investigate the main turning points in this evolutionary trajectory and to delineate the periodization that follows from this inquiry. PMID:16129826

Adaptive processes drive ecomorphological convergent evolution in antwrens (Thamnophilidae).

PubMed

Bravo, Gustavo A; Remsen, J V; Brumfield, Robb T

2014-10-01

Phylogenetic niche conservatism (PNC) and convergence are contrasting evolutionary patterns that describe phenotypic similarity across independent lineages. Assessing whether and how adaptive processes give origin to these patterns represent a fundamental step toward understanding phenotypic evolution. Phylogenetic model-based approaches offer the opportunity not only to distinguish between PNC and convergence, but also to determine the extent that adaptive processes explain phenotypic similarity. The Myrmotherula complex in the Neotropical family Thamnophilidae is a polyphyletic group of sexually dimorphic small insectivorous forest birds that are relatively homogeneous in size and shape. Here, we integrate a comprehensive species-level molecular phylogeny of the Myrmotherula complex with morphometric and ecological data within a comparative framework to test whether phenotypic similarity is described by a pattern of PNC or convergence, and to identify evolutionary mechanisms underlying body size and shape evolution. We show that antwrens in the Myrmotherula complex represent distantly related clades that exhibit adaptive convergent evolution in body size and divergent evolution in body shape. Phenotypic similarity in the group is primarily driven by their tendency to converge toward smaller body sizes. Differences in body size and shape across lineages are associated to ecological and behavioral factors. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Concerted effort of centrosomal and Golgi-derived microtubules is required for proper Golgi complex assembly but not for maintenance

PubMed Central

Vinogradova, Tatiana; Paul, Raja; Grimaldi, Ashley D.; Loncarek, Jadranka; Miller, Paul M.; Yampolsky, Dmitry; Magidson, Valentin; Khodjakov, Alexey; Mogilner, Alex; Kaverina, Irina

2012-01-01

Assembly of an integral Golgi complex is driven by microtubule (MT)-dependent transport. Conversely, the Golgi itself functions as an unconventional MT-organizing center (MTOC). This raises the question of whether Golgi assembly requires centrosomal MTs or can be self-organized, relying on its own MTOC activity. The computational model presented here predicts that each MT population is capable of gathering Golgi stacks but not of establishing Golgi complex integrity or polarity. In contrast, the concerted effort of two MT populations would assemble an integral, polarized Golgi complex. Indeed, while laser ablation of the centrosome did not alter already-formed Golgi complexes, acentrosomal cells fail to reassemble an integral complex upon nocodazole washout. Moreover, polarity of post-Golgi trafficking was compromised under these conditions, leading to strong deficiency in polarized cell migration. Our data indicate that centrosomal MTs complement Golgi self-organization for proper Golgi assembly and motile-cell polarization. PMID:22262454

Extended Kalman Filter framework for forecasting shoreline evolution

USGS Publications Warehouse

Long, Joseph; Plant, Nathaniel G.

2012-01-01

A shoreline change model incorporating both long- and short-term evolution is integrated into a data assimilation framework that uses sparse observations to generate an updated forecast of shoreline position and to estimate unobserved geophysical variables and model parameters. Application of the assimilation algorithm provides quantitative statistical estimates of combined model-data forecast uncertainty which is crucial for developing hazard vulnerability assessments, evaluation of prediction skill, and identifying future data collection needs. Significant attention is given to the estimation of four non-observable parameter values and separating two scales of shoreline evolution using only one observable morphological quantity (i.e. shoreline position).

Intermediate filament protein evolution and protists.

PubMed

Preisner, Harald; Habicht, Jörn; Garg, Sriram G; Gould, Sven B

2018-03-23

Metazoans evolved from a single protist lineage. While all eukaryotes share a conserved actin and tubulin-based cytoskeleton, it is commonly perceived that intermediate filaments (IFs), including lamin, vimentin or keratin among many others, are restricted to metazoans. Actin and tubulin proteins are conserved enough to be detectable across all eukaryotic genomes using standard phylogenetic methods, but IF proteins, in contrast, are notoriously difficult to identify by such means. Since the 1950s, dozens of cytoskeletal proteins in protists have been identified that seemingly do not belong to any of the IF families described for metazoans, yet, from a structural and functional perspective fit criteria that define metazoan IF proteins. Here, we briefly review IF protein discovery in metazoans and the implications this had for the definition of this protein family. We argue that the many cytoskeletal and filament-forming proteins of protists should be incorporated into a more comprehensive picture of IF evolution by aligning it with the recent identification of lamins across the phylogenetic diversity of eukaryotic supergroups. This then brings forth the question of how the diversity of IF proteins has unfolded. The evolution of IF proteins likely represents an example of convergent evolution, which, in combination with the speed with which these cytoskeletal proteins are evolving, generated their current diversity. IF proteins did not first emerge in metazoa, but in protists. Only the emergence of cytosolic IF proteins that appear to stem from a nuclear lamin is unique to animals and coincided with the emergence of true animal multicellularity. © 2018 Wiley Periodicals, Inc.

Transcriptional Network Analysis Identifies BACH1 as a Master Regulator of Breast Cancer Bone Metastasis

PubMed Central

Liang, Yajun; Wu, Heng; Lei, Rong; Chong, Robert A.; Wei, Yong; Lu, Xin; Tagkopoulos, Ilias; Kung, Sun-Yuan; Yang, Qifeng; Hu, Guohong; Kang, Yibin

2012-01-01

The application of functional genomic analysis of breast cancer metastasis has led to the identification of a growing number of organ-specific metastasis genes, which often function in concert to facilitate different steps of the metastatic cascade. However, the gene regulatory network that controls the expression of these metastasis genes remains largely unknown. Here, we demonstrate a computational approach for the deconvolution of transcriptional networks to discover master regulators of breast cancer bone metastasis. Several known regulators of breast cancer bone metastasis such as Smad4 and HIF1 were identified in our analysis. Experimental validation of the networks revealed BACH1, a basic leucine zipper transcription factor, as the common regulator of several functional metastasis genes, including MMP1 and CXCR4. Ectopic expression of BACH1 enhanced the malignance of breast cancer cells, and conversely, BACH1 knockdown significantly reduced bone metastasis. The expression of BACH1 and its target genes was linked to the higher risk of breast cancer recurrence in patients. This study established BACH1 as the master regulator of breast cancer bone metastasis and provided a paradigm to identify molecular determinants in complex pathological processes. PMID:22875853

Molecular organization and phylogenetic analysis of 5S rDNA in crustaceans of the genus Pollicipes reveal birth-and-death evolution and strong purifying selection

PubMed Central

2011-01-01

Background The 5S ribosomal DNA (5S rDNA) is organized in tandem arrays with repeat units that consist of a transcribing region (5S) and a variable nontranscribed spacer (NTS), in higher eukaryotes. Until recently the 5S rDNA was thought to be subject to concerted evolution, however, in several taxa, sequence divergence levels between the 5S and the NTS were found higher than expected under this model. So, many studies have shown that birth-and-death processes and selection can drive the evolution of 5S rDNA. In analyses of 5S rDNA evolution is found several 5S rDNA types in the genome, with low levels of nucleotide variation in the 5S and a spacer region highly divergent. Molecular organization and nucleotide sequence of the 5S ribosomal DNA multigene family (5S rDNA) were investigated in three Pollicipes species in an evolutionary context. Results The nucleotide sequence variation revealed that several 5S rDNA variants occur in Pollicipes genomes. They are clustered in up to seven different types based on differences in their nontranscribed spacers (NTS). Five different units of 5S rDNA were characterized in P. pollicipes and two different units in P. elegans and P. polymerus. Analysis of these sequences showed that identical types were shared among species and that two pseudogenes were present. We predicted the secondary structure and characterized the upstream and downstream conserved elements. Phylogenetic analysis showed an among-species clustering pattern of 5S rDNA types. Conclusions These results suggest that the evolution of Pollicipes 5S rDNA is driven by birth-and-death processes with strong purifying selection. PMID:22004418

The evolution of climatic niches in squamate reptiles.

PubMed

Pie, Marcio R; Campos, Leonardo L F; Meyer, Andreas L S; Duran, Andressa

2017-07-12

Despite the remarkable diversity found in squamate reptiles, most of their species tend to be found in warm/dry environments, suggesting that climatic requirements played a crucial role in their diversification, yet little is known about the evolution of their climatic niches. In this study, we integrate climatic information associated with the geographical distribution of 1882 squamate species and their phylogenetic relationships to investigate the tempo and mode of climatic niche evolution in squamates, both over time and among lineages. We found that changes in climatic niche dynamics were pronounced over their recent squamate evolutionary history, and we identified extensive evidence for rate heterogeneity in squamate climatic niche evolution. Most rate shifts involved accelerations, particularly over the past 50 Myr. Most squamates occupy similar regions of the climatic niche space, with only a few lineages diversifying into colder and humid climatic conditions. The changes from arid to mesic conditions in some regions of the globe may have provided opportunities for climatic niche evolution, although most lineages tended to remain near their ancestral niche. Variation in rates of climatic niche evolution seems common, particularly in response to the availability of new climatic conditions over evolutionary time. © 2017 The Author(s).

Concerted changes in N and C primary metabolism in alfalfa (Medicago sativa) under water restriction.

PubMed

Aranjuelo, Iker; Tcherkez, Guillaume; Molero, Gemma; Gilard, Françoise; Avice, Jean-Christophe; Nogués, Salvador

2013-02-01

Although the mechanisms of nodule N(2) fixation in legumes are now well documented, some uncertainty remains on the metabolic consequences of water deficit. In most cases, little consideration is given to other organs and, therefore, the coordinated changes in metabolism in leaves, roots, and nodules are not well known. Here, the effect of water restriction on exclusively N(2)-fixing alfalfa (Medicago sativa L.) plants was investigated, and proteomic, metabolomic, and physiological analyses were carried out. It is shown that the inhibition of nitrogenase activity caused by water restriction was accompanied by concerted alterations in metabolic pathways in nodules, leaves, and roots. The data suggest that nodule metabolism and metabolic exchange between plant organs nearly reached homeostasis in asparagine synthesis and partitioning, as well as the N demand from leaves. Typically, there was (i) a stimulation of the anaplerotic pathway to sustain the provision of C skeletons for amino acid (e.g. glutamate and proline) synthesis; (ii) re-allocation of glycolytic products to alanine and serine/glycine; and (iii) subtle changes in redox metabolites suggesting the implication of a slight oxidative stress. Furthermore, water restriction caused little change in both photosynthetic efficiency and respiratory cost of N(2) fixation by nodules. In other words, the results suggest that under water stress, nodule metabolism follows a compromise between physiological imperatives (N demand, oxidative stress) and the lower input to sustain catabolism.

Evolution of the beta-amylase gene in the temperate grasses: Non-purifying selection, recombination, semiparalogy, homeology and phylogenetic signal.

PubMed

Minaya, Miguel; Díaz-Pérez, Antonio; Mason-Gamer, Roberta; Pimentel, Manuel; Catalán, Pilar

2015-10-01

Low-copy nuclear genes (LCNGs) have complex genetic architectures and evolutionary dynamics. However, unlike multicopy nuclear genes, LCNGs are rarely subject to gene conversion or concerted evolution, and they have higher mutation rates than organellar or nuclear ribosomal DNA markers, so they have great potential for improving the robustness of phylogenetic reconstructions at all taxonomic levels. In this study, our first objective is to evaluate the evolutionary dynamics of the LCNG β-amylase by testing for potential pseudogenization, paralogy, homeology, recombination, and phylogenetic incongruence within a broad representation of the main Pooideae lineages. Our second objective is to determine whether β-amylase shows sufficient phylogenetic signal to reconstruct the evolutionary history of the Pooid grasses. A multigenic (ITS, matK, ndhF, trnTL, and trnLF) tree of the study group provided a framework for assessing the β-amylase phylogeny. Eight accessions showed complete absence of selection, suggesting putative pseudogenic copies or other relaxed selection pressures; resolution of Vulpia alopecuros 2x clones indicated its potential (semi) paralogy; and homeologous copies of allopolyploid species Festuca simensis, F. fenas, and F. arundinacea tracked their Mediterranean origin. Two recombination events were found within early-diverged Pooideae lineages, and five within the PACCMAD clade. The unexpected phylogenetic relationships of 37 grass species (26% of the sampled species) highlight the frequent occurrence of non-treelike evolutionary events, so this LCNG should be used with caution as a phylogenetic marker. However, once the pitfalls are identified and removed, the phylogenetic reconstruction of the grasses based on the β-amylase exon+intron positions is optimal at all taxonomic levels. Copyright © 2015 Elsevier Inc. All rights reserved.

Predicting Key Events in the Popularity Evolution of Online Information.

PubMed

Hu, Ying; Hu, Changjun; Fu, Shushen; Fang, Mingzhe; Xu, Wenwen

2017-01-01

The popularity of online information generally experiences a rising and falling evolution. This paper considers the "burst", "peak", and "fade" key events together as a representative summary of popularity evolution. We propose a novel prediction task-predicting when popularity undergoes these key events. It is of great importance to know when these three key events occur, because doing so helps recommendation systems, online marketing, and containment of rumors. However, it is very challenging to solve this new prediction task due to two issues. First, popularity evolution has high variation and can follow various patterns, so how can we identify "burst", "peak", and "fade" in different patterns of popularity evolution? Second, these events usually occur in a very short time, so how can we accurately yet promptly predict them? In this paper we address these two issues. To handle the first one, we use a simple moving average to smooth variation, and then a universal method is presented for different patterns to identify the key events in popularity evolution. To deal with the second one, we extract different types of features that may have an impact on the key events, and then a correlation analysis is conducted in the feature selection step to remove irrelevant and redundant features. The remaining features are used to train a machine learning model. The feature selection step improves prediction accuracy, and in order to emphasize prediction promptness, we design a new evaluation metric which considers both accuracy and promptness to evaluate our prediction task. Experimental and comparative results show the superiority of our prediction solution.

The predictability of evolution: glimpses into a post-Darwinian world.

PubMed

Conway Morris, Simon

2009-11-01

The very success of the Darwinian explanation, in not only demonstrating evolution from multiple lines of evidence but also in providing some plausible explanations, paradoxically seems to have served to have stifled explorations into other areas of investigation. The fact of evolution is now almost universally yoked to the assumption that its outcomes are random, trends are little more than drunkard's walks, and most evolutionary products are masterpieces of improvisation and far from perfect. But is this correct? Let us consider some alternatives. Is there evidence that evolution could in anyway be predictable? Can we identify alternative forms of biological organizations and if so how viable are they? Why are some molecules so extraordinarily versatile, while others can be spoken of as "molecules of choice"? How fortuitous are the major transitions in the history of life? What implications might this have for the Tree of Life? To what extent is evolutionary diversification constrained or facilitated by prior states? Are evolutionary outcomes merely sufficient or alternatively are they highly efficient, even superb? Here I argue that in sharp contradistinction to an orthodox Darwinian view, not only is evolution much more predictable than generally assumed but also investigation of its organizational substrates, including those of sensory systems, which indicates that it is possible to identify a predictability to the process and outcomes of evolution. If correct, the implications may be of some significance, not least in separating the unexceptional Darwinian mechanisms from underlying organizational principles, which may indicate evolutionary inevitabilities.

Evolution of the degree of substructures in simulated galaxy clusters

NASA Astrophysics Data System (ADS)

De Boni, Cristiano; Böhringer, Hans; Chon, Gayoung; Dolag, Klaus

2018-05-01

We study the evolution of substructure in the mass distribution with mass, redshift and radius in a sample of simulated galaxy clusters. The sample, containing 1226 objects, spans the mass range M200 = 1014 - 1.74 × 1015 M⊙ h-1 in six redshift bins from z = 0 to z = 1.179. We consider three different diagnostics: 1) subhalos identified with SUBFIND; 2) overdense regions localized by dividing the cluster into octants; 3) offset between the potential minimum and the center of mass. The octant analysis is a new method that we introduce in this work. We find that none of the diagnostics indicate a correlation between the mass of the cluster and the fraction of substructures. On the other hand, all the diagnostics suggest an evolution of substructures with redshift. For SUBFIND halos, the mass fraction is constant with redshift at Rvir, but shows a mild evolution at R200 and R500. Also, the fraction of clusters with at least a subhalo more massive than one thirtieth of the total mass is less than 20%. Our new method based on the octants returns a mass fraction in substructures which has a strong evolution with redshift at all radii. The offsets also evolve strongly with redshift. We also find a strong correlation for individual clusters between the offset and the fraction of substructures identified with the octant analysis. Our work puts strong constraints on the amount of substructures we expect to find in galaxy clusters and on their evolution with redshift.

Systems approaches in osteoarthritis: Identifying routes to novel diagnostic and therapeutic strategies

PubMed Central

Mueller, Alan J.; Peffers, Mandy J.; Proctor, Carole J.

2017-01-01

ABSTRACT Systems orientated research offers the possibility of identifying novel therapeutic targets and relevant diagnostic markers for complex diseases such as osteoarthritis. This review demonstrates that the osteoarthritis research community has been slow to incorporate systems orientated approaches into research studies, although a number of key studies reveal novel insights into the regulatory mechanisms that contribute both to joint tissue homeostasis and its dysfunction. The review introduces both top‐down and bottom‐up approaches employed in the study of osteoarthritis. A holistic and multiscale approach, where clinical measurements may predict dysregulation and progression of joint degeneration, should be a key objective in future research. The review concludes with suggestions for further research and emerging trends not least of which is the coupled development of diagnostic tests and therapeutics as part of a concerted effort by the osteoarthritis research community to meet clinical needs. © 2017 The Authors. Journal of Orthopaedic Research Published by Wiley Periodicals, Inc. on behalf of Orthopaedic Research Society. J Orthop Res 35:1573–1588, 2017. PMID:28318047

Identifying QCD Transition Using Deep Learning

NASA Astrophysics Data System (ADS)

Zhou, Kai; Pang, Long-gang; Su, Nan; Petersen, Hannah; Stoecker, Horst; Wang, Xin-Nian

2018-02-01

In this proceeding we review our recent work using supervised learning with a deep convolutional neural network (CNN) to identify the QCD equation of state (EoS) employed in hydrodynamic modeling of heavy-ion collisions given only final-state particle spectra ρ(pT, V). We showed that there is a traceable encoder of the dynamical information from phase structure (EoS) that survives the evolution and exists in the final snapshot, which enables the trained CNN to act as an effective "EoS-meter" in detecting the nature of the QCD transition.

The need for New In Situ Measurements to Understand the Climate, Geology and Evolution of Venus.

NASA Astrophysics Data System (ADS)

Grinspoon, D. H.

2017-12-01

Many measurements needed to address outstanding questions about current processes and evolution of Venus can only be made from in situ platforms such as entry probes, balloons or landers. Among these are precise determination of the value and altitude dependence of the deuterium-to-hydrogen ratio, an important tracer of water history which, while clearly greatly elevated compared to the terrestrial ratio, is still unknown within a large range of uncertainty and appears, based on Venus Express results, to display an enigmatic altitude dependence. Rare gas abundances and isotopes provide clues to volatile sources and histories of outgassing and exospheric escape. Modern mass spectrometry at Venus would yield abundances of the eight stable xenon isotopes, bulk abundances of krypton, and isotopes of neon. Altitude profiles of sulfur-containing chemical species would illuminate global geochemical cycles, including cloud formation, outgassing rates and surface-atmosphere interactions. The altitude profile of wind speeds and radiation fluxes, interpreted in light of the Venus Express and Akatsuki data, would enrich understanding of the global circulation and climate dynamics of Venus. Descent and surface images of carefully chosen locations would lend ground truth to interpretations of the near-global Magellan data sets and provide context for global remote sensing data obtained by future orbiter missions. Landed instruments would provide refinement and calibration for chemical abundance measurements by historical missions as well as direct mineralogical measurements of Venusian surface and subsurface rocks. In concert with atmospheric measurements these would greatly constrain geologic history as well as the nature of surface-atmosphere interactions. Such a suite of measurements will deepen our understanding of the origin and evolution of Venus in the context of Solar System and extrasolar terrestrial planets, determine the level and style of current geological activity

Concerted One-Electron Two-Proton Transfer Processes in Models Inspired by the Tyr-His Couple of Photosystem II

DOE PAGES

Huynh, Mioy T.; Mora, S. Jimena; Villalba, Matias; ...

2017-05-09

Nature employs a TyrZ-His pair as a redox relay that couples proton transfer to the redox process between P680 and the water oxidizing catalyst in photosystem II. Artificial redox relays composed of different benzimidazole–phenol dyads (benzimidazole models His and phenol models Tyr) with substituents designed to simulate the hydrogen bond network surrounding the TyrZ-His pair have been prepared. Furthermore, when the benzimidazole substituents are strong proton acceptors such as primary or tertiary amines, theory predicts that a concerted two proton transfer process associated with the electrochemical oxidation of the phenol will take place. Furthermore, theory predicts a decrease in themore » redox potential of the phenol by ~300 mV and a small kinetic isotope effect (KIE). Indeed, electrochemical, spectroelectrochemical, and KIE experimental data are consistent with these predictions. Our results were obtained by using theory to guide the rational design of artificial systems and have implications for managing proton activity to optimize efficiency at energy conversion sites involving water oxidation and reduction.« less

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.

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

Neurotactin functions in concert with other identified CAMs in growth cone guidance in Drosophila.

PubMed

Speicher, S; García-Alonso, L; Carmena, A; Martín-Bermudo, M D; de la Escalera, S; Jiménez, F

1998-02-01

We have isolated and characterized mutations in Drosophila neurotactin, a gene that encodes a cell adhesion protein widely expressed during neural development. Analysis of both loss and gain of gene function conditions during embryonic and postembryonic development revealed specific requirements for neurotactin during axon outgrowth, fasciculation, and guidance. Furthermore, embryos of some double mutant combinations of neurotactin and other genes encoding adhesion/signaling molecules, including neuroglian, derailed, and kekkon1, displayed phenotypic synergy. This result provides evidence for functional cooperativity in vivo between the adhesion and signaling pathways controlled by neurotactin and the other three genes.

Drug discovery: lessons from evolution

PubMed Central

Warren, John

2011-01-01

A common view within the pharmaceutical industry is that there is a problem with drug discovery and we should do something about it. There is much sympathy for this from academics, regulators and politicians. In this article I propose that lessons learnt from evolution help identify those factors that favour successful drug discovery. This personal view is influenced by a decade spent reviewing drug development programmes submitted for European regulatory approval. During the prolonged gestation of a new medicine few candidate molecules survive. This process of elimination of many variants and the survival of so few has much in common with evolution, an analogy that encourages discussion of the forces that favour, and those that hinder, successful drug discovery. Imagining a world without vaccines, anaesthetics, contraception and anti-infectives reveals how medicines revolutionized humanity. How to manipulate conditions that favour such discoveries is worth consideration. PMID:21395642

Coupled hydrological and geochemical process evolution at the Landscape Evolution Observatory

NASA Astrophysics Data System (ADS)

Troch, P. A. A.

2015-12-01

Predictions of hydrologic and biogeochemical responses to natural and anthropogenic forcing at the landscape scale are highly uncertain due to the effects of heterogeneity on the scaling of reaction, flow and transport phenomena. The physical, chemical and biological structures and processes controlling reaction, flow and transport in natural landscapes interact at multiple space and time scales and are difficult to quantify. The current paradigm of hydrological and geochemical theory is that process descriptions derived from observations at small scales in controlled systems can be applied to predict system response at much larger scales, as long as some 'equivalent' or 'effective' values of the scale-dependent parameters can be identified. Furthermore, natural systems evolve in time in a way that is hard to observe in short-run laboratory experiments or in natural landscapes with unknown initial conditions and time-variant forcing. The spatial structure of flow pathways along hillslopes determines the rate, extent and distribution of geochemical reactions (and biological colonization) that drive weathering, the transport and precipitation of solutes and sediments, and the further evolution of soil structure. The resulting evolution of structures and processes, in turn, produces spatiotemporal variability of hydrological states and flow pathways. There is thus a need for experimental research to improve our understanding of hydrology-biogeochemistry interactions and feedbacks at appropriate spatial scales larger than laboratory soil column experiments. Such research is complicated in real-world settings because of poorly constrained impacts of initial conditions, climate variability, ecosystems dynamics, and geomorphic evolution. The Landscape Evolution Observatory (LEO) at Biosphere 2 offers a unique research facility that allows real-time observations of incipient hydrologic and biogeochemical response under well-constrained initial conditions and climate

The Evolution of Research on Digital Education

ERIC Educational Resources Information Center

Dillenbourg, Pierre

2016-01-01

How does AI&EdAIED today compare to 25 years ago? This paper addresses this evolution by identifying six trends. The trends are ongoing and will influence learning technologies going forward. First, the physicality of interactions and the physical space of the learner became genuine components of digital education. The frontier between the…

Adaptive evolution of Mediterranean pines.

PubMed

Grivet, Delphine; Climent, José; Zabal-Aguirre, Mario; Neale, David B; Vendramin, Giovanni G; González-Martínez, Santiago C

2013-09-01

Mediterranean pines represent an extremely heterogeneous assembly. Although they have evolved under similar environmental conditions, they diversified long ago, ca. 10 Mya, and present distinct biogeographic and demographic histories. Therefore, it is of special interest to understand whether and to what extent they have developed specific strategies of adaptive evolution through time and space. To explore evolutionary patterns, the Mediterranean pines' phylogeny was first reconstructed analyzing a new set of 21 low-copy nuclear genes with multilocus Bayesian tree reconstruction methods. Secondly, a phylogenetic approach was used to search for footprints of natural selection and to examine the evolution of multiple phenotypic traits. We identified two genes (involved in pines' defense and stress responses) that have likely played a role in the adaptation of Mediterranean pines to their environment. Moreover, few life-history traits showed historical or evolutionary adaptive convergence in Mediterranean lineages, while patterns of character evolution revealed various evolutionary trade-offs linking growth-development, reproduction and fire-related traits. Assessing the evolutionary path of important life-history traits, as well as the genomic basis of adaptive variation is central to understanding the past evolutionary success of Mediterranean pines and their future response to environmental changes. Copyright © 2013 Elsevier Inc. All rights reserved.

Can Evolution Supply What Ecology Demands?

PubMed

Kokko, Hanna; Chaturvedi, Anurag; Croll, Daniel; Fischer, Martin C; Guillaume, Frédéric; Karrenberg, Sophie; Kerr, Ben; Rolshausen, Gregor; Stapley, Jessica

2017-03-01

A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate. In this review, we highlight how complexity in both ecological 'demands' and the evolutionary 'supply' influences organisms' ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards ecologically realistic studies of adaptation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Integrated Analysis of Genetic and Proteomic Data Identifies Biomarkers Associated with Adverse Events Following Smallpox Vaccination

EPA Science Inventory

Complex clinical outcomes, such as adverse reaction to vaccination, arise from the concerted interactions among the myriad components of a biological system. Therefore, comprehensive etiological models can be developed only through the integrated study of multiple types of experi...

Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato

USDA-ARS?s Scientific Manuscript database

This study explores the genetic architecture underling the potato evolution through a comprehensive assessment of wild and cultivated potato species based on the re-sequencing of 201 accessions of Solanum section Petota with >12 × genome coverage. We identified 450 domesticated genes, which showed e...

Concerted regulation of renal plasma flow and glomerular filtration rate by renal dopamine and NOS I in rats on high salt intake.

PubMed

Ibarra, Mariano E; Albertoni Borghese, Maria F; Majowicz, Mónica P; Ortiz, María C; Loidl, Fabián; Rey-Funes, Manuel; Di Ciano, Luis A; Ibarra, Fernando R

2017-03-01

Under high sodium intake renal dopamine (DA) increases while NOS I expression in macula densa cells (MD) decreases. To explore whether renal DA and NOS I, linked to natriuresis and to the stability of the tubuloglomerular feedback, respectively, act in concert to regulate renal plasma flow (RPF) and glomerular filtration rate (GFR). Male Wistar rats were studied under a normal sodium intake (NS, NaCl 0.24%) or a high sodium intake (HS, NaCl 1% in drinking water) during the 5 days of the study. For the last two days, the specific D 1 -like receptor antagonist SCH 23390 (1 mg kg bwt -1  day -1 , sc) or a vehicle was administered. HS intake increased natriuresis, diuresis, and urinary DA while it decreased cortical NOS I expression ( P  < 0.05 vs. NS), Nicotinamide adenine dinucleotide phosphate diaphorase (NADPH-d) activity in MD ( P  < 0.001 vs. NS) and cortical nitrates+nitrites (NOx) production (NS 2.04 ± 0.22 vs. HS 1.28 ± 0.10 nmol mg protein -1 , P  < 0.01). Treatment with SCH 23390 to rats on HS sharply decreased hydroelectrolyte excretion ( P  < 0.001 vs. HS) while NOS I expression, NADPH-d activity and NOx production increased ( P  < 0.05 vs. HS for NOS I and P  < 0.001 vs. HS for NADPH-d and NOx). SCH 23390 increased RPF and GFR in HS rats ( P  < 0.01 HS+SCH vs. HS). It did not cause variations in NS rats. Results indicate that when NS intake is shifted to a prolonged high sodium intake, renal DA through the D 1 R, and NOS I in MD cells act in concert to regulate RPF and GFR to stabilize the delivery of NaCl to the distal nephron. © 2017 Universidad De Buenos Aires. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and the American Physiological Society.

Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted, independent, or multiple evolutionary responses?

PubMed Central

Bagley, Justin C; Johnson, Jerald B

2014-01-01

A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns (“concerted-response hypothesis”); (2) independent responses, indicated by spatial incongruence (“independent-response hypothesis”); or (3) multiple responses (“multiple-response hypothesis”), indicated by spatial congruence but temporal incongruence (“pseudocongruence”) or spatial and temporal incongruence (“pseudoincongruence”). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co-occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer-scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation-with-migration models estimated incongruent timelines of among-region divergences, with A. cultratus and Xenophallus populations diverging over Miocene–mid-Pleistocene while P. gillii populations diverged over mid-late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B10] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple-response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer-scale population expansions in the other taxa. Empirical tests for phylogeographic congruence

Adaptive microclimatic evolution of the dehydrin 6 gene in wild barley at "Evolution Canyon", Israel.

PubMed

Yang, Zujun; Zhang, Tao; Li, Guangrong; Nevo, Eviatar

2011-12-01

Dehydrins are one of the major stress-induced gene families, and the expression of dehydrin 6 (Dhn6) is strictly related to drought in barley. In order to investigate how the evolution of the Dhn6 gene is associated with adaptation to environmental changes, we examined 48 genotypes of wild barley, Hordeum spontaneum, from "Evolution Canyon" at Mount Carmel, Israel. The Dhn6 sequences of the 48 genotypes were identified, and a recent insertion of 342 bp at 5'UTR was found in the sequences of 11 genotypes. Both nucleotide and haplotype diversity of single nucleotide polymorphism in Dhn6 coding regions were higher on the AS ("African" slope or dry slope) than on the ES ("European" slope or humid slope), and the applied Tajima D and Fu-Li test rejected neutrality of SNP diversity. Expression analysis indicated that the 342 bp insertion at 5'UTR was associated with the earlier up-regulation of Dhn6 after dehydration. The genetic divergence of amino acids sequences indicated significant positive selection of Dhn6 among the wild barley populations. The diversity of Dhn6 in microclimatic divergence slopes suggested that Dhn6 has been subjected to natural selection and adaptively associated with drought resistance of wild barley at "Evolution Canyon".

CMDR based differential evolution identifies the epistatic interaction in genome-wide association studies.

PubMed

Yang, Cheng-Hong; Chuang, Li-Yeh; Lin, Yu-Da

2017-08-01

Detecting epistatic interactions in genome-wide association studies (GWAS) is a computational challenge. Such huge numbers of single-nucleotide polymorphism (SNP) combinations limit the some of the powerful algorithms to be applied to detect the potential epistasis in large-scale SNP datasets. We propose a new algorithm which combines the differential evolution (DE) algorithm with a classification based multifactor-dimensionality reduction (CMDR), termed DECMDR. DECMDR uses the CMDR as a fitness measure to evaluate values of solutions in DE process for scanning the potential statistical epistasis in GWAS. The results indicated that DECMDR outperforms the existing algorithms in terms of detection success rate by the large simulation and real data obtained from the Wellcome Trust Case Control Consortium. For running time comparison, DECMDR can efficient to apply the CMDR to detect the significant association between cases and controls amongst all possible SNP combinations in GWAS. DECMDR is freely available at https://goo.gl/p9sLuJ . chuang@isu.edu.tw or e0955767257@yahoo.com.tw. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The Role of the Y-Chromosome in the Establishment of Murine Hybrid Dysgenesis and in the Analysis of the Nucleotide Sequence Organization, Genetic Transmission and Evolution of Repeated Sequences.

NASA Astrophysics Data System (ADS)

Nallaseth, Ferez Soli

The Y-chromosome presents a unique cytogenetic framework for the evolution of nucleotide sequences. Alignment of nine Y-chromosomal fragments in their increasing Y-specific/non Y-specific (male/female) sequence divergence ratios was directly and inversely related to their interspersion on these two respective genomic fractions. Sequence analysis confirmed a direct relationship between divergence ratios and the Alu, LINE-1, Satellite and their derivative oligonucleotide contents. Thus their relocation on the Y-chromosome is followed by sequence divergence rather than the well documented concerted evolution of these non-coding progenitor repeated sequences. Five of the nine Y-chromosomal fragments are non-pseudoautosomal and transcribed into heterogeneous PolyA^+ RNA and thus can be retrotransposed. Evolutionary and computer analysis identified homologous oligonucleotide tracts in several human loci suggesting common and random mechanistic origins. Dysgenic genomes represent the accelerated evolution driving sequence divergence (McClintock, 1984). Sex reversal and sterility characterizing dysgenesis occurs in C57BL/6JY ^{rm Pos} but not in 129/SvY^{rm Pos} derivative strains. High frequency, random, multi-locus deletion products of the feral Y^{ rm Pos}-chromosome are generated in the germlines of F1(C57BL/6J X 129/SvY^{ rm Pos})(male) and C57BL/6JY ^{rm Pos}(male) but not in 129/SvY^{rm Pos}(male). Equal, 10^{-1}, 10^ {-2}, and 0 copies (relative to males) of Y^{rm Pos}-specific deletion products respectively characterize C57BL/6JY ^{rm Pos} (HC), (LC), (T) and (F) females. The testes determining loci of inactive Y^{rm Pos}-chromosomes in C57BL/6JY^{rm Pos} HC females are the preferentially deleted/rearranged Y ^{rm Pos}-sequences. Disruption of regulation of plasma testosterone and hepatic MUP-A mRNA levels, TRD of a 4.7 Kbp EcoR1 fragment suggest disruption of autosomal/X-chromosomal sequences. These data and the highly repeated progenitor (Alu, GATA, LINE-1

Evolution of DNA Methylation across Insects.

PubMed

Bewick, Adam J; Vogel, Kevin J; Moore, Allen J; Schmitz, Robert J

2017-03-01

DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Effective Strategies for Teaching Evolution: The Primary Evolution Project

ERIC Educational Resources Information Center

Hatcher, Chris

2015-01-01

When Chris Hatcher joined the Primary Evolution Project team at the University of Reading, his goal was to find effective strategies to teach evolution in a way that keeps children engaged and enthused. Hatcher has collaborated with colleagues at the University's Institute of Education to break the evolution unit down into distinct topics and…

Identifying artificial selection signals in the chicken genome.

PubMed

Ma, Yunlong; Gu, Lantao; Yang, Liubin; Sun, Chenghao; Xie, Shengsong; Fang, Chengchi; Gong, Yangzhang; Li, Shijun

2018-01-01

Identifying the signals of artificial selection can contribute to further shaping economically important traits. Here, a chicken 600k SNP-array was employed to detect the signals of artificial selection using 331 individuals from 9 breeds, including Jingfen (JF), Jinghong (JH), Araucanas (AR), White Leghorn (WL), Pekin-Bantam (PB), Shamo (SH), Gallus-Gallus-Spadiceus (GA), Rheinlander (RH) and Vorwerkhuhn (VO). Per the population genetic structure, 9 breeds were combined into 5 breed-pools, and a 'two-step' strategy was used to reveal the signals of artificial selection. GA, which has little artificial selection, was defined as the reference population, and a total of 204, 155, 305 and 323 potential artificial selection signals were identified in AR_VO, PB, RH_WL and JH_JF, respectively. We also found signals derived from standing and de-novo genetic variations have contributed to adaptive evolution during artificial selection. Further enrichment analysis suggests that the genomic regions of artificial selection signals harbour genes, including THSR, PTHLH and PMCH, responsible for economic traits, such as fertility, growth and immunization. Overall, this study found a series of genes that contribute to the improvement of chicken breeds and revealed the genetic mechanisms of adaptive evolution, which can be used as fundamental information in future chicken functional genomics study.

A data dictionary approach to multilingual documentation and decision support for the diagnosis of acute abdominal pain. (COPERNICUS 555, an European concerted action).

PubMed

Ohmann, C; Eich, H P; Sippel, H

1998-01-01

This paper describes the design and development of a multilingual documentation and decision support system for the diagnosis of acute abdominal pain. The work was performed within a multi-national COPERNICUS European concerted action dealing with information technology for quality assurance in acute abdominal pain in Europe (EURO-AAP, 555). The software engineering was based on object-oriented analysis design and programming. The program cover three modules: a data dictionary, a documentation program and a knowledge based system. National versions of the software were provided and introduced into 16 centers from Central and Eastern Europe. A prospective data collection was performed in which 4020 patients were recruited. The software design has been proven to be very efficient and useful for the development of multilingual software.

Punctuated Copy Number Evolution and Clonal Stasis in Triple-Negative Breast Cancer

PubMed Central

Gao, Ruli; Davis, Alexander; McDonald, Thomas O.; Sei, Emi; Shi, Xiuqing; Wang, Yong; Tsai, Pei-Ching; Casasent, Anna; Waters, Jill; Zhang, Hong; Meric-Bernstam, Funda; Michor, Franziska; Navin, Nicholas E.

2016-01-01

Aneuploidy is a hallmark of breast cancer; however, our knowledge of how these complex genomic rearrangements evolve during tumorigenesis is limited. In this study we developed a highly multiplexed single-nucleus-sequencing method to investigate copy number evolution in triple-negative breast cancer patients. We sequenced 1000 single cells from 12 patients and identified 1–3 major clonal subpopulations in each tumor that shared a common evolutionary lineage. We also identified a minor subpopulation of non-clonal cells that were classified as: 1) metastable, 2) pseudo-diploid, or 3) chromazemic. Phylogenetic analysis and mathematical modeling suggest that these data are unlikely to be explained by the gradual accumulation of copy number events over time. In contrast, our data challenge the paradigm of gradual evolution, showing that the majority of copy number aberrations are acquired at the earliest stages of tumor evolution, in short punctuated bursts, followed by stable clonal expansions that form the tumor mass. PMID:27526321

The evolution of plant-insect mutualisms.

PubMed

Bronstein, Judith L; Alarcón, Ruben; Geber, Monica

2006-01-01

Mutualisms (cooperative interactions between species) have had a central role in the generation and maintenance of life on earth. Insects and plants are involved in diverse forms of mutualism. Here we review evolutionary features of three prominent insect-plant mutualisms: pollination, protection and seed dispersal. We focus on addressing five central phenomena: evolutionary origins and maintenance of mutualism; the evolution of mutualistic traits; the evolution of specialization and generalization; coevolutionary processes; and the existence of cheating. Several features uniting very diverse insect-plant mutualisms are identified and their evolutionary implications are discussed: the involvement of one mobile and one sedentary partner; natural selection on plant rewards; the existence of a continuum from specialization to generalization; and the ubiquity of cheating, particularly on the part of insects. Plant-insect mutualisms have apparently both arisen and been lost repeatedly. Many adaptive hypotheses have been proposed to explain these transitions, and it is unlikely that any one of them dominates across interactions differing so widely in natural history. Evolutionary theory has a potentially important, but as yet largely unfilled, role to play in explaining the origins, maintenance, breakdown and evolution of insect-plant mutualisms.

Genetics of Rapid and Extreme Size Evolution in Island Mice

PubMed Central

Gray, Melissa M.; Parmenter, Michelle D.; Hogan, Caley A.; Ford, Irene; Cuthbert, Richard J.; Ryan, Peter G.; Broman, Karl W.; Payseur, Bret A.

2015-01-01

Organisms on islands provide a revealing window into the process of adaptation. Populations that colonize islands often evolve substantial differences in body size from their mainland relatives. Although the ecological drivers of this phenomenon have received considerable attention, its genetic basis remains poorly understood. We use house mice (subspecies: Mus musculus domesticus) from remote Gough Island to provide a genetic portrait of rapid and extreme size evolution. In just a few hundred generations, Gough Island mice evolved the largest body size among wild house mice from around the world. Through comparisons with a smaller-bodied wild-derived strain from the same subspecies (WSB/EiJ), we demonstrate that Gough Island mice achieve their exceptional body weight primarily by growing faster during the 6 weeks after birth. We use genetic mapping in large F2 intercrosses between Gough Island mice and WSB/EiJ to identify 19 quantitative trait loci (QTL) responsible for the evolution of 16-week weight trajectories: 8 QTL for body weight and 11 QTL for growth rate. QTL exhibit modest effects that are mostly additive. We conclude that body size evolution on islands can be genetically complex, even when substantial size changes occur rapidly. In comparisons to published studies of laboratory strains of mice that were artificially selected for divergent body sizes, we discover that the overall genetic profile of size evolution in nature and in the laboratory is similar, but many contributing loci are distinct. Our results underscore the power of genetically characterizing the entire growth trajectory in wild populations and lay the foundation necessary for identifying the mutations responsible for extreme body size evolution in nature. PMID:26199233

Predicting Key Events in the Popularity Evolution of Online Information

PubMed Central

Fu, Shushen; Fang, Mingzhe; Xu, Wenwen

2017-01-01

The popularity of online information generally experiences a rising and falling evolution. This paper considers the “burst”, “peak”, and “fade” key events together as a representative summary of popularity evolution. We propose a novel prediction task—predicting when popularity undergoes these key events. It is of great importance to know when these three key events occur, because doing so helps recommendation systems, online marketing, and containment of rumors. However, it is very challenging to solve this new prediction task due to two issues. First, popularity evolution has high variation and can follow various patterns, so how can we identify “burst”, “peak”, and “fade” in different patterns of popularity evolution? Second, these events usually occur in a very short time, so how can we accurately yet promptly predict them? In this paper we address these two issues. To handle the first one, we use a simple moving average to smooth variation, and then a universal method is presented for different patterns to identify the key events in popularity evolution. To deal with the second one, we extract different types of features that may have an impact on the key events, and then a correlation analysis is conducted in the feature selection step to remove irrelevant and redundant features. The remaining features are used to train a machine learning model. The feature selection step improves prediction accuracy, and in order to emphasize prediction promptness, we design a new evaluation metric which considers both accuracy and promptness to evaluate our prediction task. Experimental and comparative results show the superiority of our prediction solution. PMID:28046121

The Origin and Early Evolution of Membrane Proteins

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Schweighofter, Karl; Wilson, Michael A.

2006-01-01

The origin and early evolution of membrane proteins, and in particular ion channels, are considered from the point of view that the transmembrane segments of membrane proteins are structurally quite simple and do not require specific sequences to fold. We argue that the transport of solute species, especially ions, required an early evolution of efficient transport mechanisms, and that the emergence of simple ion channels was protobiologically plausible. We also argue that, despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. These properties can be subtly modulated by local modifications to the sequence rather than global changes in molecular architecture. In order to address the evolution and development of ion channels, we focus on identifying those protein domains that are commonly associated with ion channel proteins and are conserved throughout the three main domains of life (Eukarya, Prokarya, and Archaea). We discuss the potassium-sodium-calcium superfamily of voltage-gated ion channels, mechanosensitive channels, porins, and ABC-transporters and argue that these families of membrane channels have sufficiently universal architectures that they can readily adapt to the diverse functional demands arising during evolution.

A Generative Angular Model of Protein Structure Evolution

PubMed Central

Golden, Michael; García-Portugués, Eduardo; Sørensen, Michael; Mardia, Kanti V.; Hamelryck, Thomas; Hein, Jotun

2017-01-01

Abstract Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale. The model concerns the local dependencies between sequence and structure evolution in a pair of homologous proteins. The evolutionary trajectory between the two structures in the protein pair is treated as a random walk in dihedral angle space, which is modeled using a novel angular diffusion process on the two-dimensional torus. Coupling sequence and structure evolution in our model allows for modeling both “smooth” conformational changes and “catastrophic” conformational jumps, conditioned on the amino acid changes. The model has interpretable parameters and is comparatively more realistic than previous stochastic models, providing new insights into the relationship between sequence and structure evolution. For example, using the trained model we were able to identify an apparent sequence–structure evolutionary motif present in a large number of homologous protein pairs. The generative nature of our model enables us to evaluate its validity and its ability to simulate aspects of protein evolution conditioned on an amino acid sequence, a related amino acid sequence, a related structure or any combination thereof. PMID:28453724

Quantifying long-term evolution of intra-urban spatial interactions

PubMed Central

Sun, Lijun; Jin, Jian Gang; Axhausen, Kay W.; Lee, Der-Horng; Cebrian, Manuel

2015-01-01

Understanding the long-term impact that changes in a city's transportation infrastructure have on its spatial interactions remains a challenge. The difficulty arises from the fact that the real impact may not be revealed in static or aggregated mobility measures, as these are remarkably robust to perturbations. More generally, the lack of longitudinal, cross-sectional data demonstrating the evolution of spatial interactions at a meaningful urban scale also hinders us from evaluating the sensitivity of movement indicators, limiting our capacity to understand the evolution of urban mobility in depth. Using very large mobility records distributed over 3 years, we quantify the impact of the completion of a metro line extension: the Circle Line (CCL) in Singapore. We find that the commonly used movement indicators are almost identical before and after the project was completed. However, in comparing the temporal community structure across years, we do observe significant differences in the spatial reorganization of the affected geographical areas. The completion of CCL enables travellers to re-identify their desired destinations collectively with lower transport cost, making the community structure more consistent. These changes in locality are dynamic and characterized over short timescales, offering us a different approach to identify and analyse the long-term impact of new infrastructures on cities and their evolution dynamics. PMID:25551142

A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

PubMed Central

Werner, Gijsbert D. A.; Cornwell, William K.; Sprent, Janet I.; Kattge, Jens; Kiers, E. Toby

2014-01-01

Symbiotic associations occur in every habitat on earth, but we know very little about their evolutionary histories. Current models of trait evolution cannot adequately reconstruct the deep history of symbiotic innovation, because they assume homogenous evolutionary processes across millions of years. Here we use a recently developed, heterogeneous and quantitative phylogenetic framework to study the origin of the symbiosis between angiosperms and nitrogen-fixing (N2) bacterial symbionts housed in nodules. We compile the largest database of global nodulating plant species and reconstruct the symbiosis’ evolution. We identify a single, cryptic evolutionary innovation driving symbiotic N2-fixation evolution, followed by multiple gains and losses of the symbiosis, and the subsequent emergence of ‘stable fixers’ (clades extremely unlikely to lose the symbiosis). Originating over 100 MYA, this innovation suggests deep homology in symbiotic N2-fixation. Identifying cryptic innovations on the tree of life is key to understanding the evolution of complex traits, including symbiotic partnerships. PMID:24912610

Evolutionary rescue of a parasite population by mutation rate evolution.

PubMed

Greenspoon, Philip B; Mideo, Nicole

2017-10-01

The risk of antibiotic resistance evolution in parasites is a major problem for public health. Identifying factors which promote antibiotic resistance evolution is thus a priority in evolutionary medicine. The rate at which new mutations enter the parasite population is one important predictor; however, mutation rate is not necessarily a fixed quantity, as is often assumed, but can itself evolve. Here we explore the possible impacts of mutation rate evolution on the fate of a disease circulating in a host population, which is being treated with drugs, the use of which varies over time. Using an evolutionary rescue framework, we find that mutation rate evolution provides a dramatic increase in the probability that a parasite population survives treatment in only a limited region, while providing little or no advantage in other regions. Both epidemiological features, such as the virulence of infection, and population genetic parameters, such as recombination rate, play important roles in determining the probability of evolutionary rescue and whether mutation rate evolution enhances the probability of evolutionary rescue or not. While efforts to curtail mutation rate evolution in parasites may be worthwhile under some circumstances, our results suggest that this need not always be the case. Copyright © 2017 Elsevier Inc. All rights reserved.

Cosmological evolution of the nitrogen abundance

NASA Astrophysics Data System (ADS)

Vangioni, Elisabeth; Dvorkin, Irina; Olive, Keith A.; Dubois, Yohan; Molaro, Paolo; Petitjean, Patrick; Silk, Joe; Kimm, Taysun

2018-06-01

The abundance of nitrogen in the interstellar medium is a powerful probe of star formation processes over cosmological time-scales. Since nitrogen can be produced both in massive and intermediate-mass stars with metallicity-dependent yields, its evolution is challenging to model, as evidenced by the differences between theoretical predictions and observations. In this work, we attempt to identify the sources of these discrepancies using a cosmic evolution model. To further complicate matters, there is considerable dispersion in the abundances from observations of damped Lyα absorbers (DLAs) at z ˜ 2-3. We study the evolution of nitrogen with a detailed cosmic chemical evolution model and find good agreement with these observations, including the relative abundances of (N/O) and (N/Si). We find that the principal contribution of nitrogen comes from intermediate-mass stars, with the exception of systems with the lowest N/H, where nitrogen production might possibly be dominated by massive stars. This last result could be strengthened if stellar rotation which is important at low metallicity can produce significant amounts of nitrogen. Moreover, these systems likely reside in host galaxies with stellar masses below 108.5 M⊙. We also study the origin of the observed dispersion in nitrogen abundances using the cosmological hydrodynamical simulations Horizon-AGN. We conclude that this dispersion can originate from two effects: difference in the masses of the DLA host galaxies, and difference in their position inside the galaxy.

Convergent evolution of a fused sexual cycle promotes the haploid lifestyle

NASA Astrophysics Data System (ADS)

Sherwood, Racquel Kim; Scaduto, Christine M.; Torres, Sandra E.; Bennett, Richard J.

2014-02-01

Sexual reproduction is restricted to eukaryotic species and involves the fusion of haploid gametes to form a diploid cell that subsequently undergoes meiosis to generate recombinant haploid forms. This process has been extensively studied in the unicellular yeast Saccharomyces cerevisiae, which exhibits separate regulatory control over mating and meiosis. Here we address the mechanism of sexual reproduction in the related hemiascomycete species Candida lusitaniae. We demonstrate that, in contrast to S. cerevisiae, C. lusitaniae exhibits a highly integrated sexual program in which the programs regulating mating and meiosis have fused. Profiling of the C. lusitaniae sexual cycle revealed that gene expression patterns during mating and meiosis were overlapping, indicative of co-regulation. This was particularly evident for genes involved in pheromone MAPK signalling, which were highly induced throughout the sexual cycle of C. lusitaniae. Furthermore, genetic analysis showed that the orthologue of IME2, a `diploid-specific' factor in S. cerevisiae, and STE12, the master regulator of S. cerevisiae mating, were each required for progression through both mating and meiosis in C. lusitaniae. Together, our results establish that sexual reproduction has undergone significant rewiring between S. cerevisiae and C. lusitaniae, and that a concerted sexual cycle operates in C. lusitaniae that is more reminiscent of the distantly related ascomycete, Schizosaccharomyces pombe. We discuss these results in light of the evolution of sexual reproduction in yeast, and propose that regulatory coupling of mating and meiosis has evolved multiple times as an adaptation to promote the haploid lifestyle.

Long-term radio and X-ray evolution of the tidal disruption event ASASSN-14li

NASA Astrophysics Data System (ADS)

Bright, J. S.; Fender, R. P.; Motta, S. E.; Mooley, K.; Perrott, Y. C.; van Velzen, S.; Carey, S.; Hickish, J.; Razavi-Ghods, N.; Titterington, D.; Scott, P.; Grainge, K.; Scaife, A.; Cantwell, T.; Rumsey, C.

2018-04-01

We report on late time radio and X-ray observations of the tidal disruption event candidate ASASSN-14li, covering the first 1000 d of the decay phase. For the first ˜200 d the radio and X-ray emission fade in concert. This phase is better fitted by an exponential decay at X-ray wavelengths, while the radio emission is well described by either an exponential or the canonical t-5/3 decay assumed for tidal disruption events. The correlation between radio and X-ray emission during this period can be fitted as L_R∝ L_X^{1.9± 0.2}. After 400 d the radio emission at 15.5 GHz has reached a plateau level of 244 ± 8 μJy which it maintains for at least the next 600 d, while the X-ray emission continues to fade exponentially. This steady level of radio emission is likely due to relic radio lobes from the weak AGN-like activity implied by historical radio observations. We note that while most existing models are based upon the evolution of ejecta which are decoupled from the central black hole, the radio-X-ray correlation during the declining phase is also consistent with core-jet emission coupled to a radiatively efficient accretion flow.

Soft gluon evolution and non-global logarithms

NASA Astrophysics Data System (ADS)

Martínez, René Ángeles; De Angelis, Matthew; Forshaw, Jeffrey R.; Plätzer, Simon; Seymour, Michael H.

2018-05-01

We consider soft-gluon evolution at the amplitude level. Our evolution algorithm applies to generic hard-scattering processes involving any number of coloured partons and we present a reformulation of the algorithm in such a way as to make the cancellation of infrared divergences explicit. We also emphasise the special role played by a Lorentz-invariant evolution variable, which coincides with the transverse momentum of the latest emission in a suitably defined dipole zero-momentum frame. Handling large colour matrices presents the most significant challenge to numerical implementations and we present a means to expand systematically about the leading colour approximation. Specifically, we present a systematic procedure to calculate the resulting colour traces, which is based on the colour flow basis. Identifying the leading contribution leads us to re-derive the Banfi-Marchesini-Smye equation. However, our formalism is more general and can systematically perform resummation of contributions enhanced by the t'Hooft coupling α s N ˜ 1, along with successive perturbations that are parametrically suppressed by powers of 1 /N . We also discuss how our approach relates to earlier work.

The evolution of speech: a comparative review.

PubMed

Fitch

2000-07-01

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

Conference on Early Mars: Geologic and Hydrologic Evolution, Physical and Chemical Environments, and the Implications for Life

NASA Technical Reports Server (NTRS)

Clifford, S. M. (Editor); Treiman, A. H. (Editor); Newsom, H. E. (Editor); Farmer, J. D. (Editor)

1997-01-01

Topics considered include: Geology alteration and life in an extreme environment; developing a chemical code to identify magnetic biominerals; effect of impacts on early Martin geologic evolution; spectroscopic identification of minerals in Hematite-bearing soils and sediments; exopaleontology and the search for a Fossil record on Mars; geochemical evolution of the crust of Mars; geological evolution of the early earth;solar-wind-induced erosion of the Mars atmosphere. Also included geological evolution of the crust of Mars.

Delegation to automaticity: the driving force for cognitive evolution?

PubMed

Shine, J M; Shine, R

2014-01-01

The ability to delegate control over repetitive tasks from higher to lower neural centers may be a fundamental innovation in human cognition. Plausibly, the massive neurocomputational challenges associated with the mastery of balance during the evolution of bipedality in proto-humans provided a strong selective advantage to individuals with brains capable of efficiently transferring tasks in this way. Thus, the shift from quadrupedal to bipedal locomotion may have driven the rapid evolution of distinctive features of human neuronal functioning. We review recent studies of functional neuroanatomy that bear upon this hypothesis, and identify ways to test our ideas.

Heterogeneity of link weight and the evolution of cooperation

NASA Astrophysics Data System (ADS)

Iwata, Manabu; Akiyama, Eizo

2016-04-01

In this paper, we investigate the effect of heterogeneity of link weight, heterogeneity of the frequency or amount of interactions among individuals, on the evolution of cooperation. Based on an analysis of the evolutionary prisoner's dilemma game on a weighted one-dimensional lattice network with intra-individual heterogeneity, we confirm that moderate level of link-weight heterogeneity can facilitate cooperation. Furthermore, we identify two key mechanisms by which link-weight heterogeneity promotes the evolution of cooperation: mechanisms for spread and maintenance of cooperation. We also derive the corresponding conditions under which the mechanisms can work through evolutionary dynamics.

Quantifying patterns of research interest evolution

NASA Astrophysics Data System (ADS)

Jia, Tao; Wang, Dashun; Szymanski, Boleslaw

Changing and shifting research interest is an integral part of a scientific career. Despite extensive investigations of various factors that influence a scientist's choice of research topics, quantitative assessments of mechanisms that give rise to macroscopic patterns characterizing research interest evolution of individual scientists remain limited. Here we perform a large-scale analysis of extensive publication records, finding that research interest change follows a reproducible pattern characterized by an exponential distribution. We identify three fundamental features responsible for the observed exponential distribution, which arise from a subtle interplay between exploitation and exploration in research interest evolution. We develop a random walk based model, which adequately reproduces our empirical observations. Our study presents one of the first quantitative analyses of macroscopic patterns governing research interest change, documenting a high degree of regularity underlying scientific research and individual careers.

The Nature of the Arguments for Creationism, Intelligent Design, and Evolution

NASA Astrophysics Data System (ADS)

Barnes, Ralph M.; Church, Rebecca A.; Draznin-Nagy, Samuel

2017-03-01

Seventy-two Internet documents promoting creationism, intelligent design (I.D.), or evolution were selected for analysis. The primary goal of each of the 72 documents was to present arguments for creationism, I.D., or evolution. We first identified all arguments in these documents. Each argument was then coded in terms of both argument type (appeal to authority, appeal to empirical evidence, appeal to reason, etc.) and argument topic (age of earth, mechanism of descent with modification, etc.). We then provided a quantitative summary of each argument type and topic for each of the three positions. Three clear patterns were revealed by the data. First, websites promoting evolution were characterized by a narrow focus on appeals to empirical evidence, whereas websites promoting creationism and I.D. were quite heterogeneous in regards to argument type. Second, websites promoting evolution relied primarily on a small number of empirical examples (e.g., fossils, biogeography, homology, etc.), while websites promoting creationism and I.D. used a far greater range of arguments. Finally, websites promoting evolution were narrowly focused on the topic of descent with modification. In contrast, websites promoting creationism tackled a broad range of topics, while websites promoting I.D. were narrowly focused on the issue of the existence of God. The current study provides a quantitative summary of a systematic content analysis of argument type and topic across a large number of frequently accessed websites dealing with origins. The analysis we have used may prove fruitful in identifying and understanding argumentation trends in scientific writing and pseudo-scientific writing.

Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance

PubMed Central

Mead, Rebecca; Hejmadi, Momna

2017-01-01

What is the best way to teach evolution? As microevolution may be configured as a branch of genetics, it being a short conceptual leap from understanding the concepts of mutation and alleles (i.e., genetics) to allele frequency change (i.e., evolution), we hypothesised that learning genetics prior to evolution might improve student understanding of evolution. In the UK, genetics and evolution are typically taught to 14- to 16-y-old secondary school students as separate topics with few links, in no particular order and sometimes with a large time span between. Here, then, we report the results of a large trial into teaching order of evolution and genetics. We modified extant questionnaires to ascertain students’ understanding of evolution and genetics along with acceptance of evolution. Students were assessed prior to teaching, immediately post teaching and again after several months. Teachers were not instructed what to teach, just to teach in a given order. Regardless of order, teaching increased understanding and acceptance, with robust signs of longer-term retention. Importantly, teaching genetics before teaching evolution has a significant (p < 0.001) impact on improving evolution understanding by 7% in questionnaire scores beyond the increase seen for those taught in the inverse order. For lower ability students, an improvement in evolution understanding was seen only if genetics was taught first. Teaching genetics first additionally had positive effects on genetics understanding, by increasing knowledge. These results suggest a simple, minimally disruptive, zero-cost intervention to improve evolution understanding: teach genetics first. This same alteration does not, however, result in a significantly increased acceptance of evolution, which reflects a weak correlation between knowledge and acceptance of evolution. Qualitative focus group data highlights the role of authority figures in determination of acceptance. PMID:28542179

Teaching genetics prior to teaching evolution improves evolution understanding but not acceptance.

PubMed

Mead, Rebecca; Hejmadi, Momna; Hurst, Laurence D

2017-05-01

What is the best way to teach evolution? As microevolution may be configured as a branch of genetics, it being a short conceptual leap from understanding the concepts of mutation and alleles (i.e., genetics) to allele frequency change (i.e., evolution), we hypothesised that learning genetics prior to evolution might improve student understanding of evolution. In the UK, genetics and evolution are typically taught to 14- to 16-y-old secondary school students as separate topics with few links, in no particular order and sometimes with a large time span between. Here, then, we report the results of a large trial into teaching order of evolution and genetics. We modified extant questionnaires to ascertain students' understanding of evolution and genetics along with acceptance of evolution. Students were assessed prior to teaching, immediately post teaching and again after several months. Teachers were not instructed what to teach, just to teach in a given order. Regardless of order, teaching increased understanding and acceptance, with robust signs of longer-term retention. Importantly, teaching genetics before teaching evolution has a significant (p < 0.001) impact on improving evolution understanding by 7% in questionnaire scores beyond the increase seen for those taught in the inverse order. For lower ability students, an improvement in evolution understanding was seen only if genetics was taught first. Teaching genetics first additionally had positive effects on genetics understanding, by increasing knowledge. These results suggest a simple, minimally disruptive, zero-cost intervention to improve evolution understanding: teach genetics first. This same alteration does not, however, result in a significantly increased acceptance of evolution, which reflects a weak correlation between knowledge and acceptance of evolution. Qualitative focus group data highlights the role of authority figures in determination of acceptance.

Concerted changes in N and C primary metabolism in alfalfa (Medicago sativa) under water restriction

PubMed Central

Aranjuelo, Iker

2013-01-01

Although the mechanisms of nodule N2 fixation in legumes are now well documented, some uncertainty remains on the metabolic consequences of water deficit. In most cases, little consideration is given to other organs and, therefore, the coordinated changes in metabolism in leaves, roots, and nodules are not well known. Here, the effect of water restriction on exclusively N2-fixing alfalfa (Medicago sativa L.) plants was investigated, and proteomic, metabolomic, and physiological analyses were carried out. It is shown that the inhibition of nitrogenase activity caused by water restriction was accompanied by concerted alterations in metabolic pathways in nodules, leaves, and roots. The data suggest that nodule metabolism and metabolic exchange between plant organs nearly reached homeostasis in asparagine synthesis and partitioning, as well as the N demand from leaves. Typically, there was (i) a stimulation of the anaplerotic pathway to sustain the provision of C skeletons for amino acid (e.g. glutamate and proline) synthesis; (ii) re-allocation of glycolytic products to alanine and serine/glycine; and (iii) subtle changes in redox metabolites suggesting the implication of a slight oxidative stress. Furthermore, water restriction caused little change in both photosynthetic efficiency and respiratory cost of N2 fixation by nodules. In other words, the results suggest that under water stress, nodule metabolism follows a compromise between physiological imperatives (N demand, oxidative stress) and the lower input to sustain catabolism. PMID:23440170

Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins

DOE PAGES

Zhao, Baoyu; Shu, Chang; Gao, Xinsheng; ...

2016-06-02

Type I IFNs are key cytokines mediating innate antiviral immunity. cGMP-AMP synthase, ritinoic acid-inducible protein 1 (RIG-I)–like receptors, and Toll-like receptors recognize microbial double-stranded (ds)DNA, dsRNA, and LPS to induce the expression of type I IFNs. These signaling pathways converge at the recruitment and activation of the transcription factor IRF-3 (IFN regulatory factor 3). The adaptor proteins STING (stimulator of IFN genes), MAVS (mitochondrial antiviral signaling), and TRIF (TIR domain-containing adaptor inducing IFN-β) mediate the recruitment of IRF-3 through a conserved pLxIS motif. Here in this paper, we show that the pLxIS motif of phosphorylated STING, MAVS, and TRIF bindsmore » to IRF-3 in a similar manner, whereas residues upstream of the motif confer specificity. The structure of the IRF-3 phosphomimetic mutant S386/396E bound to the cAMP response element binding protein (CREB)-binding protein reveals that the pLxIS motif also mediates IRF-3 dimerization and activation. Moreover, rotavirus NSP1 (nonstructural protein 1) employs a pLxIS motif to target IRF-3 for degradation, but phosphorylation of NSP1 is not required for its activity. These results suggest a concerted mechanism for the recruitment and activation of IRF-3 that can be subverted by viral proteins to evade innate immune responses.« less

Structural basis for concerted recruitment and activation of IRF-3 by innate immune adaptor proteins

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

Zhao, Baoyu; Shu, Chang; Gao, Xinsheng

Type I IFNs are key cytokines mediating innate antiviral immunity. cGMP-AMP synthase, ritinoic acid-inducible protein 1 (RIG-I)–like receptors, and Toll-like receptors recognize microbial double-stranded (ds)DNA, dsRNA, and LPS to induce the expression of type I IFNs. These signaling pathways converge at the recruitment and activation of the transcription factor IRF-3 (IFN regulatory factor 3). The adaptor proteins STING (stimulator of IFN genes), MAVS (mitochondrial antiviral signaling), and TRIF (TIR domain-containing adaptor inducing IFN-β) mediate the recruitment of IRF-3 through a conserved pLxIS motif. Here in this paper, we show that the pLxIS motif of phosphorylated STING, MAVS, and TRIF bindsmore » to IRF-3 in a similar manner, whereas residues upstream of the motif confer specificity. The structure of the IRF-3 phosphomimetic mutant S386/396E bound to the cAMP response element binding protein (CREB)-binding protein reveals that the pLxIS motif also mediates IRF-3 dimerization and activation. Moreover, rotavirus NSP1 (nonstructural protein 1) employs a pLxIS motif to target IRF-3 for degradation, but phosphorylation of NSP1 is not required for its activity. These results suggest a concerted mechanism for the recruitment and activation of IRF-3 that can be subverted by viral proteins to evade innate immune responses.« less

Evolution of photoperiod sensing in plants and algae.

PubMed

Serrano-Bueno, Gloria; Romero-Campero, Francisco J; Lucas-Reina, Eva; Romero, Jose M; Valverde, Federico

2017-06-01

Measuring day length confers a strong fitness improvement to photosynthetic organisms as it allows them to anticipate light phases and take the best decisions preceding diurnal transitions. In close association with signals from the circadian clock and the photoreceptors, photoperiodic sensing constitutes also a precise way to determine the passing of the seasons and to take annual decisions such as the best time to flower or the beginning of dormancy. Photoperiodic sensing in photosynthetic organisms is ancient and two major stages in its evolution could be identified, the cyanobacterial time sensing and the evolutionary tool kit that arose in green algae and developed into the photoperiodic system of modern plants. The most recent discoveries about the evolution of the perception of light, measurement of day length and relationship with the circadian clock along the evolution of the eukaryotic green lineage will be discussed in this review. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Rapid and Recent Evolution of LTR Retrotransposons Drives Rice Genome Evolution During the Speciation of AA-Genome Oryza Species

PubMed Central

Zhang, Qun-Jie; Gao, Li-Zhi

2017-01-01

The dynamics of long terminal repeat (LTR) retrotransposons and their contribution to genome evolution during plant speciation have remained largely unanswered. Here, we perform a genome-wide comparison of all eight Oryza AA-genome species, and identify 3911 intact LTR retrotransposons classified into 790 families. The top 44 most abundant LTR retrotransposon families show patterns of rapid and distinct diversification since the species split over the last ∼4.8 MY (million years). Phylogenetic and read depth analyses of 11 representative retrotransposon families further provide a comprehensive evolutionary landscape of these changes. Compared with Ty1-copia, independent bursts of Ty3-gypsy retrotransposon expansions have occurred with the three largest showing signatures of lineage-specific evolution. The estimated insertion times of 2213 complete retrotransposons from the top 23 most abundant families reveal divergent life histories marked by speedy accumulation, decline, and extinction that differed radically between species. We hypothesize that this rapid evolution of LTR retrotransposons not only divergently shaped the architecture of rice genomes but also contributed to the process of speciation and diversification of rice. PMID:28413161

Protein interactions in 3D: from interface evolution to drug discovery.

PubMed

Winter, Christof; Henschel, Andreas; Tuukkanen, Anne; Schroeder, Michael

2012-09-01

Over the past 10years, much research has been dedicated to the understanding of protein interactions. Large-scale experiments to elucidate the global structure of protein interaction networks have been complemented by detailed studies of protein interaction interfaces. Understanding the evolution of interfaces allows one to identify convergently evolved interfaces which are evolutionary unrelated but share a few key residues and hence have common binding partners. Understanding interaction interfaces and their evolution is an important basis for pharmaceutical applications in drug discovery. Here, we review the algorithms and databases on 3D protein interactions and discuss in detail applications in interface evolution, drug discovery, and interface prediction. Copyright © 2012 Elsevier Inc. All rights reserved.

Evolution of Life and SETI (Evo-SETI)

NASA Astrophysics Data System (ADS)

Maccone, Claudio

forced by us to have their peak value located on the exponential mean-value curve of the GBM (this is the so-called “Peak-Locus Theorem”). In the framework of Darwinian Evolution, the resulting mathematical construction was shown to identify with Cladistics (refs. [2], [3], [4]). 4) The (Shannon) Entropy of such b-lognormals is then seen to represent the “degree of progress” reached by each living organism or by each big set of living organisms, like historic human civilizations. Having understood this fact, Human History may then be cast into the language of b-lognormals that are more and more organized in time (i.e. having smaller and smaller entropy, or smaller and smaller “chaos”), and have their peaks located on the increasing GBM exponential. This exponential is thus the “trend of progress” in Human History. 5) But our most striking new result is about the well-known “Molecular Clock of Evolution”, namely the “constant rate of Evolution at the molecular level” as shown by Kimura’s Neutral Theory of Molecular Evolution. We showed that that the Molecular Clock identifies with Entropy in our Evo-SETI model because they both grew linearly in time since the origin of life. 6) Furthermore, we applid our Evo-SETI model to lognormal stochastic processes other then the GBMs. For instance, we showed that the Markov-Korotayev (2007-2008, refs. [5], [6]) model for Darwinian Evolution identifies with an Evo-SETI model for which the mean value of the lognormal stochastic process is a cubic (third degree polynomial) function of the time. In conclusion: we have provided a vast mathematical model capable of embracing Molecular Evolution, SETI and Entropy into a simple set of statistical equations based upon b-lognormals pdfs and lognormal stochastic processes Keywords: Molecular Clock, Darwinian evolution, statistical Drake equation, lognormal probability densities, geometric Brownian motion, entropy. REFERENCES [1] Maccone, C. (2008), “The Statistical

Understanding Evolution: An Evolution Website for Teachers

ERIC Educational Resources Information Center

Scotchmoor, Judy; Janulaw, Al

2005-01-01

While many states are facing challenges to the teaching of evolution in their science classrooms, the University of California Museum of Paleontology, working with the National Center for Science Education, has developed a useful web-based resource for science teachers of all grade- and experience-levels. Understanding Evolution (UE) was developed…

Position specific variation in the rate of evolution in transcription factor binding sites

PubMed Central

Moses, Alan M; Chiang, Derek Y; Kellis, Manolis; Lander, Eric S; Eisen, Michael B

2003-01-01

Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Results Here we analyse the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikatae to study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms. Conclusion As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the

Multiplicity evolution of identified particle charge-dependent correlations in Pb-Pb, p-Pb and pp collisions at the LHC with ALICE

NASA Astrophysics Data System (ADS)

Pan, Jinjin; Alice Collaboration

2017-09-01

The charge pair creation and transport processes in heavy-ion collisions are investigated experimentally by measurements of charge-dependent correlations of identified particle pairs, related to the Balance Function. The produced pair separation in rapidity is expected to be larger for hadrons arising from quark-antiquark pair creation in the early stages of the collision than for hadrons emerging from the later hadronization stage. Correlations are reported for charged-pion pairs in Pb-Pb, p-Pb and pp collisions at √{sNN } = 2.76, 5.02 and 7 TeV, respectively; and for charged-kaon pairs in Pb-Pb collisions at √{sNN } = 2.76 TeV. The correlations are measured as a function of relative rapidity Δy and azimuthal angle Δϕ , and are dominated by a peak centered at Δy = Δϕ = 0. We observe that the peak widths in Δy and Δϕ are narrower in higher multiplicity events in Pb-Pb, p-Pb, and pp collisions, which is consistent with the effects of radial flow, as well as the two-wave quark production mechanism. We investigate the charge transport and system evolution further by studying the Δϕ width of the peak as a function of Δy. Funded by the US Department of Energy.

Concerted ligand exchange and the roles of counter anions in the reversible structural switching of crystalline peptide metallo-macrocycles.

PubMed

Miyake, Ryosuke; Shionoya, Mitsuhiko

2014-06-02

To understand reversible structural switching in crystalline materials, we studied the mechanism of reversible crystal-to-crystal transformation of a tetranuclear Ni(II) macrocycle consisting of artificial β-dipeptides. On the basis of detailed structural analyses and thermodynamic measurements made in a comparison of pseudo-isostructural crystals (NO3 and BF4 salts), we herein discuss how ligand-exchange reactions take place in the crystal due to changes in water content and temperature. Observations of the structural transformation of NO3 salt indicated that a pseudo crystalline phase transformation takes place through concerted ligand-exchange reactions at the four Ni(II) centers of the macrocycle with hydrogen bond switching. A mechanism for this ligand exchange was supported by IR spectroscopy. Thermodynamic measurements suggested that the favorable compensation relationship of the enthalpy changes due to water uptake and structural changes are keys to the reversible structural transformation. On the basis of a comparison with the pseudo-isostructural crystals, it is apparent that the crystal packing structure and the types of counter anions are important factors for facilitating reversible ligand exchange with single crystallinity.

Bacterial examination of endodontic infections by clonal analysis in concert with denaturing high-performance liquid chromatography.

PubMed

Jacinto, R C; Gomes, B P F A; Desai, M; Rajendram, D; Shah, H N

2007-12-01

The aim of this study was to examine the diversity of bacterial species in the infected root canals of teeth associated with endodontic abscesses by cloning and sequencing techniques in concert with denaturing high-performance liquid chromatography. Samples collected from five infected root canals were subjected to polymerase chain reaction (PCR) with universal 16S ribosomal DNA primers. Products of these PCRs were cloned and sequenced. Denaturing high-performance liquid chromatography (DHPLC) was used as a screening method to reduce the number of clones necessary for DNA sequencing. All samples were positive for the presence of bacteria and a range of 7-13 different bacteria were found per root canal sample. In total, 48 different oral clones were detected among the five root canal samples. Olsenella profusa was the only species present in all samples. Porphyromonas gingivalis, Dialister pneumosintes, Dialister invisus, Lachnospiraceae oral clone, Staphylococcus aureus, Pseudoramibacter alactolyticus, Peptostreptococcus micros and Enterococcus faecalis were found in two of the five samples. The majority of the taxa were present in only one sample, for example Tannerella forsythia, Shuttleworthia satelles and Filifactor alocis. Some facultative anaerobes that are frequently isolated from endodontic infections such as E. faecalis, Streptococcus anginosus and Lactobacillus spp. were also found in this study. Clonal analysis of the microflora associated with endodontic infections revealed a wide diversity of oral species.

Thirty-Five Years of Research on Perceptual Strengths: Essential Strategies to Promote Learning

ERIC Educational Resources Information Center

Dunn, Rita; Dunn, Kenneth

2005-01-01

This article discusses the evolution of teaching approaches in concert with the findings of over three decades of researches on student perceptual strengths. Confusing reports of successes and only limited successes for students with varied perceptual strengths suggest that combined auditory, visual, tactual, and/or kinesthetic instructional…

Evolution education in Canada's museums: Where is human evolution?

NASA Astrophysics Data System (ADS)

Bean, Sarah

While an interest in the origin of human beings may be a cultural universal, there are various views and beliefs about how this event took place. In Canada, a recent (2010) Angus Reid survey revealed that only 61% of Canadians accepted that humans evolved over millions of years; 39% of the population either believed in creationism or did not accept evolution as a scientific fact. These statistics suggest that human evolution education is a topic that needs to be addressed. This thesis investigates the role of museums in public education about human evolution. Prior to this study, the number of Canadian museums with exhibits about this topic was unknown. Sixteen Canadian museums participated in this study, and the results demonstrated that only two had permanent exhibits on human evolution, and one creationist museum presented a biblically-based account of human origins. Here, it is argued that more of Canada's museums should consider incorporating human evolution education into their mandates.

The International Space Station Evolution Data Book: An Overview and Status

NASA Technical Reports Server (NTRS)

Antol, Jeffrey; Jorgensen, Catherine A.

1999-01-01

The evolution and enhancement of the International Space Station (ISS) is currently being planned in conjunction with the on-orbit construction of the baseline configuration. Three principal areas have been identified that will contribute to the evolution of ISS: Pre-Planned Program Improvement (P3I), Utilization & Commercialization, and Human Exploration and Development of Space (HEDS) missions. The ISS Evolution Strategy, under development by the Spacecraft and Sensors Branch of NASA Langley Research Center, seeks to coordinate the P3I technology development with Commercialization/Utilization activities and HEDS advanced mission accommodation to provide synergistic technology developments for all three areas. The focal point of this proposed strategy is the ISS Evolution Data Book (EDB), a tool for aiding the evolution and enhancement of ISS beyond Assembly Complete. This paper will discuss the strategy and provide an overview of the EDB, describing the contents of each section. It will also discuss potential applications of the EDB and present an example Design Reference Mission (DRM). The latest status of the EDB and the plans for completing and enhancing the book will also be summarized.

Evolution of limited seed dispersal ability on gypsum islands.

PubMed

Schenk, John J

2013-09-01

Dispersal is a major feature of plant evolution that has many advantages but is not always favored. Wide dispersal, for example, leads to greater seed loss in oceanic-island endemics, and evolution has favored morphologies that limit dispersal. I tested the hypothesis that selection favored limited dispersal on gypsum islands in western North America, where edaphic communities are sparsely vegetated except for a specialized flora that competes poorly with the surrounding flora. • I applied a series of comparative phylogenetic approaches to gypsophilic species of Mentzelia section Bartonia (Loasaceae) to investigate the evolution of limited dispersal function in seed wings, which increase primary dispersal by wind. Through these tests, I determined whether narrowed wings were selected for in gypsophilic species. • Gypsophily was derived four to seven times. Seed area was not significantly correlated with gypsophily or wing area. Wing area was significantly smaller in the derived gypsum endemics, supporting the hypothesis in favor of limited dispersal function. A model-fitting approach identified two trait optima in wing area, with gypsum endemics having a lower optimum. • Evolution into novel ecologies influences morphological evolution. Morphological characters have been selected for limited dispersal following evolution onto gypsum islands. Selection for limited dispersal ability has occurred across animals and plants, both in oceanic and terrestrial systems, which suggests that reduced dispersal ability may be a general process: selection favors limited dispersal if the difference in survival between the habitat of the parent and the surrounding area is great enough.

Paul Wittgenstein's right arm and his phantom: the saga of a famous concert pianist and his amputation.

PubMed

Boller, François; Bogousslavsky, Julien

2015-01-01

Reports of postamputation pain and problems linked to phantom limbs have increased in recent years, particularly in relation to war-related amputations. These problems are still poorly understood and are considered rather mysterious, and they are difficult to treat. In addition, they may shed light on brain physiology and neuropsychology. Functional neuroimaging techniques now enable us to better understand their pathophysiology and to consider new rehabilitation techniques. Several artists have suffered from postamputation complications and this has influenced not only their personal life but also their artistic work. Paul Wittgenstein (1887-1961), a pianist whose right arm was amputated during the First World War, became a famous left-handed concert performer. His case provides insight into Post-World War I musical and political history. More specifically, the impact on the artistic life of this pianist illustrates various postamputation complications, such as phantom limb, stump pain, and especially moving phantom. The phantom movements of his right hand helped him develop the dexterity of his left hand. Wittgenstein played piano works that were written especially for him (the most famous being Ravel's Concerto for the Left Hand) and composed some of his own. Additionally, several famous composers had previously written for the left hand. © 2015 Elsevier B.V. All rights reserved.

LEAMram (Trademark): Land Use Evolution and Impact Assessment Model Residential Attractiveness Model

DTIC Science & Technology

2006-09-01

MEPLAN are popular in both the United States and overseas, and focus on identifying growth by income and housing costs. These and other models focus...CUF-2), SLEUTH, Landuse Evolution Assessment Model (LEAM™), Smart Places, and What If?: • CUF-2 uses a set of econometric models to project...ER D C/ CE R L TR -0 6 -2 8 LEAMram™: Land use Evolution and impact Assessment Model Residential Attractiveness Model James D

Alternating high and low climate variability: The context of natural selection and speciation in Plio-Pleistocene hominin evolution.

PubMed

Potts, Richard; Faith, J Tyler

2015-10-01

Interaction of orbital insolation cycles defines a predictive model of alternating phases of high- and low-climate variability for tropical East Africa over the past 5 million years. This model, which is described in terms of climate variability stages, implies repeated increases in landscape/resource instability and intervening periods of stability in East Africa. It predicts eight prolonged (>192 kyr) eras of intensified habitat instability (high variability stages) in which hominin evolutionary innovations are likely to have occurred, potentially by variability selection. The prediction that repeated shifts toward high climate variability affected paleoenvironments and evolution is tested in three ways. In the first test, deep-sea records of northeast African terrigenous dust flux (Sites 721/722) and eastern Mediterranean sapropels (Site 967A) show increased and decreased variability in concert with predicted shifts in climate variability. These regional measurements of climate dynamics are complemented by stratigraphic observations in five basins with lengthy stratigraphic and paleoenvironmental records: the mid-Pleistocene Olorgesailie Basin, the Plio-Pleistocene Turkana and Olduvai Basins, and the Pliocene Tugen Hills sequence and Hadar Basin--all of which show that highly variable landscapes inhabited by hominin populations were indeed concentrated in predicted stages of prolonged high climate variability. Second, stringent null-model tests demonstrate a significant association of currently known first and last appearance datums (FADs and LADs) of the major hominin lineages, suites of technological behaviors, and dispersal events with the predicted intervals of prolonged high climate variability. Palynological study in the Nihewan Basin, China, provides a third test, which shows the occupation of highly diverse habitats in eastern Asia, consistent with the predicted increase in adaptability in dispersing Oldowan hominins. Integration of fossil, archeological

RNA Recombination Enhances Adaptability and Is Required for Virus Spread and Virulence.

PubMed

Xiao, Yinghong; Rouzine, Igor M; Bianco, Simone; Acevedo, Ashley; Goldstein, Elizabeth Faul; Farkov, Mikhail; Brodsky, Leonid; Andino, Raul

2016-04-13

Mutation and recombination are central processes driving microbial evolution. A high mutation rate fuels adaptation but also generates deleterious mutations. Recombination between two different genomes may resolve this paradox, alleviating effects of clonal interference and purging deleterious mutations. Here we demonstrate that recombination significantly accelerates adaptation and evolution during acute virus infection. We identified a poliovirus recombination determinant within the virus polymerase, mutation of which reduces recombination rates without altering replication fidelity. By generating a panel of variants with distinct mutation rates and recombination ability, we demonstrate that recombination is essential to enrich the population in beneficial mutations and purge it from deleterious mutations. The concerted activities of mutation and recombination are key to virus spread and virulence in infected animals. These findings inform a mathematical model to demonstrate that poliovirus adapts most rapidly at an optimal mutation rate determined by the trade-off between selection and accumulation of detrimental mutations. Copyright © 2016 Elsevier Inc. All rights reserved.

Genetics of Rapid and Extreme Size Evolution in Island Mice.

PubMed

Gray, Melissa M; Parmenter, Michelle D; Hogan, Caley A; Ford, Irene; Cuthbert, Richard J; Ryan, Peter G; Broman, Karl W; Payseur, Bret A

2015-09-01

Organisms on islands provide a revealing window into the process of adaptation. Populations that colonize islands often evolve substantial differences in body size from their mainland relatives. Although the ecological drivers of this phenomenon have received considerable attention, its genetic basis remains poorly understood. We use house mice (subspecies: Mus musculus domesticus) from remote Gough Island to provide a genetic portrait of rapid and extreme size evolution. In just a few hundred generations, Gough Island mice evolved the largest body size among wild house mice from around the world. Through comparisons with a smaller-bodied wild-derived strain from the same subspecies (WSB/EiJ), we demonstrate that Gough Island mice achieve their exceptional body weight primarily by growing faster during the 6 weeks after birth. We use genetic mapping in large F(2) intercrosses between Gough Island mice and WSB/EiJ to identify 19 quantitative trait loci (QTL) responsible for the evolution of 16-week weight trajectories: 8 QTL for body weight and 11 QTL for growth rate. QTL exhibit modest effects that are mostly additive. We conclude that body size evolution on islands can be genetically complex, even when substantial size changes occur rapidly. In comparisons to published studies of laboratory strains of mice that were artificially selected for divergent body sizes, we discover that the overall genetic profile of size evolution in nature and in the laboratory is similar, but many contributing loci are distinct. Our results underscore the power of genetically characterizing the entire growth trajectory in wild populations and lay the foundation necessary for identifying the mutations responsible for extreme body size evolution in nature. Copyright © 2015 by the Genetics Society of America.

Sixth Symposium on Chemical Evolution and the Origin and Evolution of Life

NASA Technical Reports Server (NTRS)

Acevedo, Sara (Editor); DeVincenzi, Donald L. (Editor); Chang, Sherwood (Editor)

1998-01-01

The 6th Symposium on Chemical Evolution and the Origin and Evolution of Life was convened at NASA Ames Research Center, November 17-20, 1997. This Symposium is convened every three years under the auspices of NASA's Exobiology Program Office. All Principal Investigators funded by this Program present their most recent research accomplishments at the Symposium. Scientific papers were presented in the following areas: cosmic evolution of the biogenic elements, prebiotic evolution (both planetary and chemical), evolution of early organisms and evolution of organisms in extreme environments, solar system exploration, and star and planet formation. The Symposium was attended by over 200 scientists from NASA centers and Universities nationwide.

High School Students' Perceptions of Evolution Instruction: Acceptance and Evolution Learning Experiences

ERIC Educational Resources Information Center

Donnelly, Lisa A.; Kazempour, Mahsa; Amirshokoohi, Aidin

2009-01-01

Evolution is an important and sometimes controversial component of high school biology. In this study, we used a mixed methods approach to explore students' evolution acceptance and views of evolution teaching and learning. Students explained their acceptance and rejection of evolution in terms of evidence and conflicts with religion and…

The genomic basis of adaptive evolution in threespine sticklebacks

PubMed Central

Jones, Felicity C; Grabherr, Manfred G; Chan, Yingguang Frank; Russell, Pamela; Mauceli, Evan; Johnson, Jeremy; Swofford, Ross; Pirun, Mono; Zody, Michael C; White, Simon; Birney, Ewan; Searle, Stephen; Schmutz, Jeremy; Grimwood, Jane; Dickson, Mark C; Myers, Richard M; Miller, Craig T; Summers, Brian R; Knecht, Anne K; Brady, Shannon D; Zhang, Haili; Pollen, Alex A; Howes, Timothy; Amemiya, Chris; Lander, Eric S; Di Palma, Federica

2012-01-01

Summary Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature. PMID:22481358

The genomic basis of adaptive evolution in threespine sticklebacks.

PubMed

Jones, Felicity C; Grabherr, Manfred G; Chan, Yingguang Frank; Russell, Pamela; Mauceli, Evan; Johnson, Jeremy; Swofford, Ross; Pirun, Mono; Zody, Michael C; White, Simon; Birney, Ewan; Searle, Stephen; Schmutz, Jeremy; Grimwood, Jane; Dickson, Mark C; Myers, Richard M; Miller, Craig T; Summers, Brian R; Knecht, Anne K; Brady, Shannon D; Zhang, Haili; Pollen, Alex A; Howes, Timothy; Amemiya, Chris; Baldwin, Jen; Bloom, Toby; Jaffe, David B; Nicol, Robert; Wilkinson, Jane; Lander, Eric S; Di Palma, Federica; Lindblad-Toh, Kerstin; Kingsley, David M

2012-04-04

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

The effect of selection environment on the probability of parallel evolution.

PubMed

Bailey, Susan F; Rodrigue, Nicolas; Kassen, Rees

2015-06-01

Across the great diversity of life, there are many compelling examples of parallel and convergent evolution-similar evolutionary changes arising in independently evolving populations. Parallel evolution is often taken to be strong evidence of adaptation occurring in populations that are highly constrained in their genetic variation. Theoretical models suggest a few potential factors driving the probability of parallel evolution, but experimental tests are needed. In this study, we quantify the degree of parallel evolution in 15 replicate populations of Pseudomonas fluorescens evolved in five different environments that varied in resource type and arrangement. We identified repeat changes across multiple levels of biological organization from phenotype, to gene, to nucleotide, and tested the impact of 1) selection environment, 2) the degree of adaptation, and 3) the degree of heterogeneity in the environment on the degree of parallel evolution at the gene-level. We saw, as expected, that parallel evolution occurred more often between populations evolved in the same environment; however, the extent of parallel evolution varied widely. The degree of adaptation did not significantly explain variation in the extent of parallelism in our system but number of available beneficial mutations correlated negatively with parallel evolution. In addition, degree of parallel evolution was significantly higher in populations evolved in a spatially structured, multiresource environment, suggesting that environmental heterogeneity may be an important factor constraining adaptation. Overall, our results stress the importance of environment in driving parallel evolutionary changes and point to a number of avenues for future work for understanding when evolution is predictable. © The Author 2015. 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.

The recognition signal hypothesis for the adaptive evolution of religion : a phylogenetic test with Christian denominations.

PubMed

Matthews, Luke J

2012-06-01

Recent research on the evolution of religion has focused on whether religion is an unselected by-product of evolutionary processes or if it is instead an adaptation by natural selection. Adaptive hypotheses for religion include direct fitness benefits from improved health and indirect fitness benefits mediated by costly signals and/or cultural group selection. Herein, I propose that religious denominations achieve indirect fitness gains for members through the use of ecologically arbitrary beliefs, rituals, and moral rules that function as recognition markers of cultural inheritance analogous to kin and species recognition of genetic inheritance in biology. This recognition signal hypotheses could act in concert with either costly signaling or cultural group selection to produce evolutionarily altruistic behaviors within denominations. Using a cultural phylogenetic analysis, I show that a large set of religious behaviors among extant Christian denominations supports the prediction of the recognition signal hypothesis that characters change more frequently near historical schisms. By incorporating demographic data into the model, I show that more-distinctive denominations, as measured through dissimilar characteristics, appear to be protected from intrusion by nonmembers in mixed-denomination households, and that they may be experiencing greater biological growth of their populations even in the present day.

Galaxy evolution spectroscopic explorer: scientific rationale

NASA Astrophysics Data System (ADS)

Heap, Sara; Ninkov, Zoran; Robberto, Massimo; Hull, Tony; Purves, Lloyd

2016-07-01

GESE is a mission concept consisting of a 1.5-m space telescope and UV multi-object slit spectrograph designed to help understand galaxy evolution in a critical era in the history of the universe, where the rate of star-formation stopped increasing and started to decline. To isolate and identify the various processes driving the evolution of these galaxies, GESE will obtain rest-frame far-UV spectra of 100,000 galaxies at redshifts, z 1-2. To obtain such a large number of spectra, multiplexing over a wide field is an absolute necessity. A slit device such as a digital micro-mirror device (DMD) or a micro-shutter array (MSA) enables spectroscopy of a hundred or more sources in a single exposure while eliminating overlapping spectra of other sources and blocking unwanted background like zodiacal light. We find that a 1.5-m space telescope with a MSA slit device combined with a custom orbit enabling long, uninterrupted exposures ( 10 hr) are optimal for this spectroscopic survey. GESE will not be operating alone in this endeavor. Together with x-ray telescopes and optical/near-IR telescopes like Subaru/Prime Focus Spectrograph, GESE will detect "feedback" from young massive stars and massive black holes (AGN's), and other drivers of galaxy evolution.

Galaxy Evolution Spectroscopic Explorer: Scientific Rationale

NASA Technical Reports Server (NTRS)

Heap, Sara; Ninkov, Zoran; Robberto, Massimo; Hull, Tony; Purves, Lloyd

2016-01-01

GESE is a mission concept consisting of a 1.5-m space telescope and UV multi-object slit spectrograph designed to help understand galaxy evolution in a critical era in the history of the universe, where the rate of star-formation stopped increasing and started to decline. To isolate and identify the various processes driving the evolution of these galaxies, GESE will obtain rest-frame far-UV spectra of 100,000 galaxies at redshifts, z approximately 1-2. To obtain such a large number of spectra, multiplexing over a wide field is an absolute necessity. A slit device such as a digital micro-mirror device (DMD) or a micro-shutter array (MSA) enables spectroscopy of a hundred or more sources in a single exposure while eliminating overlapping spectra of other sources and blocking unwanted background like zodiacal light. We find that a 1.5-m space telescope with a MSA slit device combined with a custom orbit enabling long, uninterrupted exposures (approximately 10 hr) are optimal for this spectroscopic survey. GESE will not be operating alone in this endeavor. Together with x-ray telescopes and optical/near-IR telescopes like Subaru/Prime Focus Spectrograph, GESE will detect "feedback" from young massive stars and massive black holes (AGN's), and other drivers of galaxy evolution.

Evolution of DNA Methylation across Insects

PubMed Central

Vogel, Kevin J.; Moore, Allen J.; Schmitz, Robert J.

2017-01-01

DNA methylation contributes to gene and transcriptional regulation in eukaryotes, and therefore has been hypothesized to facilitate the evolution of plastic traits such as sociality in insects. However, DNA methylation is sparsely studied in insects. Therefore, we documented patterns of DNA methylation across a wide diversity of insects. We predicted that underlying enzymatic machinery is concordant with patterns of DNA methylation. Finally, given the suggestion that DNA methylation facilitated social evolution in Hymenoptera, we tested the hypothesis that the DNA methylation system will be associated with presence/absence of sociality among other insect orders. We found DNA methylation to be widespread, detected in all orders examined except Diptera (flies). Whole genome bisulfite sequencing showed that orders differed in levels of DNA methylation. Hymenopteran (ants, bees, wasps and sawflies) had some of the lowest levels, including several potential losses. Blattodea (cockroaches and termites) show all possible patterns, including a potential loss of DNA methylation in a eusocial species whereas solitary species had the highest levels. Species with DNA methylation do not always possess the typical enzymatic machinery. We identified a gene duplication event in the maintenance DNA methyltransferase 1 (DNMT1) that is shared by some Hymenoptera, and paralogs have experienced divergent, nonneutral evolution. This diversity and nonneutral evolution of underlying machinery suggests alternative DNA methylation pathways may exist. Phylogenetically corrected comparisons revealed no evidence that supports evolutionary association between sociality and DNA methylation. Future functional studies will be required to advance our understanding of DNA methylation in insects. PMID:28025279

A new paradigma on the plant evolution: from a natural evolution to an artificial evolution?

PubMed

Bennici, Andrea

2005-01-01

After evidencing the great importance of plants for animals and humans in consequence of the photosynthesis, several considerations on plant evolution are made. One of the peculiar characteristics of the plant is the sessile property, due especially to the cell wall. This factor, principally, strengthened by the photosynthetic process, determined the particular developmental pattern of the plant, which is characterized by the continuous formation of new organs. The plant immobility, although negative for its survival, has been, in great part, overcome by the acquisition of the capacity of adaptation (plasticity) to the environmental stresses and changes, and the establishment of more adapted genotypes. This capacity to react to the external signals induced Trewavas to speak of "plant intelligence". The plant movement incapacity and the evolution of the sexual reproduction system were strongly correlated. In this context, the evolution of the flower in the Angiosperms has been particularly important to allow the male gamete to fertilize the immobile female gamete. Moreover, the formation of fruit and seed greatly improved the dispersal and conservation of the progeny in the environment. With the flower, mechanisms to favour the outcrossing among different individuals appeared, which are essential to increase the genetic variability and, then, the plant evolution itself. Although the Angiosperms seem highly evolved, the plant evolution is not surely finished, because many reported morpho-physiological processes may be still considered susceptible of further improvement. In the last years the relationships among humans, plants and environment are becoming closer and closer. This is due to the use of the DNA recombinant techniques with the aim to modify artificially plant characters. Therefore, the risk of a plant evolution strongly directed towards practical or commercial objectives, or "an artificial evolution", may be hypothesized.

Integrative molecular network analysis identifies emergent enzalutamide resistance mechanisms in prostate cancer

PubMed Central

King, Carly J.; Woodward, Josha; Schwartzman, Jacob; Coleman, Daniel J.; Lisac, Robert; Wang, Nicholas J.; Van Hook, Kathryn; Gao, Lina; Urrutia, Joshua; Dane, Mark A.; Heiser, Laura M.; Alumkal, Joshi J.

2017-01-01

Recent work demonstrates that castration-resistant prostate cancer (CRPC) tumors harbor countless genomic aberrations that control many hallmarks of cancer. While some specific mutations in CRPC may be actionable, many others are not. We hypothesized that genomic aberrations in cancer may operate in concert to promote drug resistance and tumor progression, and that organization of these genomic aberrations into therapeutically targetable pathways may improve our ability to treat CRPC. To identify the molecular underpinnings of enzalutamide-resistant CRPC, we performed transcriptional and copy number profiling studies using paired enzalutamide-sensitive and resistant LNCaP prostate cancer cell lines. Gene networks associated with enzalutamide resistance were revealed by performing an integrative genomic analysis with the PAthway Representation and Analysis by Direct Reference on Graphical Models (PARADIGM) tool. Amongst the pathways enriched in the enzalutamide-resistant cells were those associated with MEK, EGFR, RAS, and NFKB. Functional validation studies of 64 genes identified 10 candidate genes whose suppression led to greater effects on cell viability in enzalutamide-resistant cells as compared to sensitive parental cells. Examination of a patient cohort demonstrated that several of our functionally-validated gene hits are deregulated in metastatic CRPC tumor samples, suggesting that they may be clinically relevant therapeutic targets for patients with enzalutamide-resistant CRPC. Altogether, our approach demonstrates the potential of integrative genomic analyses to clarify determinants of drug resistance and rational co-targeting strategies to overcome resistance. PMID:29340039

Systems approaches in osteoarthritis: Identifying routes to novel diagnostic and therapeutic strategies.

PubMed

Mueller, Alan J; Peffers, Mandy J; Proctor, Carole J; Clegg, Peter D

2017-08-01

Systems orientated research offers the possibility of identifying novel therapeutic targets and relevant diagnostic markers for complex diseases such as osteoarthritis. This review demonstrates that the osteoarthritis research community has been slow to incorporate systems orientated approaches into research studies, although a number of key studies reveal novel insights into the regulatory mechanisms that contribute both to joint tissue homeostasis and its dysfunction. The review introduces both top-down and bottom-up approaches employed in the study of osteoarthritis. A holistic and multiscale approach, where clinical measurements may predict dysregulation and progression of joint degeneration, should be a key objective in future research. The review concludes with suggestions for further research and emerging trends not least of which is the coupled development of diagnostic tests and therapeutics as part of a concerted effort by the osteoarthritis research community to meet clinical needs. © 2017 The Authors. Journal of Orthopaedic Research Published by Wiley Periodicals, Inc. on behalf of Orthopaedic Research Society. J Orthop Res 35:1573-1588, 2017. © 2017 The Authors. Journal of Orthopaedic Research Published by Wiley Periodicals, Inc. on behalf of Orthopaedic Research Society.

The relativistic equations of stellar structure and evolution

NASA Technical Reports Server (NTRS)

Thorne, K. S.

1975-01-01

The general relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. A general relativistic version of the mixing-length formalism for convection is presented. It is argued that in work on spherical systems, general relativity theorists have identified the wrong quantity as total mass-energy inside radius r.

Current Status of Research in Teaching and Learning Evolution: II. Pedagogical Issues

NASA Astrophysics Data System (ADS)

Smith, Mike U.

2010-06-01

This is the second of two articles that address recent scholarship about teaching and learning about evolution. This second review seeks to summarize this state of affairs and address the implications of this work for the classroom by addressing four basic questions: (1) What is evolution?/What components of the theory are important at the introductory level? (2) Why do students and members of the public at large need to understand evolution? (3) What makes evolution difficult to teach and learn? and (4) What promising instructional approaches have been developed and tested? The paper will also focus on concerns about both the research designs and the measures used in this work. Based on this review, I will then propose a set of pedagogical implications and recommendations for the classroom instructor and call for studies to address specific gaps identified.

Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates.

PubMed

Bao, Yongbo; Xu, Fei; Shimeld, Sebastian M

2017-04-01

The gain and loss of genes encoding transcription factors is of importance to understanding the evolution of gene regulatory complexity. The basic helix-loop-helix (bHLH) genes encode a large superfamily of transcription factors. We systematically classify the bHLH genes from five mollusc, two annelid and one brachiopod genomes, tracing the pattern of bHLH gene evolution across these poorly studied Phyla. In total, 56-88 bHLH genes were identified in each genome, with most identifiable as members of previously described bilaterian families, or of new families we define. Of such families only one, Mesp, appears lost by all these species. Additional duplications have also played a role in the evolution of the bHLH gene repertoire, with many new lophotrochozoan-, mollusc-, bivalve-, or gastropod-specific genes defined. Using a combination of transcriptome mining, RT-PCR, and in situ hybridization we compared the expression of several of these novel genes in tissues and embryos of the molluscs Crassostrea gigas and Patella vulgata, finding both conserved expression and evidence for neofunctionalization. We also map the positions of the genes across these genomes, identifying numerous gene linkages. Some reflect recent paralog divergence by tandem duplication, others are remnants of ancient tandem duplications dating to the lophotrochozoan or bilaterian common ancestors. These data are built into a model of the evolution of bHLH genes in molluscs, showing formidable evolutionary stasis at the family level but considerable within-family diversification by tandem gene duplication. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Galapagos III World Evolution Summit: why evolution matters

PubMed Central

Paz-y-Miño-C, Guillermo; Espinosa, Avelina

2016-01-01

There is no place on Earth like the Galapagos Islands and no better destination to discuss the reality of evolution. Under the theme ‘Why Does Evolution Matter’, the University San Francisco of Quito (USFQ), Ecuador, and its Galapagos Institute for the Arts and Sciences (GAIAS), organized the III World Evolution Summit in San Cristóbal Island. The 200-attendee meeting took place on 1 to 5 June 2013; it included 12 keynote speakers, 20 oral presentations by international scholars, and 31 posters by faculty, postdocs, and graduate and undergraduate students. The Summit encompassed five sessions: evolution and society, pre-cellular evolution and the RNA world, behavior and environment, genome, and microbes and diseases. USFQ and GAIAS launched officially the Lynn Margulis Center for Evolutionary Biology and showcased the Galapagos Science Center, in San Cristóbal, an impressive research facility conceptualized in partnership with the University of North Carolina at Chapel Hill, USA. USFQ and GAIAS excelled at managing the conference with exceptional vision and at highlighting the relevance of Galapagos in the history of modern evolutionary thinking; Charles Darwin’s visit to this volcanic archipelago in 1835 unfolded unprecedented scientific interest in what today is a matchless World Heritage. PMID:26925190

Divergent evolution of life span associated with mitochondrial DNA evolution.

PubMed

Stojković, Biljana; Sayadi, Ahmed; Đorđević, Mirko; Jović, Jelena; Savković, Uroš; Arnqvist, Göran

2017-01-01

Mitochondria play a key role in ageing. The pursuit of genes that regulate variation in life span and ageing have shown that several nuclear-encoded mitochondrial genes are important. However, the role of mitochondrial encoded genes (mtDNA) is more controversial and our appreciation of the role of mtDNA for the evolution of life span is limited. We use replicated lines of seed beetles that have been artificially selected for long or short life for >190 generations, now showing dramatic phenotypic differences, to test for a possible role of mtDNA in the divergent evolution of ageing and life span. We show that these divergent selection regimes led to the evolution of significantly different mtDNA haplotype frequencies. Selection for a long life and late reproduction generated positive selection for one specific haplotype, which was fixed in most such lines. In contrast, selection for reproduction early in life led to both positive selection as well as negative frequency-dependent selection on two different haplotypes, which were both present in all such lines. Our findings suggest that the evolution of life span was in part mediated by mtDNA, providing support for the emerging general tenet that adaptive evolution of life-history syndromes may involve mtDNA. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Invasive forest pathogens: Summary of issues, critical needs, and future goals for Forest Service Research and Development

Treesearch

Ned B. Klopfenstein; Jennifer Juzwik; Michael E. Ostry; Mee-Sook Kim; Paul J. Zambino; Robert C. Venette; Bryce A. Richardson; John E. Lundquist; D. Jean Lodge; Jessie A. Glaeser; Susan J. Frankel; William J. Otrosina; Pauline Spaine; Brian W. Geils

2010-01-01

Invasive pathogens have caused immeasurable ecological and economic damage to forest ecosystems. Damage will undoubtedly increase over time due to increased introductions and evolution of invasive pathogens in concert with complex environmental disturbances, such as climate change. Forest Service Research and Development must fulfill critical roles and responsibilities...

Inlet Geomorphology Evolution

DTIC Science & Technology

2015-04-01

APR 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE Inlet Geomorphology Evolution 5a. CONTRACT NUMBER 5b...Std Z39-18 Coastal Inlets Research Program Inlet Geomorphology Evolution The Inlet Geomorphology Evolution work unit of the CIRP evaluates

Molecular mechanisms of dominance evolution in Müllerian mimicry.

PubMed

Llaurens, V; Joron, M; Billiard, S

2015-12-01

Natural selection acting on dominance between adaptive alleles at polymorphic loci can be sufficiently strong for dominance to evolve. However, the molecular mechanisms underlying such evolution are generally unknown. Here, using Müllerian mimicry as a case-study for adaptive morphological variation, we present a theoretical analysis of the invasion of dominance modifiers altering gene expression through different molecular mechanisms. Toxic species involved in Müllerian mimicry exhibit warning coloration, and converge morphologically with other toxic species of the local community, due to positive frequency-dependent selection acting on these colorations. Polymorphism in warning coloration may be maintained by migration-selection balance with fine scale spatial heterogeneity. We modeled a dominance modifier locus altering the expression of the warning coloration locus, targeting one or several alleles, acting in cis or trans, and either enhancing or repressing expression. We confirmed that dominance could evolve when balanced polymorphism was maintained at the color locus. Dominance evolution could result from modifiers enhancing one allele specifically, irrespective of their linkage with the targeted locus. Nonspecific enhancers could also persist in populations, at frequencies tightly depending on their linkage with the targeted locus. Altogether, our results identify which mechanisms of expression alteration could lead to dominance evolution in polymorphic mimicry. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The roles of tolerance in the evolution, maintenance and breakdown of mutualism

NASA Astrophysics Data System (ADS)

Edwards, David P.

2009-10-01

Tolerance strategies are cost-reduction mechanisms that enable organisms to recover some of the fitness lost to damage, but impose limited or no cost on antagonists. They are frequently invoked in studies of plant-herbivore and of host-parasite interactions, but the possible roles of tolerance in mutualism (interspecific cooperation) have yet to be thoroughly examined. This review identifies candidate roles for tolerance in the evolution, maintenance and breakdown of mutualism. Firstly, by reducing the cost of damage, tolerance provides a key pathway by which pre-mutualistic hosts can reduce the cost of association with their parasites, promoting cooperation. This holds for the evolution of ‘evolved dependency’ type mutualism, where a host requires an antagonist that does not direct any reward to their partner for some resource, and of ‘outright mutualism’, where participants directly trade benefits. Secondly, in outright mutualism, tolerance might maintain cooperation by reducing the cost of a persisting negative trait in a symbiotic partner. Finally, the evolution of tolerance might also provide a pathway out of mutualism because the host could evolve a cheaper alternative to continued cooperation with its mutualistic partner, permitting autonomy. A key consequence of tolerance is that it contrasts with partner choice mechanisms that impose large costs on cheats, and I highlight understanding any trade-off between tolerance and partner choice as an important research topic in the evolution of cooperation. I conclude by identifying tolerance as part of a more general phenomenon of co-adaptation in mutualism and parasitism that drives the evolution of the cost/benefit ratio from the interaction.

Untangling the origin of viruses and their impact on cellular evolution.

PubMed

Nasir, Arshan; Sun, Feng-Jie; Kim, Kyung Mo; Caetano-Anollés, Gustavo

2015-04-01

The origin and evolution of viruses remain mysterious. Here, we focus on the distribution of viral replicons in host organisms, their morphological features, and the evolution of highly conserved protein and nucleic acid structures. The apparent inability of RNA viral replicons to infect contemporary akaryotic species suggests an early origin of RNA viruses and their subsequent loss in akaryotes. A census of virion morphotypes reveals that advanced forms were unique to viruses infecting a specific supergroup, while simpler forms were observed in viruses infecting organisms in all forms of cellular life. Results hint toward an ancient origin of viruses from an ancestral virus harboring either filamentous or spherical virions. Finally, phylogenetic trees built from protein domain and tRNA structures in thousands of genomes suggest that viruses evolved via reductive evolution from ancient cells. The analysis presents a complete account of the evolutionary history of cells and viruses and identifies viruses as crucial agents influencing cellular evolution. © 2015 New York Academy of Sciences.

[The motive force of evolution based on the principle of organismal adjustment evolution.].

PubMed

Cao, Jia-Shu

2010-08-01

From the analysis of the existing problems of the prevalent theories of evolution, this paper discussed the motive force of evolution based on the knowledge of the principle of organismal adjustment evolution to get a new understanding of the evolution mechanism. In the guide of Schrodinger's theory - "life feeds on negative entropy", the author proposed that "negative entropy flow" actually includes material flow, energy flow and information flow, and the "negative entropy flow" is the motive force for living and development. By modifying my own theory of principle of organismal adjustment evolution (not adaptation evolution), a new theory of "regulation system of organismal adjustment evolution involved in DNA, RNA and protein interacting with environment" is proposed. According to the view that phylogenetic development is the "integral" of individual development, the difference of negative entropy flow between organisms and environment is considered to be a motive force for evolution, which is a new understanding of the mechanism of evolution. Based on such understanding, evolution is regarded as "a changing process that one subsystem passes all or part of its genetic information to the next generation in a larger system, and during the adaptation process produces some new elements, stops some old ones, and thereby lasts in the larger system". Some other controversial questions related to evolution are also discussed.

Next Generation Epigenetic Detection Technique: Identifying Methylated DNA using Graphene Nanopore

NASA Astrophysics Data System (ADS)

Ahmed, Towfiq; Haraldsen, Jason T.; Zhu, Jian-Xin; Balatsky, A. V.

2014-03-01

DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells.Unusual methylation on CPG islands are identified as the prime causes for silencing the tumor suppressant genes. Early detection of such methylation can diagnose the potentially harmful oncogenic evolution of cells, and provide a promising guideline for cancer prevention.We propose a detection technique and calculate the transport current through punctured graphene as the cytosine and methylated cytosine translocate through the nanopore. We also calculate the transport properties for uracil and cyano-cytosine to compare. Our calculations of transmission, current and tunneling conductance show distinct signatures in their spectrum for each molecular type. Our theoretical study provides a next generation detection technique for identifying DNA methylation using graphene based nanopore device. This work was supported by U.S. DOE Office of Basic Energy Sciences, and by VR 621-2012-2983 and ERC 321031-DM. This work was, in part, supported by the Center for Integrated Nanotechnologies, a U.S. DOE BES user facility.

Secular Evolution of Galaxies

NASA Astrophysics Data System (ADS)

Falcón-Barroso, Jesús; Knapen, Johan H.

2013-10-01

Preface; 1. Secular evolution in disk galaxies John Kormendy; 2. Galaxy morphology Ronald J. Buta; 3. Dynamics of secular evolution James Binney; 4. Bars and secular evolution in disk galaxies: theoretical input E. Athanassoula; 5. Stellar populations Reynier F. Peletier; 6. Star formation rate indicators Daniela Calzetti; 7. The evolving interstellar medium Jacqueline van Gorkom; 8. Evolution of star formation and gas Nick Z. Scoville; 9. Cosmological evolution of galaxies Isaac Shlosman.

Arguing for Evolution.

ERIC Educational Resources Information Center

Ayala, Francisco J.

2000-01-01

Discusses the Kansas State Board of Education's decision to remove references to evolution and cosmology from the state's education standards and assessment. Advocates the need to teach evolution in high schools for a meaningful biology education. Addresses the question whether the teaching of evolution poses a threat to Christianity or other…

Biomimetic perfusion and electrical stimulation applied in concert improved the assembly of engineered cardiac tissue

PubMed Central

Lee, Eun Jung; Luo, Jianwen; Duan, Yi; Yeager, Keith; Konofagou, Elisa; Vunjak-Novakovic, Gordana

2012-01-01

Maintenance of normal myocardial function depends intimately on synchronous tissue contraction driven by electrical activation and on adequate nutrient perfusion in support thereof. Bioreactors have been used to mimic aspects of these factors in vitro to engineer cardiac tissue, but due to design limitations, previous bioreactor systems have yet to simultaneously support nutrient perfusion, electrical stimulation, and unconstrained (i.e., not isometric) tissue contraction. To the best of our knowledge, the bioreactor system described herein is the first to integrate in concert these three key factors. We present the design of our bioreactor and characterize its capability in integrated experimental and mathematical modeling studies. We then culture cardiac cells obtained from neonatal rats in porous, channeled elastomer scaffolds with the simultaneous application of perfusion and electrical stimulation, with controls excluding either one or both of these two conditions. After eight days of culture, constructs grown with the simultaneous perfusion and electrical stimulation exhibited substantially improved functional properties, as evidenced by a significant increase in contraction amplitude (0.23±0.10% vs. 0.14±0.05, 0.13±0.08, or 0.09±0.02% in control constructs grown without stimulation, without perfusion, or either stimulation or perfusion, respectively). Consistently, these constructs had significantly improved DNA contents, cell distribution throughout the scaffold thickness, cardiac protein expression, cell morphology and overall tissue organization than either control group. Thus, the simultaneous application of medium perfusion and electrical conditioning enabled by the use of the novel bioreactor system may accelerate the generation of fully functional, clinically sized cardiac tissue constructs. PMID:22170772

Developing biology teachers' pedagogical content knowledge through learning study: the case of teaching human evolution

NASA Astrophysics Data System (ADS)

Bravo, Paulina; Cofré, Hernán

2016-11-01

This work explores how pedagogical content knowledge (PCK) on evolution was modified by two biology teachers who participated in a professional development programme (PDP) that included a subsequent follow-up in the classroom. The PDP spanned a semester and included activities such as content updates, collaborative lesson planning, and the presentation of planned lessons. In the follow-up part, the lessons were videotaped and analysed, identifying strategies, activities, and conditions based on student learning about the theory of evolution. Data were collected in the first round with an interview before the training process, identifying these teachers' initial content representation (CoRe) for evolution. Then, a group interview was conducted after the lessons, and, finally, an interview of stimulated recall with each teacher was conducted regarding the subject taught to allow teachers to reflect on their practice (final CoRe). This information was analysed by the teachers and the researchers, reflecting on the components of the PCK, possible changes, and the rationale behind their actions. The results show that teachers changed their beliefs and knowledge about the best methods and strategies to teach evolution, and about students' learning obstacles and misconceptions on evolution. They realised how a review of their own practices promotes this transformation.

Criticality and big brake singularities in the tachyonic evolutions of closed Friedmann universes with cold dark matter

NASA Astrophysics Data System (ADS)

Horváth, Zsolt; Keresztes, Zoltán; Kamenshchik, Alexander Yu.; Gergely, László Á.

2015-05-01

The evolution of a closed Friedmann universe filled by a tachyon scalar field with a trigonometric potential and cold dark matter (CDM) is investigated. A subset of the evolutions consistent to 1 σ confidence level with the Union 2.1 supernova data set is identified. The evolutions of the tachyon field are classified. Some of them evolve into a de Sitter attractor, while others proceed through a pseudotachyonic regime into a sudden future singularity. Critical evolutions leading to big brake singularities in the presence of CDM are found and a new type of cosmological evolution characterized by singularity avoidance in the pseudotachyon regime is presented.

Health, Education, and the Post-Retirement Evolution of Household Assets

PubMed Central

Poterba, James; Venti, Steven; Wise, David A.

2013-01-01

We explore the relationship between education and the evolution of wealth after retirement. Asset growth following retirement depends in part on health capital and financial capital accumulated prior to retirement, which in turn are strongly related to educational attainment. These “initial conditions” at retirement can have a lingering effect on subsequent asset evolution. We aim to disentangle the effects of education that operate through health and financial pathways (such as Social Security benefits and the general level of health) prior to retirement from the effects of education that impinge directly on asset evolution after retirement. We also consider the additional effects of education that are not captured through these pathways. We find a substantial effect of education on asset growth through each of the pathways as well as a substantial additional effect not captured by the identified pathways. PMID:24904710

Spin period evolution of the newly identified ULX pulsar (NGC 300 ULX1) associated with the supernova impostor SN2010da

NASA Astrophysics Data System (ADS)

Vasilopoulos, G.; Haberl, F.; Carpano, S.; Maitra, C.

2018-01-01

Following the discovery of the newly discovered ULX pulsar in NGC 300 (ATel #11158) we searched the available X-ray data for the evolution of the spin period of the neutron star and the X-ray luminosity.

The mitochondrial genome of Frankliniella intonsa: insights into the evolution of mitochondrial genomes at lower taxonomic levels in Thysanoptera.

PubMed

Yan, Dankan; Tang, Yunxia; Hu, Min; Liu, Fengquan; Zhang, Dongfang; Fan, Jiaqin

2014-10-01

Thrips is an ideal group for studying the evolution of mitochondrial (mt) genomes in the genus and family due to independent rearrangements within this order. The complete sequence of the mitochondrial DNA (mtDNA) of the flower thrips Frankliniella intonsa has been completed and annotated in this study. The circular genome is 15,215bp in length with an A+T content of 75.9% and contains the typical 37 genes and it has triplicate putative control regions. Nucleotide composition is A+T biased, and the majority of the protein-coding genes present opposite CG skew which is reflected by the nucleotide composition, codon and amino acid usage. Although the known thrips have massive gene rearrangements, it showed no reversal of strand asymmetry. Gene rearrangements have been found in the lower taxonomic levels of thrips. Three tRNA genes were translocated in the genus Frankliniella and eight tRNA genes in the family Thripidae. Although the gene arrangements of mt genomes of all three thrips species differ massively from the ancestral insect, they are all very similar to each other, indicating that there was a large rearrangement somewhere before the most recent common ancestor of these three species and very little genomic evolution or rearrangements after then. The extremely similar sequences among the CRs suggest that they are ongoing concerted evolution. Analyses of the up and downstream sequence of CRs reveal that the CR2 is actually the ancestral CR. The three CRs are in the same spot in each of the three thrips mt genomes which have the identical inverted genes. These characteristics might be obtained from the most recent common ancestor of this three thrips. Above observations suggest that the mt genomes of the three thrips keep a single massive rearrangement from the common ancestor and have low evolutionary rates among them. Copyright © 2014 Elsevier Inc. All rights reserved.

Microcephaly genes evolved adaptively throughout the evolution of eutherian mammals

PubMed Central

2014-01-01

Background Genes associated with the neurodevelopmental disorder microcephaly display a strong signature of adaptive evolution in primates. Comparative data suggest a link between selection on some of these loci and the evolution of primate brain size. Whether or not either positive selection or this phenotypic association are unique to primates is unclear, but recent studies in cetaceans suggest at least two microcephaly genes evolved adaptively in other large brained mammalian clades. Results Here we analyse the evolution of seven microcephaly loci, including three recently identified loci, across 33 eutherian mammals. We find extensive evidence for positive selection having acted on the majority of these loci not just in primates but also across non-primate mammals. Furthermore, the patterns of selection in major mammalian clades are not significantly different. Using phylogenetically corrected comparative analyses, we find that the evolution of two microcephaly loci, ASPM and CDK5RAP2, are correlated with neonatal brain size in Glires and Euungulata, the two most densely sampled non-primate clades. Conclusions Together with previous results, this suggests that ASPM and CDK5RAP2 may have had a consistent role in the evolution of brain size in mammals. Nevertheless, several limitations of currently available data and gene-phenotype tests are discussed, including sparse sampling across large evolutionary distances, averaging gene-wide rates of evolution, potential phenotypic variation and evolutionary reversals. We discuss the implications of our results for studies of the genetic basis of brain evolution, and explicit tests of gene-phenotype hypotheses. PMID:24898820

Temporal evolution of age data under transient pumping conditions

NASA Astrophysics Data System (ADS)

Leray, S.; de Dreuzy, J.-R.; Aquilina, L.; Vergnaud-Ayraud, V.; Labasque, T.; Bour, O.; Le Borgne, T.

2014-04-01

While most age data derived from tracers have been analyzed in steady-state flow conditions, we determine their temporal evolution when starting a pumping. Our study is based on a model made up of a shallowly dipping aquifer overlain by a less permeable aquitard characteristic of the crystalline aquifer of Plœmeur (Brittany, France). Under a pseudo transient flow assumption (instantaneous shift between two steady-state flow fields), we solve the transport equation with a backward particle-tracking method and determine the temporal evolution of the concentrations at the pumping well of CFC-11, CFC-12, CFC-113 and SF6. Apparent ages evolve because of the modifications of the flow pattern and because of the non-linear evolution of the tracer atmospheric concentrations. To identify the respective role of these two causes, we propose two successive analyses. We first convolute residence time distributions initially arising at different times at the same sampling time. We secondly convolute one residence time distribution at various sampling times. We show that flow pattern modifications control the apparent ages evolution in the first pumping year when the residence time distribution is modified from a piston-like distribution to a much broader distribution. In the first pumping year, the apparent age evolution contains transient information that can be used to better constrain hydrogeological systems and slightly compensate for the small number of tracers. Later, the residence time distribution hardly evolves and apparent ages only evolve because of the tracer atmospheric concentrations. In this phase, apparent age time-series do not reflect any evolution in the flow pattern.

A Statistical Approach to Identify Superluminous Supernovae and Probe Their Diversity

NASA Astrophysics Data System (ADS)

Inserra, C.; Prajs, S.; Gutierrez, C. P.; Angus, C.; Smith, M.; Sullivan, M.

2018-02-01

We investigate the identification of hydrogen-poor superluminous supernovae (SLSNe I) using a photometric analysis, without including an arbitrary magnitude threshold. We assemble a homogeneous sample of previously classified SLSNe I from the literature, and fit their light curves using Gaussian processes. From the fits, we identify four photometric parameters that have a high statistical significance when correlated, and combine them in a parameter space that conveys information on their luminosity and color evolution. This parameter space presents a new definition for SLSNe I, which can be used to analyze existing and future transient data sets. We find that 90% of previously classified SLSNe I meet our new definition. We also examine the evidence for two subclasses of SLSNe I, combining their photometric evolution with spectroscopic information, namely the photospheric velocity and its gradient. A cluster analysis reveals the presence of two distinct groups. “Fast” SLSNe show fast light curves and color evolution, large velocities, and a large velocity gradient. “Slow” SLSNe show slow light curve and color evolution, small expansion velocities, and an almost non-existent velocity gradient. Finally, we discuss the impact of our analyses in the understanding of the powering engine of SLSNe, and their implementation as cosmological probes in current and future surveys.

Parasitism drives host genome evolution: Insights from the Pasteuria ramosa-Daphnia magna system.

PubMed

Bourgeois, Yann; Roulin, Anne C; Müller, Kristina; Ebert, Dieter

2017-04-01

Because parasitism is thought to play a major role in shaping host genomes, it has been predicted that genomic regions associated with resistance to parasites should stand out in genome scans, revealing signals of selection above the genomic background. To test whether parasitism is indeed such a major factor in host evolution and to better understand host-parasite interaction at the molecular level, we studied genome-wide polymorphisms in 97 genotypes of the planktonic crustacean Daphnia magna originating from three localities across Europe. Daphnia magna is known to coevolve with the bacterial pathogen Pasteuria ramosa for which host genotypes (clonal lines) are either resistant or susceptible. Using association mapping, we identified two genomic regions involved in resistance to P. ramosa, one of which was already known from a previous QTL analysis. We then performed a naïve genome scan to test for signatures of positive selection and found that the two regions identified with the association mapping further stood out as outliers. Several other regions with evidence for selection were also found, but no link between these regions and phenotypic variation could be established. Our results are consistent with the hypothesis that parasitism is driving host genome evolution. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Fourth Symposium on Chemical Evolution and the Origin and Evolution of Life

NASA Technical Reports Server (NTRS)

Wharton, Robert A., Jr. (Editor); Andersen, Dale T. (Editor); Bzik, Sara E. (Editor); Rummel, John D. (Editor)

1991-01-01

This symposium was held at the NASA Ames Research Center, Moffett Field, California, July 24-27, 1990. The NASA exobiology investigators reported their recent research findings. Scientific papers were presented in the following areas: cosmic evolution of biogenic compounds, prebiotic evolution (planetary and molecular), early evolution of life (biological and geochemical), evolution of advanced life, solar system exploration, and the Search for Extraterrestrial Intelligence (SETI).

Evolution of the SOUL Heme-Binding Protein Superfamily Across Eukarya.

PubMed

Fortunato, Antonio Emidio; Sordino, Paolo; Andreakis, Nikos

2016-06-01

SOUL homologs constitute a heme-binding protein superfamily putatively involved in heme and tetrapyrrole metabolisms associated with a number of physiological processes. Despite their omnipresence across the tree of life and the biochemical characterization of many SOUL members, their functional role and the evolutionary events leading to such remarkable protein repertoire still remain cryptic. To explore SOUL evolution, we apply a computational phylogenetic approach, including a relevant number of SOUL homologs, to identify paralog forms and reconstruct their genealogy across the tree of life and within species. In animal lineages, multiple gene duplication or loss events and paralog functional specializations underlie SOUL evolution from the dawn of ancestral echinoderm and mollusc SOUL forms. In photosynthetic organisms, SOUL evolution is linked to the endosymbiosis events leading to plastid acquisition in eukaryotes. Derivative features, such as the F2L peptide and BH3 domain, evolved in vertebrates and provided innovative functionality to support immune response and apoptosis. The evolution of elements such as the N-terminal protein domain DUF2358, the His42 residue, or the tetrapyrrole heme-binding site is modern, and their functional implications still unresolved. This study represents the first in-depth analysis of SOUL protein evolution and provides novel insights in the understanding of their obscure physiological role.

The evolution of eyes and visually guided behaviour

PubMed Central

Nilsson, Dan-Eric

2009-01-01

The morphology and molecular mechanisms of animal photoreceptor cells and eyes reveal a complex pattern of duplications and co-option of genetic modules, leading to a number of different light-sensitive systems that share many components, in which clear-cut homologies are rare. On the basis of molecular and morphological findings, I discuss the functional requirements for vision and how these have constrained the evolution of eyes. The fact that natural selection on eyes acts through the consequences of visually guided behaviour leads to a concept of task-punctuated evolution, where sensory systems evolve by a sequential acquisition of sensory tasks. I identify four key innovations that, one after the other, paved the way for the evolution of efficient eyes. These innovations are (i) efficient photopigments, (ii) directionality through screening pigment, (iii) photoreceptor membrane folding, and (iv) focusing optics. A corresponding evolutionary sequence is suggested, starting at non-directional monitoring of ambient luminance and leading to comparisons of luminances within a scene, first by a scanning mode and later by parallel spatial channels in imaging eyes. PMID:19720648

Molecular hyperdiversity and evolution in very large populations.

PubMed

Cutter, Asher D; Jovelin, Richard; Dey, Alivia

2013-04-01

The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of noncrossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on noncoding regulatory elements. © 2013 Blackwell Publishing Ltd.

Evolution of semilocal string networks. II. Velocity estimators

NASA Astrophysics Data System (ADS)

Lopez-Eiguren, A.; Urrestilla, J.; Achúcarro, A.; Avgoustidis, A.; Martins, C. J. A. P.

2017-07-01

We continue a comprehensive numerical study of semilocal string networks and their cosmological evolution. These can be thought of as hybrid networks comprised of (nontopological) string segments, whose core structure is similar to that of Abelian Higgs vortices, and whose ends have long-range interactions and behavior similar to that of global monopoles. Our study provides further evidence of a linear scaling regime, already reported in previous studies, for the typical length scale and velocity of the network. We introduce a new algorithm to identify the position of the segment cores. This allows us to determine the length and velocity of each individual segment and follow their evolution in time. We study the statistical distribution of segment lengths and velocities for radiation- and matter-dominated evolution in the regime where the strings are stable. Our segment detection algorithm gives higher length values than previous studies based on indirect detection methods. The statistical distribution shows no evidence of (anti)correlation between the speed and the length of the segments.

FTS evolution

NASA Technical Reports Server (NTRS)

Provost, David E.

1990-01-01

Viewgraphs on flight telerobotic servicer evolution are presented. Topics covered include: paths for FTS evolution; frequently performed actions; primary task states; EPS radiator panel installation; generic task definitions; path planning; non-contact alignment; contact planning and control; and human operator interface.

Classifying stages of cirrus life-cycle evolution

NASA Astrophysics Data System (ADS)

Urbanek, Benedikt; Groß, Silke; Schäfler, Andreas; Wirth, Martin

2018-04-01

Airborne lidar backscatter data is used to determine in- and out-of-cloud regions. Lidar measurements of water vapor together with model temperature fields are used to calculate relative humidity over ice (RHi). Based on temperature and RHi we identify different stages of cirrus evolution: homogeneous and heterogeneous freezing, depositional growth, ice sublimation and sedimentation. We will present our classification scheme and first applications on mid-latitude cirrus clouds.

Brain reorganization, not relative brain size, primarily characterizes anthropoid brain evolution.

PubMed

Smaers, J B; Soligo, C

2013-05-22

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning.

Brain reorganization, not relative brain size, primarily characterizes anthropoid brain evolution

PubMed Central

Smaers, J. B.; Soligo, C.

2013-01-01

Comparative analyses of primate brain evolution have highlighted changes in size and internal organization as key factors underlying species diversity. It remains, however, unclear (i) how much variation in mosaic brain reorganization versus variation in relative brain size contributes to explaining the structural neural diversity observed across species, (ii) which mosaic changes contribute most to explaining diversity, and (iii) what the temporal origin, rates and processes are that underlie evolutionary shifts in mosaic reorganization for individual branches of the primate tree of life. We address these questions by combining novel comparative methods that allow assessing the temporal origin, rate and process of evolutionary changes on individual branches of the tree of life, with newly available data on volumes of key brain structures (prefrontal cortex, frontal motor areas and cerebrocerebellum) for a sample of 17 species (including humans). We identify patterns of mosaic change in brain evolution that mirror brain systems previously identified by electrophysiological and anatomical tract-tracing studies in non-human primates and functional connectivity MRI studies in humans. Across more than 40 Myr of anthropoid primate evolution, mosaic changes contribute more to explaining neural diversity than changes in relative brain size, and different mosaic patterns are differentially selected for when brains increase or decrease in size. We identify lineage-specific evolutionary specializations for all branches of the tree of life covered by our sample and demonstrate deep evolutionary roots for mosaic patterns associated with motor control and learning. PMID:23536600

Towards identifying the active sites on RuO 2 (110) in catalyzing oxygen evolution

DOE PAGES

Rao, Reshma R.; Kolb, Manuel J.; Halck, Niels Bendtsen; ...

2017-11-17

While the surface atomic structure of RuO 2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO 2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used to determine the surface structural changes on single-crystal RuO2(110) as a function of potential in acidic electrolyte. The redox peaks at 0.7, 1.1 and 1.4 V vs. reversible hydrogen electrode (RHE) could be attributed to surface transitions associated with the successive deprotonation of –H 2O on the coordinatively unsaturated Ru sites (CUS)more » and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring –OH group on the Ru CUS or bridge site. Combining potential-dependent surface structures with their energetics from DFT led to a new OER pathway, where the deprotonation of the –OH group used to stabilize –OO was found to be rate-limiting.« less

Towards identifying the active sites on RuO 2 (110) in catalyzing oxygen evolution

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

Rao, Reshma R.; Kolb, Manuel J.; Halck, Niels Bendtsen

While the surface atomic structure of RuO 2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO 2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used to determine the surface structural changes on single-crystal RuO2(110) as a function of potential in acidic electrolyte. The redox peaks at 0.7, 1.1 and 1.4 V vs. reversible hydrogen electrode (RHE) could be attributed to surface transitions associated with the successive deprotonation of –H 2O on the coordinatively unsaturated Ru sites (CUS)more » and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring –OH group on the Ru CUS or bridge site. Combining potential-dependent surface structures with their energetics from DFT led to a new OER pathway, where the deprotonation of the –OH group used to stabilize –OO was found to be rate-limiting.« less

Evolution: Help for the Confused.

ERIC Educational Resources Information Center

Scheer, Bradley T.

1979-01-01

Written in response to an earlier article questioning certain aspects of evolution theory. Discusses ontogeny and phylogeny, the basis of evolution, chance or purpose in evolution, micro and macro-evolution, reversibility, and the evolution processes today. (MA)

Dynamical evolution of topology of large-scale structure. [in distribution of galaxies

NASA Technical Reports Server (NTRS)

Park, Changbom; Gott, J. R., III

1991-01-01

The nonlinear effects of statistical biasing and gravitational evolution on the genus are studied. The biased galaxy subset is picked for the first time by actually identifying galaxy-sized peaks above a fixed threshold in the initial conditions, and their subsequent evolution is followed. It is found that in the standard cold dark matter (CDM) model the statistical biasing in the locations of galaxies produces asymmetry in the genus curve and coupling with gravitational evolution gives rise to a shift in the genus curve to the left in moderately nonlinear regimes. Gravitational evolution alone reduces the amplitude of the genus curve due to strong phase correlations in the density field and also produces asymmetry in the curve. Results on the genus of the mass density field for both CDM and hot dark matter models are consistent with previous work by Melott, Weinberg, and Gott (1987).

Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system.

PubMed

Satler, Jordan D; Carstens, Bryan C

2016-05-01

Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co-distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long-standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs of phylogeographic congruence because ancestral polymorphism has not completely sorted. Here, we introduce Phylogeographic Concordance Factors (PCFs), a novel method for quantifying phylogeographic congruence across species. We apply this method to the Sarracenia alata pitcher plant system, a carnivorous plant with a diverse array of commensal organisms. We explore whether a group of ecologically associated arthropods have co-diversified with the host pitcher plant, and identify if there is a positive correlation between ecological interaction and PCFs. Results demonstrate that multiple arthropods share congruent phylogeographic breaks with S. alata, and provide evidence that the level of ecological association can be used to predict the degree of similarity in the phylogeographic pattern. This study outlines an approach for quantifying phylogeographic congruence, a central concept in biogeographic research. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Another ``new'' metric for outdoor amphitheater criteria

NASA Astrophysics Data System (ADS)

Berens, Robert S.

2005-09-01

Since the late 1960s, when amplified musical performances began being held there, Atlanta's open-air Chastain Park Amphitheater has been the source of enormous friction between the City, the venue's owner, and the wealthy, politically-connected residential community abutting the Park. To identify the characteristics of concert event sound to which neighbors are particularly sensitive, sound levels were monitored during 17 concerts, ranging from quiet jazz and classical performances to rock-and-roll and hip-hop. Community sound levels were monitored at 25 locations, including nine where measurements were made simultaneously inside and outside homes. The study team confirmed that low-frequency sound was the one feature of concert-related sound that community residents identified as most problematic, but that only a relatively small proportion of the Chastain concerts resulted in any significant community annoyance. After assessing the spectral characteristics of the most troublesome concerts, a new compliance metric has been proposed to address low-frequency annoyance issues: a two-tiered exceedence threshold, based on 1-minute LEQ levels in the 63 Hz octave band measured at the rear of the amphitheater, with a concert-event ``exceedence'' defined to be either a 1-minute LEQ(63 Hz) level greater than 95 dB or more than ten 1-minute LEQ(63 Hz) levels greater than 90 dB.

Tightly congruent bursts of lineage and phenotypic diversification identified in a continental ant radiation.

PubMed

Price, Shauna L; Etienne, Rampal S; Powell, Scott

2016-04-01

Adaptive diversification is thought to be shaped by ecological opportunity. A prediction of this ecological process of diversification is that it should result in congruent bursts of lineage and phenotypic diversification, but few studies have found this expected association. Here, we study the relationship between rates of lineage diversification and body size evolution in the turtle ants, a diverse Neotropical clade. Using a near complete, time-calibrated phylogeny we investigated lineage diversification dynamics and body size disparity through model fitting analyses and estimation of per-lineage rates of cladogenesis and phenotypic evolution. We identify an exceptionally high degree of congruence between the high rates of lineage and body size diversification in a young clade undergoing renewed diversification in the ecologically distinct Chacoan biogeographical region of South America. It is likely that the region presented turtle ants with novel ecological opportunity, which facilitated a nested burst of diversification and phenotypic evolution within the group. Our results provide a compelling quantitative example of tight congruence between rates of lineage and phenotypic diversification, meeting the key predicted pattern of adaptive diversification shaped by ecological opportunity. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Adaptability and evolution.

PubMed

Bateson, Patrick

2017-10-06

The capacity of organisms to respond in their own lifetimes to new challenges in their environments probably appeared early in biological evolution. At present few studies have shown how such adaptability could influence the inherited characteristics of an organism's descendants. In part, this has been because organisms have been treated as passive in evolution. Nevertheless, their effects on biological evolution are likely to have been important and, when they occurred, accelerated the pace of evolution. Ways in which this might have happened have been suggested many times since the 1870s. I review these proposals and discuss their relevance to modern thought.

Evolution and immunity.

PubMed

Kaufman, Jim

2010-08-01

This report describes a meeting organized by Ken Smith and Jim Kaufman, entitled Evolution and Immunity, which took place at the University of Cambridge on 24 September 2009 to honour the anniversaries of the birth of Darwin and the first publication of The Origin of Species. Ten internationally-known speakers described the effects of evolution on immunity, ranging in timescales from the deep-time evolution of adaptive immune systems in vertebrates and invertebrates to the evolution of pathogens and lymphocytes within a single individual. The final talk explored the application of phylogenetic analysis to non-biological systems.

Evolution and immunity

PubMed Central

Kaufman, Jim

2010-01-01

This report describes a meeting organized by Ken Smith and Jim Kaufman, entitled Evolution and Immunity, which took place at the University of Cambridge on 24 September 2009 to honour the anniversaries of the birth of Darwin and the first publication of The Origin of Species. Ten internationally-known speakers described the effects of evolution on immunity, ranging in timescales from the deep-time evolution of adaptive immune systems in vertebrates and invertebrates to the evolution of pathogens and lymphocytes within a single individual. The final talk explored the application of phylogenetic analysis to non-biological systems. PMID:20465576

Evolution of genome size and complexity in the rhabdoviridae.

PubMed

Walker, Peter J; Firth, Cadhla; Widen, Steven G; Blasdell, Kim R; Guzman, Hilda; Wood, Thomas G; Paradkar, Prasad N; Holmes, Edward C; Tesh, Robert B; Vasilakis, Nikos

2015-02-01

RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.

Evolution of Genome Size and Complexity in the Rhabdoviridae

PubMed Central

Walker, Peter J.; Firth, Cadhla; Widen, Steven G.; Blasdell, Kim R.; Guzman, Hilda; Wood, Thomas G.; Paradkar, Prasad N.; Holmes, Edward C.; Tesh, Robert B.; Vasilakis, Nikos

2015-01-01

RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae. PMID:25679389

Asteroid Secular Dynamics: Ceres’ Fingerprint Identified

NASA Astrophysics Data System (ADS)

Novaković, Bojan; Maurel, Clara; Tsirvoulis, Georgios; Knežević, Zoran

2015-07-01

Here we report on the significant role of a so far overlooked dynamical aspect, namely, a secular resonance between the dwarf planet Ceres and other asteroids. We demonstrate that this type of secular resonance can be the dominant dynamical factor in certain regions of the main asteroid belt. Specifically, we performed a dynamical analysis of the asteroids belonging to the (1726) Hoffmeister family. To identify which dynamical mechanisms are actually at work in this part of the main asteroid belt, i.e., to isolate the main perturber(s), we study the evolution of this family in time. The study is accomplished using numerical integrations of test particles performed within different dynamical models. The obtained results reveal that the post-impact evolution of the Hoffmeister asteroid family is a direct consequence of the nodal secular resonance with Ceres. This leads us to the conclusion that similar effects must exist in other parts of the asteroid belt. In this respect, the obtained results shed light on an important and entirely new aspect of the long-term dynamics of small bodies. Ceres’ fingerprint in asteroid dynamics, expressed through the discovered secular resonance effect, completely changes our understanding of the way in which perturbations by Ceres-like objects affect the orbits of nearby bodies.

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

PubMed Central

2013-01-01

Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome. PMID:24267946

Frontiers of stellar evolution

NASA Technical Reports Server (NTRS)

Lambert, David L. (Editor)

1991-01-01

The present conference discusses theoretical and observational views of star formation, spectroscopic constraints on the evolution of massive stars, very low mass stars and brown dwarfs, asteroseismology, globular clusters as tests of stellar evolution, observational tests of stellar evolution, and mass loss from cool evolved giant stars. Also discussed are white dwarfs and hot subdwarfs, neutron stars and black holes, supernovae from single stars, close binaries with evolved components, accretion disks in interacting binaries, supernovae in binary systems, stellar evolution and galactic chemical evolution, and interacting binaries containing compact components.

Efficacy of Histone Deacetylase and Estrogen Receptor Inhibition in Breast Cancer Cells Due to Concerted down Regulation of Akt

PubMed Central

Thomas, Scott; Thurn, K. Ted; Raha, Paromita; Chen, Stephanie; Munster, Pamela N.

2013-01-01

Hormonal therapy resistance remains a considerable barrier in the treatment of breast cancer. Activation of the Akt-PI3K-mTOR pathway plays an important role in hormonal therapy resistance. Our recent preclinical and clinical studies showed that the addition of a histone deacetylase inhibitor re-sensitized hormonal therapy resistant breast cancer to tamoxifen. As histone deacetylases are key regulators of Akt, we evaluated the effect of combined treatment with the histone deacetylase inhibitor PCI-24781 and tamoxifen on Akt in breast cancer cells. We demonstrate that while both histone deacetylase and estrogen receptor inhibition down regulate AKT mRNA and protein, their concerted effort results in down regulation of AKT activity with induction of cell death. Histone deacetylase inhibition exerts its effect on AKT mRNA through an estrogen receptor-dependent mechanism, primarily down regulating the most abundant isoform AKT1. Although siRNA depletion of AKT modestly induces cell death, when combined with an anti-estrogen, cytotoxicity is significantly enhanced. Thus, histone deacetylase regulation of AKT mRNA is a key mediator of this therapeutic combination and may represent a novel biomarker for predicting response to this regimen. PMID:23874830

Evolution with Stochastic Fitness and Stochastic Migration

PubMed Central

Rice, Sean H.; Papadopoulos, Anthony

2009-01-01

Background Migration between local populations plays an important role in evolution - influencing local adaptation, speciation, extinction, and the maintenance of genetic variation. Like other evolutionary mechanisms, migration is a stochastic process, involving both random and deterministic elements. Many models of evolution have incorporated migration, but these have all been based on simplifying assumptions, such as low migration rate, weak selection, or large population size. We thus have no truly general and exact mathematical description of evolution that incorporates migration. Methodology/Principal Findings We derive an exact equation for directional evolution, essentially a stochastic Price equation with migration, that encompasses all processes, both deterministic and stochastic, contributing to directional change in an open population. Using this result, we show that increasing the variance in migration rates reduces the impact of migration relative to selection. This means that models that treat migration as a single parameter tend to be biassed - overestimating the relative impact of immigration. We further show that selection and migration interact in complex ways, one result being that a strategy for which fitness is negatively correlated with migration rates (high fitness when migration is low) will tend to increase in frequency, even if it has lower mean fitness than do other strategies. Finally, we derive an equation for the effective migration rate, which allows some of the complex stochastic processes that we identify to be incorporated into models with a single migration parameter. Conclusions/Significance As has previously been shown with selection, the role of migration in evolution is determined by the entire distributions of immigration and emigration rates, not just by the mean values. The interactions of stochastic migration with stochastic selection produce evolutionary processes that are invisible to deterministic evolutionary theory

Has pollination mode shaped the evolution of ficus pollen?

PubMed

Wang, Gang; Chen, Jin; Li, Zong-Bo; Zhang, Feng-Ping; Yang, Da-Rong

2014-01-01

The extent to which co-evolutionary processes shape morphological traits is one of the most fascinating topics in evolutionary biology. Both passive and active pollination modes coexist in the fig tree (Ficus, Moraceae) and fig wasp (Agaonidae, Hymenoptera) mutualism. This classic obligate relationship that is about 75 million years old provides an ideal system to consider the role of pollination mode shifts on pollen evolution. Twenty-five fig species, which cover all six Ficus subgenera, and are native to the Xishuangbanna region of southwest China, were used to investigate pollen morphology with scanning electron microscope (SEM). Pollination mode was identified by the Anther/Ovule ratio in each species. Phylogenetic free regression and a correlated evolution test between binary traits were conducted based on a strong phylogenetic tree. Seventeen of the 25 fig species were actively pollinated and eight species were passively pollinated. Three pollen shape types and three kinds of exine ornamentation were recognized among these species. Pollen grains with ellipsoid shape and rugulate ornamentation were dominant. Ellipsoid pollen occurred in all 17 species of actively pollinated figs, while for the passively pollinated species, two obtuse end shapes were identified: cylinder and sphere shapes were identified in six of the eight species. All passively pollinated figs presented rugulate ornamentation, while for actively pollinated species, the smoother types - psilate and granulate-rugulate ornamentations - accounted for just five and two among the 17 species, respectively. The relationship between pollen shape and pollination mode was shown by both the phylogenetic free regression and the correlated evolution tests. Three pollen shape and ornamentation types were found in Ficus, which show characteristics related to passive or active pollination mode. Thus, the pollen shape is very likely shaped by pollination mode in this unique obligate mutualism.

Has Pollination Mode Shaped the Evolution of Ficus Pollen?

PubMed Central

Wang, Gang; Chen, Jin; Li, Zong-Bo; Zhang, Feng-Ping; Yang, Da-Rong

2014-01-01

Background The extent to which co-evolutionary processes shape morphological traits is one of the most fascinating topics in evolutionary biology. Both passive and active pollination modes coexist in the fig tree (Ficus, Moraceae) and fig wasp (Agaonidae, Hymenoptera) mutualism. This classic obligate relationship that is about 75 million years old provides an ideal system to consider the role of pollination mode shifts on pollen evolution. Methods and Main Findings Twenty-five fig species, which cover all six Ficus subgenera, and are native to the Xishuangbanna region of southwest China, were used to investigate pollen morphology with scanning electron microscope (SEM). Pollination mode was identified by the Anther/Ovule ratio in each species. Phylogenetic free regression and a correlated evolution test between binary traits were conducted based on a strong phylogenetic tree. Seventeen of the 25 fig species were actively pollinated and eight species were passively pollinated. Three pollen shape types and three kinds of exine ornamentation were recognized among these species. Pollen grains with ellipsoid shape and rugulate ornamentation were dominant. Ellipsoid pollen occurred in all 17 species of actively pollinated figs, while for the passively pollinated species, two obtuse end shapes were identified: cylinder and sphere shapes were identified in six of the eight species. All passively pollinated figs presented rugulate ornamentation, while for actively pollinated species, the smoother types - psilate and granulate-rugulate ornamentations - accounted for just five and two among the 17 species, respectively. The relationship between pollen shape and pollination mode was shown by both the phylogenetic free regression and the correlated evolution tests. Conclusions Three pollen shape and ornamentation types were found in Ficus, which show characteristics related to passive or active pollination mode. Thus, the pollen shape is very likely shaped by pollination mode

Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae).

PubMed

Prebus, Matthew

2017-12-13

Temnothorax (Formicidae: Myrmicinae) is a diverse genus of ants found in a broad spectrum of ecosystems across the northern hemisphere. These diminutive ants have long served as models for social insect behavior, leading to discoveries about social learning and inspiring hypotheses about the process of speciation and the evolution of social parasitism. This genus is highly morphologically and behaviorally diverse, and this has caused a great deal of taxonomic confusion in recent years. Past efforts to estimate the phylogeny of this genus have been limited in taxonomic scope, leaving the broader evolutionary patterns in Temnothorax unclear. To establish the monophyly of Temnothorax, resolve the evolutionary relationships, reconstruct the historical biogeography and investigate trends in the evolution of key traits, I generated, assembled, and analyzed two molecular datasets: a traditional multi-locus Sanger sequencing dataset, and an ultra-conserved element (UCE) dataset. Using maximum likelihood, Bayesian, and summary-coalescent based approaches, I analyzed 22 data subsets consisting of 103 ingroup taxa and a maximum of 1.8 million base pairs in 2485 loci. The results of this study suggest an origin of Temnothorax at the Eocene-Oligocene transition, concerted transitions to arboreal nesting habits in several clades during the Oligocene, coinciding with ancient global cooling, and several convergent origins of social parasitism in the Miocene and Pliocene. As with other Holarctic taxa, Temnothorax has a history of migration across Beringia during the Miocene. Temnothorax is corroborated as a natural group, and the notion that many of the historical subgeneric and species group concepts are artificial is reinforced. The strict form of Emery's Rule, in which a socially parasitic species is sister to its host species, is not well supported in Temnothorax.

Variability in group size and the evolution of collective action.

PubMed

Peña, Jorge; Nöldeke, Georg

2016-01-21

Models of the evolution of collective action typically assume that interactions occur in groups of identical size. In contrast, social interactions between animals occur in groups of widely dispersed size. This paper models collective action problems as two-strategy multiplayer games and studies the effect of variability in group size on the evolution of cooperative behavior under the replicator dynamics. The analysis identifies elementary conditions on the payoff structure of the game implying that the evolution of cooperative behavior is promoted or inhibited when the group size experienced by a focal player is more or less variable. Similar but more stringent conditions are applicable when the confounding effect of size-biased sampling, which causes the group-size distribution experienced by a focal player to differ from the statistical distribution of group sizes, is taken into account. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genetic variability, individuality and the evolution of the mammalian brain.

PubMed

Lipp, H P

1995-12-01

The neo-Darwinian theory of evolution has difficulty in explaining the rapid evolution of mammalian brain and behavior. I shall argue that the plasticity mechanisms of the brain (i.e., system homeostasis, developmental reorganization, structural adult plasticity, and cognition and learning) have evolved primarily as genetic buffer systems which protect subtle mutations influencing brain structures from natural selection. These buffer systems permit accumulation of genetic variation in the higher system levels of the brain (simply defined as structures with late differentiation), while low-level systems are kept constant by natural selection. The organization of this intrinsic genetic buffering system provides several features facilitating neo-Darwinian evolution: In conclusion, the evolutionary appearance of cognition and intelligence is an ordinary biological mechanism compensating evolutionary drags such as long lifespans and fewer offspring. The concept has heuristic value for identifying gene-brain-behavior relationships and for explaining behavioral consequences of artifical gene deletions.

A limited role for gene duplications in the evolution of platypus venom.

PubMed

Wong, Emily S W; Papenfuss, Anthony T; Whittington, Camilla M; Warren, Wesley C; Belov, Katherine

2012-01-01

Gene duplication followed by adaptive selection is believed to be the primary driver of venom evolution. However, to date, no studies have evaluated the importance of gene duplications for venom evolution using a genomic approach. The availability of a sequenced genome and a venom gland transcriptome for the enigmatic platypus provides a unique opportunity to explore the role that gene duplication plays in venom evolution. Here, we identify gene duplication events and correlate them with expressed transcripts in an in-season venom gland. Gene duplicates (1,508) were identified. These duplicated pairs (421), including genes that have undergone multiple rounds of gene duplications, were expressed in the venom gland. The majority of these genes are involved in metabolism and protein synthesis not toxin functions. Twelve secretory genes including serine proteases, metalloproteinases, and protease inhibitors likely to produce symptoms of envenomation such as vasodilation and pain were detected. Only 16 of 107 platypus genes with high similarity to known toxins evolved through gene duplication. Platypus venom C-type natriuretic peptides and nerve growth factor do not possess lineage-specific gene duplicates. Extensive duplications, believed to increase the potency of toxic content and promote toxin diversification, were not found. This is the first study to take a genome-wide approach in order to examine the impact of gene duplication on venom evolution. Our findings support the idea that adaptive selection acts on gene duplicates to drive the independent evolution and functional diversification of similar venom genes in venomous species. However, gene duplications alone do not explain the "venome" of the platypus. Other mechanisms, such as alternative splicing and mutation, may be important in venom innovation.

A Limited Role for Gene Duplications in the Evolution of Platypus Venom

PubMed Central

Wong, Emily S. W.; Papenfuss, Anthony T.; Whittington, Camilla M.; Warren, Wesley C.; Belov, Katherine

2012-01-01

Gene duplication followed by adaptive selection is believed to be the primary driver of venom evolution. However, to date, no studies have evaluated the importance of gene duplications for venom evolution using a genomic approach. The availability of a sequenced genome and a venom gland transcriptome for the enigmatic platypus provides a unique opportunity to explore the role that gene duplication plays in venom evolution. Here, we identify gene duplication events and correlate them with expressed transcripts in an in-season venom gland. Gene duplicates (1,508) were identified. These duplicated pairs (421), including genes that have undergone multiple rounds of gene duplications, were expressed in the venom gland. The majority of these genes are involved in metabolism and protein synthesis not toxin functions. Twelve secretory genes including serine proteases, metalloproteinases, and protease inhibitors likely to produce symptoms of envenomation such as vasodilation and pain were detected. Only 16 of 107 platypus genes with high similarity to known toxins evolved through gene duplication. Platypus venom C-type natriuretic peptides and nerve growth factor do not possess lineage-specific gene duplicates. Extensive duplications, believed to increase the potency of toxic content and promote toxin diversification, were not found. This is the first study to take a genome-wide approach in order to examine the impact of gene duplication on venom evolution. Our findings support the idea that adaptive selection acts on gene duplicates to drive the independent evolution and functional diversification of similar venom genes in venomous species. However, gene duplications alone do not explain the “venome” of the platypus. Other mechanisms, such as alternative splicing and mutation, may be important in venom innovation. PMID:21816864

Spectral evolution of GRBs with negative spectral lag using Fermi GBM observations

NASA Astrophysics Data System (ADS)

Chakrabarti, Arundhati; Chaudhury, Kishor; Sarkar, Samir K.; Bhadra, Arunava

2018-06-01

The positive spectral lag of Gamma Ray Bursts (GRBs) is often explained in terms of hard-to-soft spectral evolution of GRB pulses. While positive lags of GRBs is very common, there are few GRB pulses that exhibits negative spectral lags. In the present work we examine whether negative lags of GRBs also can be interpreted in terms of spectral evolution of GRB pulses or not. Using Fermi-GBM data, we identify two GRBs, GRB 090426C and GRB 150213A, with clean pulses that exhibit negative spectral lag. An indication of soft to hard transition has been noticed for the negative spectral lag events from the spectral evolution study. The implication of the present findings on the models of GRB spectral lags are discussed.

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

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

Frese, Steven A.; Benson, Andrew K.; Tannock, Gerald W.

Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order tomore » differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process.« less

The evolution of phenotypic integration: How directional selection reshapes covariation in mice.

PubMed

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-10-01

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

How does pollen versus seed dispersal affect niche evolution?

PubMed

Aguilée, Robin; Shaw, Frank H; Rousset, François; Shaw, Ruth G; Ronce, Ophélie

2013-03-01

In heterogeneous landscapes, the genetic and demographic consequences of dispersal influence the evolution of niche width. Unless pollen is limiting, pollen dispersal does not contribute directly to population growth. However, by disrupting local adaptation, it indirectly affects population dynamics. We compare the effect of pollen versus seed dispersal on the evolution of niche width in heterogeneous habitats, explicitly considering the feedback between maladaptation and demography. We consider two scenarios: the secondary contact of two subpopulations, in distinct, formerly isolated habitats, and the colonization of an empty habitat with dispersal between the new and ancestral habitat. With an analytical model, we identify critical levels of genetic variance leading to niche contraction (secondary contact scenario), or expansion (new habitat scenario). We confront these predictions with simulations where the genetic variance freely evolves. Niche contraction occurs when habitats are very different. It is faster as total gene flow increases or as pollen predominates in overall gene flow. Niche expansion occurs when habitat heterogeneity is not too high. Seed dispersal accelerates it, whereas pollen dispersal tends to retard it. In both scenarios very high seed dispersal leads to extinction. Overall, our results predict a wider niche for species dispersing seeds more than pollen. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Evolution patterns and parameter regimes in edge localized modes on the National Spherical Torus Experiment

DOE Data Explorer

Smith, D. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Bell, R. E. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Podesta, M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Smith, D. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Fonck, R. J. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); McKee, G. R. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Diallo, A. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Kaye, S. M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); LeBlanc, B. P. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Sabbagh, S. A. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)

2015-09-01

We implement unsupervised machine learning techniques to identify characteristic evolution patterns and associated parameter regimes in edge localized mode (ELM) events observed on the National Spherical Torus Experiment. Multi-channel, localized measurements spanning the pedestal region capture the complex evolution patterns of ELM events on Alfven timescales. Some ELM events are active for less than 100~microsec, but others persist for up to 1~ms. Also, some ELM events exhibit a single dominant perturbation, but others are oscillatory. Clustering calculations with time-series similarity metrics indicate the ELM database contains at least two and possibly three groups of ELMs with similar evolution patterns. The identified ELM groups trigger similar stored energy loss, but the groups occupy distinct parameter regimes for ELM-relevant quantities like plasma current, triangularity, and pedestal height. Notably, the pedestal electron pressure gradient is not an effective parameter for distinguishing the ELM groups, but the ELM groups segregate in terms of electron density gradient and electron temperature gradient. The ELM evolution patterns and corresponding parameter regimes can shape the formulation or validation of nonlinear ELM models. Finally, the techniques and results demonstrate an application of unsupervised machine learning at a data-rich fusion facility.

OncoNEM: inferring tumor evolution from single-cell sequencing data.

PubMed

Ross, Edith M; Markowetz, Florian

2016-04-15

Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. OncoNEM identifies homogeneous cellular subpopulations and infers their genotypes as well as a tree describing their evolutionary relationships. In simulation studies, we assess OncoNEM's robustness and benchmark its performance against competing methods. Finally, we show its applicability in case studies of muscle-invasive bladder cancer and essential thrombocythemia.

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

Treesearch

Daniel L. Lindner; Mark T. Banik

2011-01-01

Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus...

Cospeciation of gut microbiota with hominids

PubMed Central

Moeller, Andrew H.; Caro-Quintero, Alejandro; Mjungu, Deus; Georgiev, Alexander V.; Lonsdorf, Elizabeth V.; Muller, Martin N.; Pusey, Anne E.; Peeters, Martine; Hahn, Beatrice H.; Ochman, Howard

2016-01-01

The evolutionary origins of the bacterial lineages that populate the human gut are unknown. Here we show that multiple lineages of the predominant bacterial taxa in the gut arose via cospeciation with humans, chimpanzees, bonobos, and gorillas over the past 15 million years. Analyses of strain-level bacterial diversity within hominid gut microbiomes revealed that clades of Bacteroidaceae and Bifidobacteriaceae have been maintained exclusively within host lineages across hundreds of thousands of host generations. Divergence times of these cospeciating gut bacteria are congruent with those of hominids, indicating that nuclear, mitochondrial, and gut bacterial genomes diversified in concert during hominid evolution. This study identifies human gut bacteria descended from ancient symbionts that speciated simultaneously with humans and the African apes. PMID:27463672

Cross-Modal Perception of Noise-in-Music: Audiences Generate Spiky Shapes in Response to Auditory Roughness in a Novel Electroacoustic Concert Setting.

PubMed

Liew, Kongmeng; Lindborg, PerMagnus; Rodrigues, Ruth; Styles, Suzy J

2018-01-01

Noise has become integral to electroacoustic music aesthetics. In this paper, we define noise as sound that is high in auditory roughness, and examine its effect on cross-modal mapping between sound and visual shape in participants. In order to preserve the ecological validity of contemporary music aesthetics, we developed Rama , a novel interface, for presenting experimentally controlled blocks of electronically generated sounds that varied systematically in roughness, and actively collected data from audience interaction. These sounds were then embedded as musical drones within the overall sound design of a multimedia performance with live musicians, Audience members listened to these sounds, and collectively voted to create the shape of a visual graphic, presented as part of the audio-visual performance. The results of the concert setting were replicated in a controlled laboratory environment to corroborate the findings. Results show a consistent effect of auditory roughness on shape design, with rougher sounds corresponding to spikier shapes. We discuss the implications, as well as evaluate the audience interface.

Evolution and mass extinctions as lognormal stochastic processes

NASA Astrophysics Data System (ADS)

Maccone, Claudio

2014-10-01

-terrestrial civilizations existing in the Galaxy (as a consequence of the central limit theorem of statistics). (5) But the most striking new result is that the well-known `Molecular Clock of Evolution', namely the `constant rate of Evolution at the molecular level' as shown by Kimura's Neutral Theory of Molecular Evolution, identifies with growth rate of the entropy of our Evo-SETI model, because they both grew linearly in time since the origin of life. (6) Furthermore, we apply our Evo-SETI model to lognormal stochastic processes other than GBMs. For instance, we provide two models for the mass extinctions that occurred in the past: (a) one based on GBMs and (b) the other based on a parabolic mean value capable of covering both the extinction and the subsequent recovery of life forms. (7) Finally, we show that the Markov & Korotayev (2007, 2008) model for Darwinian Evolution identifies with an Evo-SETI model for which the mean value of the underlying lognormal stochastic process is a cubic function of the time. In conclusion: we have provided a new mathematical model capable of embracing molecular evolution, SETI and entropy into a simple set of statistical equations based upon b-lognormals and lognormal stochastic processes with arbitrary mean, of which the GBMs are the particular case of exponential growth.

Biomimetic perfusion and electrical stimulation applied in concert improved the assembly of engineered cardiac tissue.

PubMed

Maidhof, Robert; Tandon, Nina; Lee, Eun Jung; Luo, Jianwen; Duan, Yi; Yeager, Keith; Konofagou, Elisa; Vunjak-Novakovic, Gordana

2012-11-01

Maintenance of normal myocardial function depends intimately on synchronous tissue contraction, driven by electrical activation and on adequate nutrient perfusion in support thereof. Bioreactors have been used to mimic aspects of these factors in vitro to engineer cardiac tissue but, due to design limitations, previous bioreactor systems have yet to simultaneously support nutrient perfusion, electrical stimulation and unconstrained (i.e. not isometric) tissue contraction. To the best of our knowledge, the bioreactor system described herein is the first to integrate these three key factors in concert. We present the design of our bioreactor and characterize its capability in integrated experimental and mathematical modelling studies. We then cultured cardiac cells obtained from neonatal rats in porous, channelled elastomer scaffolds with the simultaneous application of perfusion and electrical stimulation, with controls excluding either one or both of these two conditions. After 8 days of culture, constructs grown with simultaneous perfusion and electrical stimulation exhibited substantially improved functional properties, as evidenced by a significant increase in contraction amplitude (0.23 ± 0.10% vs 0.14 ± 0.05%, 0.13 ± 0.08% or 0.09 ± 0.02% in control constructs grown without stimulation, without perfusion, or either stimulation or perfusion, respectively). Consistently, these constructs had significantly improved DNA contents, cell distribution throughout the scaffold thickness, cardiac protein expression, cell morphology and overall tissue organization compared to control groups. Thus, the simultaneous application of medium perfusion and electrical conditioning enabled by the use of the novel bioreactor system may accelerate the generation of fully functional, clinically sized cardiac tissue constructs. Copyright © 2011 John Wiley & Sons, Ltd.

Molecular Evolution of Phosphoprotein Phosphatases in Drosophila

PubMed Central

Miskei, Márton; Ádám, Csaba; Kovács, László; Karányi, Zsolt; Dombrádi, Viktor

2011-01-01

Phosphoprotein phosphatases (PPP), these ancient and important regulatory enzymes are present in all eukaryotic organisms. Based on the genome sequences of 12 Drosophila species we traced the evolution of the PPP catalytic subunits and noted a substantial expansion of the gene family. We concluded that the 18–22 PPP genes of Drosophilidae were generated from a core set of 8 indispensable phosphatases that are present in most of the insects. Retropositons followed by tandem gene duplications extended the phosphatase repertoire, and sporadic gene losses contributed to the species specific variations in the PPP complement. During the course of these studies we identified 5, up till now uncharacterized phosphatase retrogenes: PpY+, PpD5+, PpD6+, Pp4+, and Pp6+ which are found only in some ancient Drosophila. We demonstrated that all of these new PPP genes exhibit a distinct male specific expression. In addition to the changes in gene numbers, the intron-exon structure and the chromosomal localization of several PPP genes was also altered during evolution. The G−C content of the coding regions decreased when a gene moved into the heterochromatic region of chromosome Y. Thus the PPP enzymes exemplify the various types of dynamic rearrangements that accompany the molecular evolution of a gene family in Drosophilidae. PMID:21789237

Evolution of transcriptional enhancers and animal diversity

PubMed Central

Rubinstein, Marcelo; de Souza, Flávio S. J.

2013-01-01

Deciphering the genetic bases that drive animal diversity is one of the major challenges of modern biology. Although four decades ago it was proposed that animal evolution was mainly driven by changes in cis-regulatory DNA elements controlling gene expression rather than in protein-coding sequences, only now are powerful bioinformatics and experimental approaches available to accelerate studies into how the evolution of transcriptional enhancers contributes to novel forms and functions. In the introduction to this Theme Issue, we start by defining the general properties of transcriptional enhancers, such as modularity and the coexistence of tight sequence conservation with transcription factor-binding site shuffling as different mechanisms that maintain the enhancer grammar over evolutionary time. We discuss past and current methods used to identify cell-type-specific enhancers and provide examples of how enhancers originate de novo, change and are lost in particular lineages. We then focus in the central part of this Theme Issue on analysing examples of how the molecular evolution of enhancers may change form and function. Throughout this introduction, we present the main findings of the articles, reviews and perspectives contributed to this Theme Issue that together illustrate some of the great advances and current frontiers in the field. PMID:24218630

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes.

PubMed

Schnitzler, Christine E; Pang, Kevin; Powers, Meghan L; Reitzel, Adam M; Ryan, Joseph F; Simmons, David; Tada, Takashi; Park, Morgan; Gupta, Jyoti; Brooks, Shelise Y; Blakesley, Robert W; Yokoyama, Shozo; Haddock, Steven Hd; Martindale, Mark Q; Baxevanis, Andreas D

2012-12-21

Calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (Phylum Cnidaria) and comb jellies (Phylum Ctenophora). The complete genomic sequence from the ctenophore Mnemiopsis leidyi, a representative of the earliest branch of animals that emit light, provided an opportunity to examine the genome of an organism that uses this class of luciferase for bioluminescence and to look for genes involved in light reception. To determine when photoprotein genes first arose, we examined the genomic sequence from other early-branching taxa. We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis. The Mnemiopsis genome has 10 full-length photoprotein genes situated within two genomic clusters with high sequence conservation that are maintained due to strong purifying selection and concerted evolution. Photoprotein-like genes were also identified in the genomes of the non-luminescent sponge Amphimedon queenslandica and the non-luminescent cnidarian Nematostella vectensis, and phylogenomic analysis demonstrated that photoprotein genes arose at the base of all animals. Photoprotein gene expression in Mnemiopsis embryos begins during gastrulation in migrating precursors to photocytes and persists throughout development in the canals where photocytes reside. We identified three putative opsin genes in the Mnemiopsis genome and show that they do not group with well-known bilaterian opsin subfamilies. Interestingly, photoprotein transcripts are co-expressed with two of the putative opsins in developing photocytes. Opsin expression is also seen in the apical sensory organ. We present evidence that one opsin functions as a photopigment in vitro, absorbing light at wavelengths that overlap with peak photoprotein light emission, raising the hypothesis that light

Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes

PubMed Central

2012-01-01

Background Calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (Phylum Cnidaria) and comb jellies (Phylum Ctenophora). The complete genomic sequence from the ctenophore Mnemiopsis leidyi, a representative of the earliest branch of animals that emit light, provided an opportunity to examine the genome of an organism that uses this class of luciferase for bioluminescence and to look for genes involved in light reception. To determine when photoprotein genes first arose, we examined the genomic sequence from other early-branching taxa. We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis. Results The Mnemiopsis genome has 10 full-length photoprotein genes situated within two genomic clusters with high sequence conservation that are maintained due to strong purifying selection and concerted evolution. Photoprotein-like genes were also identified in the genomes of the non-luminescent sponge Amphimedon queenslandica and the non-luminescent cnidarian Nematostella vectensis, and phylogenomic analysis demonstrated that photoprotein genes arose at the base of all animals. Photoprotein gene expression in Mnemiopsis embryos begins during gastrulation in migrating precursors to photocytes and persists throughout development in the canals where photocytes reside. We identified three putative opsin genes in the Mnemiopsis genome and show that they do not group with well-known bilaterian opsin subfamilies. Interestingly, photoprotein transcripts are co-expressed with two of the putative opsins in developing photocytes. Opsin expression is also seen in the apical sensory organ. We present evidence that one opsin functions as a photopigment in vitro, absorbing light at wavelengths that overlap with peak photoprotein light emission, raising the hypothesis

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

An ecological and behavioural approach to hominin evolution during the Pliocene

NASA Astrophysics Data System (ADS)

Macho, Gabriele A.

2014-07-01

The study considers the turnover in hominins, together with carnivorans and other primates, at 3.5 Ma against an environmental backdrop. Communalities are identified between evolving guilds that may directly inform hominin evolution. These are the evolution of (a) dietary generalists and (b) evidence for sociality in carnivores, baboons and hominins. Sociality and behavioural flexibility are regarded advantageous for the procurement of resources while, at the same time, reducing intraspecific competition; in primates it may initially also have served to reduce predation risk. Behavioural flexibility explains the evolutionary success of Panthera leo, Papio and Homo. Viewed within a wider palaeoecological and environmental context, it is possible that sociality in hominins, including allocare, were triggered by abiotic changes at about 3.5 Ma. If confirmed in future studies, this would mark the beginning of hominin life history evolution.

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast

PubMed Central

Hope, Elyse A.; Amorosi, Clara J.; Miller, Aaron W.; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J.

2017-01-01

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. PMID:28450459

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast.

PubMed

Hope, Elyse A; Amorosi, Clara J; Miller, Aaron W; Dang, Kolena; Heil, Caiti Smukowski; Dunham, Maitreya J

2017-06-01

Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1 , and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1 , which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits. Copyright © 2017 Hope et al.

Wing serial homologs and the origin and evolution of the insect wing.

PubMed

Ohde, Takahiro; Yaginuma, Toshinobu; Niimi, Teruyuki

2014-04-01

The origin and evolution of insect wings has been the subject of extensive debate. The issue has remained controversial largely because of the absence of definitive fossil evidence or direct developmental evidence of homology between wings and a putative wing origin. Recent identification of wing serial homologs (WSHs) has provided researchers with a potential strategy for identifying WSHs in other species. Future comparative developmental analyses between wings and WSHs may clarify the important steps underlying the evolution of insect wings. Copyright © 2013 The Authors. Published by Elsevier GmbH.. All rights reserved.

Teaching Evolution

ERIC Educational Resources Information Center

Bryner, Jeanna

2005-01-01

Eighty years after the famous 1925 Scopes "monkey trial," which tested a teacher's right to discuss the theory of evolution in the classroom, evolution--and its most recent counterview, called "intelligent design"--are in the headlines again, and just about everyone seems to have an opinion. This past July, President Bush weighed in, telling…

Pigment cell interactions and differential xanthophore recruitment underlying zebrafish stripe reiteration and Danio pattern evolution

PubMed Central

Patterson, Larissa B.; Bain, Emily J.; Parichy, David M.

2014-01-01

Fishes have diverse pigment patterns, yet mechanisms of pattern evolution remain poorly understood. In zebrafish, Danio rerio, pigment-cell autonomous interactions generate dark stripes of melanophores that alternate with light interstripes of xanthophores and iridophores. Here, we identify mechanisms underlying the evolution of a uniform pattern in D. albolineatus in which all three pigment cell classes are intermingled. We show that in this species xanthophores differentiate precociously over a wider area, and that cis regulatory evolution has increased expression of xanthogenic Colony Stimulating Factor-1 (Csf1). Expressing Csf1 similarly in D. rerio has cascading effects, driving the intermingling of all three pigment cell classes and resulting in the loss of stripes, as in D. albolineatus. Our results identify novel mechanisms of pattern development and illustrate how pattern diversity can be generated when a core network of pigment-cell autonomous interactions is coupled with changes in pigment cell differentiation. PMID:25374113

The landscape of Titan as witness to its climate evolution

NASA Astrophysics Data System (ADS)

Moore, Jeffrey M.; Howard, Alan D.; Morgan, Alexander M.

2014-09-01

We investigated the range of Titan climate evolution hypotheses regulated by the role, sources, and availability of methane. We analyzed all available image data (principally synthetic aperture radar (SAR)) of Titan's landscape through the T-86 encounter, starting with focused examinations of terrains that carry the markers of climate evolution. Traditional geologic and geomorphic landscape analysis was used to perform morphometric characterization, establish time-stratigraphic relationships, and interpret local and regional geologic process-oriented evolutionary histories. We then assayed the distribution of terrains we identified with respect to both their latitudinal and altimetric occurrence. Our analysis of the terrain types and distributions was used to evaluate and rank the various climate evolution scenarios. We favor progressive hypotheses, which include a relatively brief period in which precipitation was able to affect geomorphic change in low latitudes at scales perceivable in SAR data, with subsequent gradual decline of precipitation intensity coupled with an increasing poleward restriction.

Ligand binding was acquired during evolution of nuclear receptors

PubMed Central

Escriva, Hector; Safi, Rachid; Hänni, Catherine; Langlois, Marie-Claire; Saumitou-Laprade, Pierre; Stehelin, Dominique; Capron, André; Pierce, Raymond; Laudet, Vincent

1997-01-01

The nuclear receptor (NR) superfamily comprises, in addition to ligand-activated transcription factors, members for which no ligand has been identified to date. We demonstrate that orphan receptors are randomly distributed in the evolutionary tree and that there is no relationship between the position of a given liganded receptor in the tree and the chemical nature of its ligand. NRs are specific to metazoans, as revealed by a screen of NR-related sequences in early- and non-metazoan organisms. The analysis of the NR gene duplication pattern during the evolution of metazoans shows that the present NR diversity arose from two waves of gene duplications. Strikingly, our results suggest that the ancestral NR was an orphan receptor that acquired ligand-binding ability during subsequent evolution. PMID:9192646

Achieving cost reductions in EOSDIS operations through technology evolution

NASA Technical Reports Server (NTRS)

Newsome, Penny; Moe, Karen; Harberts, Robert

1996-01-01

The earth observing system (EOS) data information system (EOSDIS) mission includes the cost-effective management and distribution of large amounts of data to the earth science community. The effect of the introduction of new information system technologies on the evolution of EOSDIS is considered. One of the steps taken by NASA to enable the introduction of new information system technologies into the EOSDIS is the funding of technology development through prototyping. Recent and ongoing prototyping efforts and their potential impact on the performance and cost-effectiveness of the EOSDIS are discussed. The technology evolution process as it related to the effective operation of EOSDIS is described, and methods are identified for the support of the transfer of relevant technology to EOSDIS components.

Evolution of complex dynamics

NASA Astrophysics Data System (ADS)

Wilds, Roy; Kauffman, Stuart A.; Glass, Leon

2008-09-01

We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.

QCDNUM: Fast QCD evolution and convolution

NASA Astrophysics Data System (ADS)

Botje, M.

2011-02-01

The QCDNUM program numerically solves the evolution equations for parton densities and fragmentation functions in perturbative QCD. Un-polarised parton densities can be evolved up to next-to-next-to-leading order in powers of the strong coupling constant, while polarised densities or fragmentation functions can be evolved up to next-to-leading order. Other types of evolution can be accessed by feeding alternative sets of evolution kernels into the program. A versatile convolution engine provides tools to compute parton luminosities, cross-sections in hadron-hadron scattering, and deep inelastic structure functions in the zero-mass scheme or in generalised mass schemes. Input to these calculations are either the QCDNUM evolved densities, or those read in from an external parton density repository. Included in the software distribution are packages to calculate zero-mass structure functions in un-polarised deep inelastic scattering, and heavy flavour contributions to these structure functions in the fixed flavour number scheme. Program summaryProgram title: QCDNUM version: 17.00 Catalogue identifier: AEHV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public Licence No. of lines in distributed program, including test data, etc.: 45 736 No. of bytes in distributed program, including test data, etc.: 911 569 Distribution format: tar.gz Programming language: Fortran-77 Computer: All Operating system: All RAM: Typically 3 Mbytes Classification: 11.5 Nature of problem: Evolution of the strong coupling constant and parton densities, up to next-to-next-to-leading order in perturbative QCD. Computation of observable quantities by Mellin convolution of the evolved densities with partonic cross-sections. Solution method: Parametrisation of the parton densities as linear or quadratic splines on a discrete grid, and evolution of the spline

Concerted functions of Streptococcus gordonii surface proteins PadA and Hsa mediate activation of human platelets and interactions with extracellular matrix.

PubMed

Haworth, Jennifer A; Jenkinson, Howard F; Petersen, Helen J; Back, Catherine R; Brittan, Jane L; Kerrigan, Steve W; Nobbs, Angela H

2017-01-01

A range of Streptococcus bacteria are able to interact with blood platelets to form a thrombus (clot). Streptococcus gordonii is ubiquitous within the human oral cavity and amongst the common pathogens isolated from subjects with infective endocarditis. Two cell surface proteins, Hsa and Platelet adherence protein A (PadA), in S. gordonii mediate adherence and activation of platelets. In this study, we demonstrate that PadA binds activated platelets and that an NGR (Asparagine-Glycine-Arginine) motif within a 657 amino acid residue N-terminal fragment of PadA is responsible for this, together with two other integrin-like recognition motifs RGT and AGD. PadA also acts in concert with Hsa to mediate binding of S. gordonii to cellular fibronectin and vitronectin, and to promote formation of biofilms. Evidence is presented that PadA and Hsa are each reliant on the other's active presentation on the bacterial cell surface, suggesting cooperativity in functions impacting both colonization and pathogenesis. © 2016 The Authors Cellular Microbiology Published by John Wiley & Sons Ltd.

Feminist Pedagogy, Body Image, and the Dance Technique Class

ERIC Educational Resources Information Center

Barr, Sherrie; Oliver, Wendy

2016-01-01

This paper investigates the evolution of feminist consciousness in dance technique class as related to body image, the myth of the perfect body, and the development of feminist pedagogy. Western concert dance forms have often been taught in a manner where imitating the teacher is primary in the learning process. In this traditional scenario,…

It's not all about us: evolution and maintenance of Cryptococcus virulence requires selection outside the human host.

PubMed

Gerstein, Aleeza C; Nielsen, Kirsten

2017-04-01

Cryptococcus is predominantly an AIDS-related pathogen that causes significant morbidity and mortality in immunocompromised patients. Research studies have historically focused on understanding how the organism causes human disease through the use of in vivo and in vitro model systems to identify virulence factors. Cryptococcus is not an obligate pathogen, however, as human-human transmission is either absent or rare. Selection in the environment must thus be invoked to shape the evolution of this taxa, and directly influences genotypic and trait diversity. Importantly, the evolution and maintenance of pathogenicity must also stem directly from environmental selection. To that end, here we examine abiotic and biotic stresses in the environment, and discuss how they could shape the factors that are commonly identified as important virulence traits. We identify a number of important unanswered questions about Cryptococcus diversity and evolution that are critical for understanding this deadly pathogen, and discuss how implementation of modern sampling and genomic tools could be utilized to answer these questions. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

The evolution of airplanes

NASA Astrophysics Data System (ADS)

Bejan, A.; Charles, J. D.; Lorente, S.

2014-07-01

The prevailing view is that we cannot witness biological evolution because it occurred on a time scale immensely greater than our lifetime. Here, we show that we can witness evolution in our lifetime by watching the evolution of the flying human-and-machine species: the airplane. We document this evolution, and we also predict it based on a physics principle: the constructal law. We show that the airplanes must obey theoretical allometric rules that unite them with the birds and other animals. For example, the larger airplanes are faster, more efficient as vehicles, and have greater range. The engine mass is proportional to the body size: this scaling is analogous to animal design, where the mass of the motive organs (muscle, heart, lung) is proportional to the body size. Large or small, airplanes exhibit a proportionality between wing span and fuselage length, and between fuel load and body size. The animal-design counterparts of these features are evident. The view that emerges is that the evolution phenomenon is broader than biological evolution. The evolution of technology, river basins, and animal design is one phenomenon, and it belongs in physics.

Evolution of forensic odontology: An overview

PubMed Central

Balachander, N.; Babu, N. Aravindha; Jimson, Sudha; Priyadharsini, C.; Masthan, K. M. K.

2015-01-01

Forensic dentistry or forensic odontology admits dentists’ participation or identification of the victim and assisting legal and criminal issues. It refers to the proper handling, examination, identification and evaluation of dental evidence. This article summarizes the evolution of forensic odontology that started right from Garden of Eden to the modern scenario in identification of the gang rape case which happened in the state capital. Forensic dentistry plays a significant role in identifying the victims of crime, deceased individuals through the examination of anatomical structures, dental appliances and dental restorations. PMID:26015703

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.

Major transitions in human evolution.

PubMed

Foley, Robert A; Martin, Lawrence; Mirazón Lahr, Marta; Stringer, Chris

2016-07-05

Evolutionary problems are often considered in terms of 'origins', and research in human evolution seen as a search for human origins. However, evolution, including human evolution, is a process of transitions from one state to another, and so questions are best put in terms of understanding the nature of those transitions. This paper discusses how the contributions to the themed issue 'Major transitions in human evolution' throw light on the pattern of change in hominin evolution. Four questions are addressed: (1) Is there a major divide between early (australopithecine) and later (Homo) evolution? (2) Does the pattern of change fit a model of short transformations, or gradual evolution? (3) Why is the role of Africa so prominent? (4) How are different aspects of adaptation-genes, phenotypes and behaviour-integrated across the transitions? The importance of developing technologies and approaches and the enduring role of fieldwork are emphasized.This article is part of the themed issue 'Major transitions in human evolution'. © 2016 The Author(s).

Constrained evolution in numerical relativity

NASA Astrophysics Data System (ADS)

Anderson, Matthew William

The strongest potential source of gravitational radiation for current and future detectors is the merger of binary black holes. Full numerical simulation of such mergers can provide realistic signal predictions and enhance the probability of detection. Numerical simulation of the Einstein equations, however, is fraught with difficulty. Stability even in static test cases of single black holes has proven elusive. Common to unstable simulations is the growth of constraint violations. This work examines the effect of controlling the growth of constraint violations by solving the constraints periodically during a simulation, an approach called constrained evolution. The effects of constrained evolution are contrasted with the results of unconstrained evolution, evolution where the constraints are not solved during the course of a simulation. Two different formulations of the Einstein equations are examined: the standard ADM formulation and the generalized Frittelli-Reula formulation. In most cases constrained evolution vastly improves the stability of a simulation at minimal computational cost when compared with unconstrained evolution. However, in the more demanding test cases examined, constrained evolution fails to produce simulations with long-term stability in spite of producing improvements in simulation lifetime when compared with unconstrained evolution. Constrained evolution is also examined in conjunction with a wide variety of promising numerical techniques, including mesh refinement and overlapping Cartesian and spherical computational grids. Constrained evolution in boosted black hole spacetimes is investigated using overlapping grids. Constrained evolution proves to be central to the host of innovations required in carrying out such intensive simulations.

Dynamics in genome evolution of Vibrio cholerae.

PubMed

Banerjee, Rachana; Das, Bhabatosh; Balakrish Nair, G; Basak, Surajit

2014-04-01

Vibrio cholerae, the etiological agent of the acute secretary diarrheal disease cholera, is still a major public health concern in developing countries. In former centuries cholera was a permanent threat even to the highly developed populations of Europe, North America, and the northern part of Asia. Extensive studies on the cholera bug over more than a century have made significant advances in our understanding of the disease and ways of treating patients. V. cholerae has more than 200 serogroups, but only few serogroups have caused disease on a worldwide scale. Until the present, the evolutionary relationship of these pandemic causing serogroups was not clear. In the last decades, we have witnessed a shift involving genetically and phenotypically varied pandemic clones of V. cholerae in Asia and Africa. The exponential knowledge on the genome of several representatives V. cholerae strains has been used to identify and analyze the key determinants for rapid evolution of cholera pathogen. Recent comparative genomic studies have identified the presence of various integrative mobile genetic elements (IMGEs) in V. cholerae genome, which can be used as a marker of differentiation of all seventh pandemic clones with very similar core genome. This review attempts to bring together some of the important researches in recent times that have contributed towards understanding the genetics, epidemiology and evolution of toxigenic V. cholerae strains. Copyright © 2014 Elsevier B.V. All rights reserved.

Evolution & Diversity in Plants.

ERIC Educational Resources Information Center

Pearson, Lorentz C.

1988-01-01

Summarizes recent findings that help in understanding how evolution has brought about the diversity of plant life that presently exists. Discusses basic concepts of evolution, diversity and classification, the three-line hypothesis of plant evolution, the origin of fungi, and the geologic time table. Included are 31 references. (CW)

Evolution-guided optimization of biosynthetic pathways.

PubMed

Raman, Srivatsan; Rogers, Jameson K; Taylor, Noah D; Church, George M

2014-12-16

Engineering biosynthetic pathways for chemical production requires extensive optimization of the host cellular metabolic machinery. Because it is challenging to specify a priori an optimal design, metabolic engineers often need to construct and evaluate a large number of variants of the pathway. We report a general strategy that combines targeted genome-wide mutagenesis to generate pathway variants with evolution to enrich for rare high producers. We convert the intracellular presence of the target chemical into a fitness advantage for the cell by using a sensor domain responsive to the chemical to control a reporter gene necessary for survival under selective conditions. Because artificial selection tends to amplify unproductive cheaters, we devised a negative selection scheme to eliminate cheaters while preserving library diversity. This scheme allows us to perform multiple rounds of evolution (addressing ∼10(9) cells per round) with minimal carryover of cheaters after each round. Based on candidate genes identified by flux balance analysis, we used targeted genome-wide mutagenesis to vary the expression of pathway genes involved in the production of naringenin and glucaric acid. Through up to four rounds of evolution, we increased production of naringenin and glucaric acid by 36- and 22-fold, respectively. Naringenin production (61 mg/L) from glucose was more than double the previous highest titer reported. Whole-genome sequencing of evolved strains revealed additional untargeted mutations that likely benefit production, suggesting new routes for optimization.

Galaxy Evolution

NASA Astrophysics Data System (ADS)

Matteucci, F.

We review both the observational and theoretical constraints on the evolution of the abundances of heavy elements in gas and stars in galaxies of different morphological type. The main aim of this work is to document the progress made in our understanding of the physical processes regulating the chemical evolution of galaxies during the last sixteen years since the appearance, in this same journal (volume 5, page 287), of the well know review of Beatrice Tinsley, to whom I dedicate this paper. Finally, this article is addressed particularly to readers who do not actively work on galactic chemical evolution and who might use it as a cook book where the main ingredients are discussed and useful recipes can be found.

Probing the Evolution of the Galaxy Interaction/Merger Rate Using Distant Collisional Ring Galaxies

NASA Astrophysics Data System (ADS)

Lavery, Russell J.; Remijan, Anthony J.

We present the initial results from our long-term program of identifying distant collisional ring galaxies (CRGS) in deep HST WFPC-2 images. The unique morphological characteristics of these galaxies make them easily identifiable out to a redshift of z = 1. To date, we have visually scanned 100 WFPC-2 fields and identified 14 excellent collisional ring galaxy (CRG) candidates. Based on estimated redshifts, these 14 galaxies are expected to lie in the redshift interval of 0.1 to 1. We have used this sample of CRGs to estimate the evolution of the galaxy interaction/merger rate with redshift. To account for the number of CRGs we have identified in these fields, the galaxy interaction/merger rate, parameterized as (1 + z)m, must increase steeply with redshift, with m = 5.7 +/- 1.5. We can rule out a non-evolving galaxy merger rate (m = 0) at greater than the 3σ level. We compare our results with other programs to determine the value of m using the evolution of galaxy pairs.

Giant hub Src and Syk tyrosine kinase thermodynamic profiles recapitulate evolution

NASA Astrophysics Data System (ADS)

Phillips, J. C.

2017-10-01

Thermodynamic scaling theory, previously applied mainly to small proteins, here analyzes quantitative evolution of the titled functional network giant hub enzymes. The broad domain structure identified homologically is confirmed hydropathically using amino acid sequences only. The most surprising results concern the evolution of the tyrosine kinase globular surface roughness from avians to mammals, which is first order, compared to the evolution within mammals from rodents to humans, which is second order. The mystery of the unique amide terminal region of proto oncogene tyrosine protein kinase is resolved by the discovery there of a rare hydroneutral septad targeting cluster, which is paralleled by an equally rare octad catalytic cluster in tyrosine kinase in humans and a few other species (cat and dog). These results, which go far towards explaining why these proteins are among the largest giant hubs in protein interaction networks, use no adjustable parameters.