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

Science.gov (United States)

Suárez-Díaz, Edna

2017-03-28

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

Electrochemically assisted mechanically controllable break junction studies on the stacking configurations of oligo(phenylene ethynylene)s molecular junctions

International Nuclear Information System (INIS)

Zheng, Jue-Ting; Yan, Run-Wen; Tian, Jing-Hua; Liu, Jun-Yang; Pei, Lin-Qi; Wu, De-Yin; Dai, Ke; Yang, Yang; Jin, Shan

2016-01-01

Highlights: • I-V characteristics of a series of oligo(phenylene ethynylene)s molecular junctions were measured. • Conductance values were found to be dependent on molecular length and substituent group. • The measured low conductance values were explained by theoretical calculations. • EC-MCBJ is feasible to fabricate and characterize molecular junctions. - Abstract: We demonstrate an electrochemically assisted mechanically controllable break junction (EC-MCBJ) approach for current-voltage characteristic (I-V curve) measurements of metal/molecule/metal junctions. A series of oligo(phenylene ethynylene)s compounds (OPEs), including those involving electron withdrawing substituent group and different backbone lengths, had been successfully designed, synthesized, and placed onto the fabricated nanogap to form molecular junctions. The observed evolution in the measured conductances of OPEs indicates that there is a dependence of conductance on molecular length and substituent group. Compared with those extracted from conductance histogram construction, the conductances of OPEs measured from I-V curves are considerably lower. Based on the transmission spectra of OPEs that calculated by density functional theory (DFT) combined with non-equilibrium Green’s function (NEGF) method, this difference was attributed to our distinct experimental operation, which may give rise to a stacking configuration of two OPE molecules.

DNA Re-EvolutioN: a game for learning molecular genetics and evolution.

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Miralles, Laura; Moran, Paloma; Dopico, Eduardo; Garcia-Vazquez, Eva

2013-01-01

Evolution is a main concept in biology, but not many students understand how it works. In this article we introduce the game DNA Re-EvolutioN as an active learning tool that uses genetic concepts (DNA structure, transcription and translation, mutations, natural selection, etc.) as playing rules. Students will learn about molecular evolution while playing a game that mixes up theory and entertainment. The game can be easily adapted to different educational levels. The main goal of this play is to arrive at the end of the game with the longest protein. Students play with pawns and dices, a board containing hypothetical events (mutations, selection) that happen to molecules, "Evolution cards" with indications for DNA mutations, prototypes of a DNA and a mRNA chain with colored "nucleotides" (plasticine balls), and small pieces simulating t-RNA with aminoacids that will serve to construct a "protein" based on the DNA chain. Students will understand how changes in DNA affect the final protein product and may be subjected to positive or negative selection, using a didactic tool funnier than classical theory lectures and easier than molecular laboratory experiments: a flexible and feasible game to learn and enjoy molecular evolution at no-cost. The game was tested by majors and non-majors in genetics from 13 different countries and evaluated with pre- and post-tests obtaining very positive results. © 2013 by The International Union of Biochemistry and Molecular Biology.

Molecular evolution, intracellular organization, and the quinary structure of proteins.

OpenAIRE

McConkey, E H

1982-01-01

High-resolution two-dimensional polyacrylamide gel electrophoresis shows that at least half of 370 denatured polypeptides from hamster cells and human cells are indistinguishable in terms of isoelectric points and molecular weights. Molecular evolution may have been more conservative for this set of proteins than sequence studies on soluble proteins have implied. This may be a consequence of complexities of intracellular organization and the numerous macromolecular interactions in which most ...

A redox-assisted molecular assembly of molybdenum oxide amine composite nanobelts

International Nuclear Information System (INIS)

Luo Haiyan; Wei Mingdeng; Wei Kemei

2011-01-01

Research highlights: → Nanobelts of molybdenum oxide amine were first synthesized via a redox-assisted molecular assembly route. → These nanobelts are highly crystalline with a several tens of micrometers in length and 20-30 nm in thickness. - Abstract: In this paper, the nanobelts of molybdenum oxide amine composite were successfully synthesized via a redox-assisted molecular assembly route under the hydrothermal conditions. The synthesized nanobelts were characterized by XRD, SEM, TEM, TG and FT-IR measurements. The thickness of nanobelts is found to be ca. 20-30 nm and their lengths are up to several tens of micrometers. Based on a series of the experimental results, a possible model, redox-intercalation-exfoliation, was suggested for the formation of nanobelts of molybdenum oxide amine composite.

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology.

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Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V

2017-04-01

Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era. Copyright © 2016 Elsevier B.V. All rights reserved.

Bayesian semiparametric regression models to characterize molecular evolution

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Datta Saheli

2012-10-01

Full Text Available Abstract Background Statistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the molecular level typically do not take into account the correlations between such properties. We propose a Bayesian hierarchical regression model with a generalization of the Dirichlet process prior on the distribution of the regression coefficients that describes the relationship between the changes in amino acid distances and natural selection in protein-coding DNA sequence alignments. Results The Bayesian semiparametric approach is illustrated with simulated data and the abalone lysin sperm data. Our method identifies groups of properties which, for this particular dataset, have a similar effect on evolution. The model also provides nonparametric site-specific estimates for the strength of conservation of these properties. Conclusions The model described here is distinguished by its ability to handle a large number of amino acid properties simultaneously, while taking into account that such data can be correlated. The multi-level clustering ability of the model allows for appealing interpretations of the results in terms of properties that are roughly equivalent from the standpoint of molecular evolution.

Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

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Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

2017-06-28

Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

Rates of molecular evolution in tree ferns are associated with body size, environmental temperature, and biological productivity.

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Barrera-Redondo, Josué; Ramírez-Barahona, Santiago; Eguiarte, Luis E

2018-05-01

Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution. In addition, we found that variation in the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the chloroplast rbcL gene was significantly correlated with ecological and morphological variables. Heterotachy in tree ferns may be influenced by effective population size associated with variation in body size and productivity. Macroevolutionary hypotheses should go beyond explaining heterotachy in terms of mutation rates and instead, should integrate population-level factors to better understand the processes affecting the tempo of evolution at the molecular level. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Non-Molecular-Clock-Like Evolution following Viral Origins in Homo sapiens

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Wendy Mok

2007-01-01

Full Text Available Researchers routinely adopt molecular clock assumptions in conducting sequence analyses to estimate dates for viral origins in humans. We used computational methods to examine the extent to which this practice can result in inaccurate ‘retrodiction.’ Failing to account for dynamic molecular evolution can affect greatly estimating index case dates, resulting in an overestimated age for the SARS-CoV-human infection, for instance.

Multisample matrix-assisted laser desorption source for molecular beams of neutral peptides

International Nuclear Information System (INIS)

Lupulescu, C.; Abd El Rahim, M.; Antoine, R.; Barbaire, M.; Broyer, M.; Dagany, X.; Maurelli, J.; Rayane, D.; Dugourd, Ph.

2006-01-01

We developed and tested a multisample laser desorption source for producing stable molecular beams of neutral peptides. Our apparatus is based on matrix-assisted laser desorption technique. The source consists of 96 different targets which may be scanned by a software control procedure. Examples of molecular beams of neutral peptides are presented, as well as the influence of the different source parameters on the jet

Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers.

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Greenwold, Matthew J; Sawyer, Roger H

2011-12-15

Feathers of today's birds are constructed of beta (β)-keratins, structural proteins of the epidermis that are found solely in reptiles and birds. Discoveries of "feathered dinosaurs" continue to stimulate interest in the evolutionary origin of feathers, but few studies have attempted to link the molecular evolution of their major structural proteins (β-keratins) to the appearance of feathers in the fossil record. Using molecular dating methods, we show that before the appearance of Anchiornis (∼155 Million years ago (Ma)) the basal β-keratins of birds began diverging from their archosaurian ancestor ∼216 Ma. However, the subfamily of feather β-keratins, as found in living birds, did not begin diverging until ∼143 Ma. Thus, the pennaceous feathers on Anchiornis, while being constructed of avian β-keratins, most likely did not contain the feather β-keratins found in the feathers of modern birds. Our results demonstrate that the evolutionary origin of feathers does not coincide with the molecular evolution of the feather β-keratins found in modern birds. More likely, during the Late Jurassic, the epidermal structures that appeared on organisms in the lineage leading to birds, including early forms of feathers, were constructed of avian β-keratins other than those found in the feathers of modern birds. Recent biophysical studies of the β-keratins in feathers support the view that the appearance of the subfamily of feather β-keratins altered the biophysical nature of the feather establishing its role in powered flight. Copyright © 2011 Wiley Periodicals, Inc., A Wiley Company.

Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

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Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

2004-01-01

To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented. Copyright 2004 S. Karger AG, Basel

Molecular evolution of the primate antiviral restriction factor tetherin.

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Jun Liu

Full Text Available BACKGROUND: Tetherin is a recently identified antiviral restriction factor that restricts HIV-1 particle release in the absence of the HIV-1 viral protein U (Vpu. It is reminiscent of APOBEC3G and TRIM5a that also antagonize HIV. APOBEC3G and TRIM5a have been demonstrated to evolve under pervasive positive selection throughout primate evolution, supporting the red-queen hypothesis. Therefore, one naturally presumes that Tetherin also evolves under pervasive positive selection throughout primate evolution and supports the red-queen hypothesis. Here, we performed a detailed evolutionary analysis to address this presumption. METHODOLOGY/PRINCIPAL FINDINGS: Results of non-synonymous and synonymous substitution rates reveal that Tetherin as a whole experiences neutral evolution rather than pervasive positive selection throughout primate evolution, as well as in non-primate mammal evolution. Sliding-window analyses show that the regions of the primate Tetherin that interact with viral proteins are under positive selection or relaxed purifying selection. In particular, the sites identified under positive selection generally focus on these regions, indicating that the main selective pressure acting on the primate Tetherin comes from virus infection. The branch-site model detected positive selection acting on the ancestral branch of the New World Monkey lineage, suggesting an episodic adaptive evolution. The positive selection was also found in duplicated Tetherins in ruminants. Moreover, there is no bias in the alterations of amino acids in the evolution of the primate Tetherin, implying that the primate Tetherin may retain broad spectrum of antiviral activity by maintaining structure stability. CONCLUSIONS/SIGNIFICANCE: These results conclude that the molecular evolution of Tetherin may be attributed to the host-virus arms race, supporting the Red Queen hypothesis, and Tetherin may be in an intermediate stage in transition from neutral to pervasive

Amino acid properties conserved in molecular evolution.

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Witold R Rudnicki

Full Text Available That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata.

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Maurer-Alcalá, Xyrus X; Katz, Laura A

2016-06-08

The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a "heteromeric" macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into "gene-sized" chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a "gene bank" that facilitates rapid changes in expression of genes required only in specific life history stages. By using "nonmodel" organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Clinical and molecular analyses of Beckwith-Wiedemann syndrome: Comparison between spontaneous conception and assisted reproduction techniques.

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Tenorio, Jair; Romanelli, Valeria; Martin-Trujillo, Alex; Fernández, García-Moya; Segovia, Mabel; Perandones, Claudia; Pérez Jurado, Luis A; Esteller, Manel; Fraga, Mario; Arias, Pedro; Gordo, Gema; Dapía, Irene; Mena, Rocío; Palomares, María; Pérez de Nanclares, Guiomar; Nevado, Julián; García-Miñaur, Sixto; Santos-Simarro, Fernando; Martinez-Glez, Víctor; Vallespín, Elena; Monk, David; Lapunzina, Pablo

2016-10-01

Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome characterized by an excessive prenatal and postnatal growth, macrosomia, macroglossia, and hemihyperplasia. The molecular basis of this syndrome is complex and heterogeneous, involving genes located at 11p15.5. BWS is correlated with assisted reproductive techniques. BWS in individuals born following assisted reproductive techniques has been found to occur four to nine times higher compared to children with to BWS born after spontaneous conception. Here, we report a series of 187 patients with to BWS born either after assisted reproductive techniques or conceived naturally. Eighty-eight percent of BWS patients born via assisted reproductive techniques had hypomethylation of KCNQ1OT1:TSS-DMR in comparison with 49% for patients with BWS conceived naturally. None of the patients with BWS born via assisted reproductive techniques had hypermethylation of H19/IGF2:IG-DMR, neither CDKN1 C mutations nor patUPD11. We did not find differences in the frequency of multi-locus imprinting disturbances between groups. Patients with BWS born via assisted reproductive techniques had an increased frequency of advanced bone age, congenital heart disease, and decreased frequency of earlobe anomalies but these differences may be explained by the different molecular background compared to those with BWS and spontaneous fertilization. We conclude there is a correlation of the molecular etiology of BWS with the type of conception. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

THE MOLECULAR EVOLUTION OF THE MOST DANGEROUS EMERGING VIRUS INFECTIONS

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Popov NN

2016-03-01

barriers and infect new hosts. Really, many recently emerged human diseases are caused by viruses that display active recombination or reassortment. The continual shuffling of genes of influenza A represents a example of the key role of reassortment for the new virus emergence. Available data demonstrate the possible origin of SARS-CoV from recombination of different bat SL-CoVs viruses strains. However in other cases the emergence of a specific virus cannot be directly attributed to its ability to recombine. For example, although SIV recombines at a high rate in natural reservoirs, there is no evidence that recombination assisted the cross-species transfer of the virus from the chimpanzee into humans. But mutagenesis and recombination actively shape the further molecular history of HIV in humans. Also it is not proved that recombination precede the cross-species jump of the Ebola virus. In summary, the available data suggest that although recombination, reassortment and mutagenesis is sometimes directly involved to the process of cross-species transmission, it is not a necessary precursor to successful viral emergence. Further investigations are required to reveal the role of genetic change in the history of virus emergence. We believe that comprehensive description of molecular evolution of new viruses has led to a better understanding of the causes and predictability of infection emergence.

The interface of protein structure, protein biophysics, and molecular evolution

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Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

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Xia Xuhua

2005-03-01

Full Text Available Abstract Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454.

Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity

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Madelaine eBartlett

2013-10-01

Full Text Available Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism’s phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic diversity could come to represent part of natural selection’s source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; hypomorphic and hypermorphic alleles; altered protein-protein interactions; altered domain content; altered protein stability; and altered activity as an activator or repressor. Variability was also observed in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.

The molecular biology and evolution of feline immunodeficiency viruses of cougars

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Poss, Mary; Ross, Howard; Rodrigo, Allen; Terwee, Julie; VandeWoude, Sue; Biek, Roman

2008-01-01

Feline immunodeficiency virus (FIV) is a lentivirus that has been identified in many members of the family Felidae but domestic cats are the only FIV host in which infection results in disease. We studied FIVpco infection of cougars (Puma concolor) as a model for asymptomatic lentivirus infections to understand the mechanisms of host-virus coexistence. Several natural cougar populations were evaluated to determine if there are any consequences of FIVpco infection on cougar fecundity, survival, or susceptibility to other infections. We have sequenced full length viral genomes and conducted a detailed analysis of viral molecular evolution on these sequences and on genome fragments of serially sampled animals to determine the evolutionary forces experienced by this virus in cougars. In addition, we have evaluated the molecular genetics of FIVpco in a new host, domestic cats, to determine the evolutionary consequences to a host-adapted virus associated with cross-species infection. Our results indicate that there are no significant differences in survival, fecundity or susceptibility to other infections between FIVpco-infected and uninfected cougars. The molecular evolution of FIVpco is characterized by a slower evolutionary rate and an absence of positive selection, but also by proviral and plasma viral loads comparable to those of epidemic lentiviruses such as HIV-1 or FIVfca. Evolutionary and recombination rates and selection profiles change significantly when FIVpco replicates in a new host. PMID:18295904

Thermal force approach to molecular evolution.

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Braun, Dieter; Libchaber, Albert

2004-06-01

Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life.

PAL: an object-oriented programming library for molecular evolution and phylogenetics.

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Drummond, A; Strimmer, K

2001-07-01

Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License.

Left ventricular assist device: exercise capacity evolution and rehabilitation added value.

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Lamotte, Michel X; Chimenti, Sara; Deboeck, Gael; Gillet, Alexis; Kacelenenbogen, Raymond; Strapart, Jonathan; Vandeneynde, Frédéric; Van Nooten, Guido; Antoine, Martine

2018-06-01

With more than 15,000 implanted patients worldwide and a survival rate of 80% at 1-year and 59% at 5-years, left ventricular assist device (LVAD) implantation has become an interesting strategy in the management of heart failure patients who are resistant to other kinds of treatment. There are limited data in the literature on the change over time of exercise capacity in LVAD patients, as well as limited knowledge about the beneficial effects that rehabilitation might have on these patients. Therefore, the aim of our study was to evaluate the evolution of exercise capacity on a cohort of patients implanted with the same device (HeartWare © ) and to analyse the potential impact of rehabilitation. Sixty-two patients implanted with a LVAD between June 2011 and June 2015 were screened. Exercise capacity was evaluated by cardiopulmonary exercise testing at 6 weeks, 6 and 12 months after implantation. We have observed significant differences in the exercise capacity and evolution between the trained and non-trained patients. Some of the trained patients nearly normalised their exercise capacity at the end of the rehabilitation programme. Exercise capacity of patient implanted with a HeartWare © LVAD increased in the early period after implantation. Rehabilitation allowed implanted patients to have a significantly better evolution compared to non-rehabilitated patients.

Molecular Evolution of the dotA Gene in Legionella pneumophila

OpenAIRE

Ko, Kwan Soo; Hong, Seong Karp; Lee, Hae Kyung; Park, Mi-Yeoun; Kook, Yoon-Hoh

2003-01-01

The molecular evolution of dotA, which is related to the virulence of Legionella pneumophila, was investigated by comparing the sequences of 15 reference strains (serogroups 1 to 15). It was found that dotA has a complex mosaic structure. The whole dotA gene of Legionella pneumophila subsp. pneumophila serogroups 2, 6, and 12 has been transferred from Legionella pneumophila subsp. fraseri. A discrepancy was found between the trees inferred from the nucleotide and deduced amino acid sequences ...

The molecular origin and evolution of dim-light vision in mammals.

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Bickelmann, Constanze; Morrow, James M; Du, Jing; Schott, Ryan K; van Hazel, Ilke; Lim, Steve; Müller, Johannes; Chang, Belinda S W

2015-11-01

The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin--the vertebrate visual pigment mediating the first step in phototransduction at low-light levels--via codon-based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λMAX values similar to the well-studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Microwave assisted synthesis of CdS nanoparticles and their size evolution

International Nuclear Information System (INIS)

Lopez, I. A.; Vazquez, A.; Gomez, I.

2013-01-01

The study of the size evolution of CdS nanoparticles in aqueous dispersion is presented in this paper. The sodium citrate was employed as stabilizer of CdS nanoparticles synthesized by microwave assisted synthesis. Analysis of this study was carried out by UV-Vis spectrophotometry, by comparison of the band gap energy using theoretical and empirical models. Results obtained show that the synthesis conditions produce CdS nanoparticles with diameters below of 6 nm, which remains stabilized by at least 14 days. These characteristics were confirmed by transmission electron microscopy. The X-ray diffraction pattern confirms cubic phase of the CdS nanoparticles. (Author)

Microwave assisted synthesis of CdS nanoparticles and their size evolution

Energy Technology Data Exchange (ETDEWEB)

Lopez, I. A.; Vazquez, A.; Gomez, I., E-mail: idaliagomezmx@yahoo.com.mx [Universidad Autonoma de Nuevo Leon, Facultad de Ciencias Quimicas, Laboratorio de Materiales I, Av. Universidad, Cd. Universitaria, 66451 San Nicolas de los Garza, Nuevo Leon (Mexico)

2013-05-01

The study of the size evolution of CdS nanoparticles in aqueous dispersion is presented in this paper. The sodium citrate was employed as stabilizer of CdS nanoparticles synthesized by microwave assisted synthesis. Analysis of this study was carried out by UV-Vis spectrophotometry, by comparison of the band gap energy using theoretical and empirical models. Results obtained show that the synthesis conditions produce CdS nanoparticles with diameters below of 6 nm, which remains stabilized by at least 14 days. These characteristics were confirmed by transmission electron microscopy. The X-ray diffraction pattern confirms cubic phase of the CdS nanoparticles. (Author)

Information Theory Broadens the Spectrum of Molecular Ecology and Evolution.

Science.gov (United States)

Sherwin, W B; Chao, A; Jost, L; Smouse, P E

2017-12-01

Information or entropy analysis of diversity is used extensively in community ecology, and has recently been exploited for prediction and analysis in molecular ecology and evolution. Information measures belong to a spectrum (or q profile) of measures whose contrasting properties provide a rich summary of diversity, including allelic richness (q=0), Shannon information (q=1), and heterozygosity (q=2). We present the merits of information measures for describing and forecasting molecular variation within and among groups, comparing forecasts with data, and evaluating underlying processes such as dispersal. Importantly, information measures directly link causal processes and divergence outcomes, have straightforward relationship to allele frequency differences (including monotonicity that q=2 lacks), and show additivity across hierarchical layers such as ecology, behaviour, cellular processes, and nongenetic inheritance. Copyright © 2017 Elsevier Ltd. All rights reserved.

The structural evolution of InN nanorods to microstructures on Si (111) by molecular beam epitaxy

International Nuclear Information System (INIS)

Anyebe, E A; Zhuang, Q; Kesaria, M; Krier, A

2014-01-01

We report the catalyst free growth of wurtzite InN nanorods (NRs) and microislands on bare Si (111) by plasma-assisted molecular beam epitaxy at various temperatures. The morphological evolution from NRs to three dimensional (3D) islands as a function of growth temperature is investigated. A combination of tapered, non-tapered, and pyramidal InN NRs are observed at 490 °C, whereas the InN evolves to faceted microislands with an increase in growth temperature to 540 °C and further developed to indented and smooth hemispherical structures at extremely high temperatures (630 °C). The evolution from NRs to microislands with increase in growth temperature is attributed to the lowering of the surface free energy of the growing crystals with disproportionate growth velocities along different growth fronts. The preferential adsorption of In atoms on the (0001) c-plane and (10-10) m-plane promotes the growth of NRs at relatively low growth temperature and 3D microislands at higher temperatures. The growth rate imbalance along different planes facilitates the development of facets on 3D microislands. A strong correlation between the morphological and structural properties of the 3D films is established. XRD studies reveal that the NRs and the faceted microislands are crystalline, whereas the hemispherical microislands grown at extremely high growth temperature contain In adlayers. Finally, photoluminescent emissions were observed at ∼0.75 eV from the InN NRs. (paper)

Environment-Assisted Speed-up of the Field Evolution in Cavity Quantum Electrodynamics.

Science.gov (United States)

Cimmarusti, A D; Yan, Z; Patterson, B D; Corcos, L P; Orozco, L A; Deffner, S

2015-06-12

We measure the quantum speed of the state evolution of the field in a weakly driven optical cavity QED system. To this end, the mode of the electromagnetic field is considered as a quantum system of interest with a preferential coupling to a tunable environment: the atoms. By controlling the environment, i.e., changing the number of atoms coupled to the optical cavity mode, an environment-assisted speed-up is realized: the quantum speed of the state repopulation in the optical cavity increases with the coupling strength between the optical cavity mode and this non-Markovian environment (the number of atoms).

Environment-Assisted Speed-up of the Field Evolution in Cavity Quantum Electrodynamics

International Nuclear Information System (INIS)

Cimmarusti, A. D.; Yan, Z.; Patterson, B. D.; Corcos, L. P.; Orozco, L. A.; Deffner, S.

2015-01-01

We measure the quantum speed of the state evolution of the field in a weakly-driven optical cavity QED system. To this end, the mode of the electromagnetic field is considered as a quantum system of interest with a preferential coupling to a tunable environment: the atoms. By controlling the environment, i.e., changing the number of atoms coupled to the optical cavity mode, an environment assisted speed-up is realized: the quantum speed of the state re-population in the optical cavity increases with the coupling strength between the optical cavity mode and this non-Markovian environment (the number of atoms)

Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey

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Jia Li

2015-12-01

Full Text Available All living organisms synchronize biological functions with environmental changes; melatonin plays a vital role in regulating daily and seasonal variations. Due to rhythmic activity of the timezyme aralkylamine N-acetyltransferase (AANAT, the blood level of melatonin increases at night and decreases during daytime. Whereas other vertebrates have a single form of AANAT, bony fishes possess various isoforms of aanat genes, though the reasons are still unclear. Here, we have taken advantage of multiple unpublished teleost aanat sequences to explore and expand our understanding of the molecular evolution of aanat in fish. Our results confirm that two rounds of whole-genome duplication (WGD led to the existence of three fish isoforms of aanat, i.e., aanat1a, aanat1b, and aanat2; in addition, gene loss led to the absence of some forms from certain special fish species. Furthermore, we suggest the different roles of two aanat1s in amphibious mudskippers, and speculate that the loss of aanat1a, may be related to terrestrial vision change. Several important sites of AANAT proteins and regulatory elements of aanat genes were analyzed for structural comparison and functional forecasting, respectively, which provides insights into the molecular evolution of the differences between AANAT1 and AANAT2.

Increase in Complexity and Information through Molecular Evolution

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Peter Schuster

2016-11-01

Full Text Available Biological evolution progresses by essentially three different mechanisms: (I optimization of properties through natural selection in a population of competitors; (II development of new capabilities through cooperation of competitors caused by catalyzed reproduction; and (III variation of genetic information through mutation or recombination. Simplified evolutionary processes combine two out of the three mechanisms: Darwinian evolution combines competition (I and variation (III and is represented by the quasispecies model, major transitions involve cooperation (II of competitors (I, and the third combination, cooperation (II and variation (III provides new insights in the role of mutations in evolution. A minimal kinetic model based on simple molecular mechanisms for reproduction, catalyzed reproduction and mutation is introduced, cast into ordinary differential equations (ODEs, and analyzed mathematically in form of its implementation in a flow reactor. Stochastic aspects are investigated through computer simulation of trajectories of the corresponding chemical master equations. The competition-cooperation model, mechanisms (I and (II, gives rise to selection at low levels of resources and leads to symbiontic cooperation in case the material required is abundant. Accordingly, it provides a kind of minimal system that can undergo a (major transition. Stochastic effects leading to extinction of the population through self-enhancing oscillations destabilize symbioses of four or more partners. Mutations (III are not only the basis of change in phenotypic properties but can also prevent extinction provided the mutation rates are sufficiently large. Threshold phenomena are observed for all three combinations: The quasispecies model leads to an error threshold, the competition-cooperation model allows for an identification of a resource-triggered bifurcation with the transition, and for the cooperation-mutation model a kind of stochastic threshold for

Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis.

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Koufopanou, Vassiliki; Burt, Austin

2005-07-01

VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including horizontal transmission, degeneration, and domestication into the mating-type switching locus HO. We investigate here the effects of these features on its molecular evolution. In addition, we correlate rates of evolution with results from site-directed mutagenesis studies. Functional elements have lower rates of evolution than degenerate ones and higher conservation at functionally important sites. However, functionally important and unimportant sites are equally likely to have been involved in the evolution of new function during the domestication of VDE into HO. The domestication event also indicates that VDE has been lost in some species and that VDE has been present in yeasts for more than 50 Myr.

Molecular marker-assisted selection for resistance to pathogens in tomato

International Nuclear Information System (INIS)

Barone, A.; Frusciante, L.

2007-01-01

Since the 1980s, the use of molecular markers has been suggested to improve the efficiency of releasing resistant varieties, thus overcoming difficulties met with classical breeding. For tomato, a high-density molecular map is available in which more than 40 resistance genes are localized. Markers linked to these genes can be used to speed up gene transfer and pyramiding. Suitable PCR markers targeting resistance genes were constructed directly on the sequences of resistance genes or on restriction fragment length polymorphisms (RFLPs) tightly linked to them, and used to select resistant genotypes in backcross schemes. In some cases, the BC 5 generation was reached, and genotypes that cumulated two homozygous resistant genes were also obtained. These results supported the feasibility of using marker-assisted selection (MAS) in tomato and reinforcing the potential of this approach for other genes, which is today also driven by the development of new techniques and increasing knowledge about the tomato genome. (author)

Contrasted patterns of molecular evolution in dominant and recessive self-incompatibility haplotypes in Arabidopsis.

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Pauline M Goubet

Full Text Available Self-incompatibility has been considered by geneticists a model system for reproductive biology and balancing selection, but our understanding of the genetic basis and evolution of this molecular lock-and-key system has remained limited by the extreme level of sequence divergence among haplotypes, resulting in a lack of appropriate genomic sequences. In this study, we report and analyze the full sequence of eleven distinct haplotypes of the self-incompatibility locus (S-locus in two closely related Arabidopsis species, obtained from individual BAC libraries. We use this extensive dataset to highlight sharply contrasted patterns of molecular evolution of each of the two genes controlling self-incompatibility themselves, as well as of the genomic region surrounding them. We find strong collinearity of the flanking regions among haplotypes on each side of the S-locus together with high levels of sequence similarity. In contrast, the S-locus region itself shows spectacularly deep gene genealogies, high variability in size and gene organization, as well as complete absence of sequence similarity in intergenic sequences and striking accumulation of transposable elements. Of particular interest, we demonstrate that dominant and recessive S-haplotypes experience sharply contrasted patterns of molecular evolution. Indeed, dominant haplotypes exhibit larger size and a much higher density of transposable elements, being matched only by that in the centromere. Overall, these properties highlight that the S-locus presents many striking similarities with other regions involved in the determination of mating-types, such as sex chromosomes in animals or in plants, or the mating-type locus in fungi and green algae.

Dracula's children: molecular evolution of vampire bat venom.

Science.gov (United States)

Low, Dolyce H W; Sunagar, Kartik; Undheim, Eivind A B; Ali, Syed A; Alagon, Alejandro C; Ruder, Tim; Jackson, Timothy N W; Pineda Gonzalez, Sandy; King, Glenn F; Jones, Alun; Antunes, Agostinho; Fry, Bryan G

2013-08-26

While vampire bat oral secretions have been the subject of intense research, efforts have concentrated only on two components: DSPA (Desmodus rotundus salivary plasminogen activator) and Draculin. The molecular evolutionary history of DSPA has been elucidated, while conversely draculin has long been known from only a very small fragment and thus even the basic protein class was not even established. Despite the fact that vampire bat venom has a multitude of effects unaccounted by the documented bioactivities of DSPA and draculin, efforts have not been made to establish what other bioactive proteins are secreted by their submaxillary gland. In addition, it has remained unclear whether the anatomically distinct anterior and posterior lobes of the submaxillary gland are evolving on separate gene expression trajectories or if they remain under the shared genetic control. Using a combined proteomic and transcriptomic approach, we show that identical proteins are simultaneously expressed in both lobes. In addition to recovering the known structural classes of DSPA, we recovered a novel DSPA isoform as well as obtained a very large sequence stretch of draculin and thus established that it is a mutated version of the lactotransferrin scaffold. This study reveals a much more complex secretion profile than previously recognised. In addition to obtaining novel versions of scaffolds convergently recruited into other venoms (allergen-like, CRiSP, kallikrein, Kunitz, lysozyme), we also documented novel expression of small peptides related to calcitonin, PACAP, and statherin. Other overexpressed protein types included BPI-fold, lacritin, and secretoglobin. Further, we investigate the molecular evolution of various vampire bat venom-components and highlight the dominant role of positive selection in the evolution of these proteins. Conspicuously many of the proteins identified in the proteome were found to be homologous to proteins with known activities affecting vasodilation and

In-situ Mass Spectrometric Determination of Molecular Structural Evolution at the Solid Electrolyte Interphase in Lithium-Ion Batteries

Energy Technology Data Exchange (ETDEWEB)

Zhu, Zihua; Zhou, Yufan; Yan, Pengfei; Vemuri, Venkata Rama Ses; Xu, Wu; Zhao, Rui; Wang, Xuelin; Thevuthasan, Suntharampillai; Baer, Donald R.; Wang, Chong M.

2015-08-19

Dynamic molecular evolution at solid/liquid electrolyte interface is always a mystery for a rechargeable battery due to the challenge to directly probe/observe the solid/liquid interface under reaction conditions, which in essence appears to be similarly true for all the fields involving solid/liquid phases, such as electrocatalysis, electrodeposition, biofuel conversion, biofilm, and biomineralization, We use in-situ liquid secondary ion mass spectroscopy (SIMS) for the first time to directly observe the molecular structural evolution at the solid electrode/liquid electrolyte interface for a lithium (Li)-ion battery under dynamic operating conditions. We have discovered that the deposition of Li metal on copper electrode leads to the condensation of solvent molecules around the electrode. Chemically, this layer of solvent condensate tends to deplete the salt anion and with low concentration of Li+ ions, which essentially leads to the formation of a lean electrolyte layer adjacent to the electrode and therefore contributes to the overpotential of the cell. This unprecedented molecular level dynamic observation at the solid electrode/liquid electrolyte interface provides vital chemical information that is needed for designing of better battery chemistry for enhanced performance, and ultimately opens new avenues for using liquid SIMS to probe molecular evolution at solid/liquid interface in general.

Molecular epidemiology and evolution of fish Novirhabdoviruses

Science.gov (United States)

Kurath, Gael

2014-01-01

The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus(HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

Molecular evolution of peptide ligands with custom-tailored characteristics for targeting of glycostructures.

Directory of Open Access Journals (Sweden)

Niels Röckendorf

Full Text Available As an advanced approach to identify suitable targeting molecules required for various diagnostic and therapeutic interventions, we developed a procedure to devise peptides with customizable features by an iterative computer-assisted optimization strategy. An evolutionary algorithm was utilized to breed peptides in silico and the "fitness" of peptides was determined in an appropriate laboratory in vitro assay. The influence of different evolutional parameters and mechanisms such as mutation rate, crossover probability, gaussian variation and fitness value scaling on the course of this artificial evolutional process was investigated. As a proof of concept peptidic ligands for a model target molecule, the cell surface glycolipid ganglioside G(M1, were identified. Consensus sequences describing local fitness optima were reached from diverse sets of L- and proteolytically stable D lead peptides. Ten rounds of evolutional optimization encompassing a total of just 4400 peptides lead to an increase in affinity of the peptides towards fluorescently labeled ganglioside G(M1 by a factor of 100 for L- and 400 for D-peptides.

Near neutrality: leading edge of the neutral theory of molecular evolution.

Science.gov (United States)

Hughes, Austin L

2008-01-01

The nearly neutral theory represents a development of Kimura's neutral theory of molecular evolution that makes testable predictions that go beyond a mere null model. Recent evidence has strongly supported several of these predictions, including the prediction that slightly deleterious variants will accumulate in a species that has undergone a severe bottleneck or in cases where recombination is reduced or absent. Because bottlenecks often occur in speciation and slightly deleterious mutations in coding regions will usually be nonsynonymous, we should expect that the ratio of nonsynonymous to synonymous fixed differences between species should often exceed the ratio of nonsynonymous to synonymous polymorphisms within species. Many data support this prediction, although they have often been wrongly interpreted as evidence for positive Darwinian selection. The use of conceptually flawed tests for positive selection has become widespread in recent years, seriously harming the quest for an understanding of genome evolution. When properly analyzed, many (probably most) claimed cases of positive selection will turn out to involve the fixation of slightly deleterious mutations by genetic drift in bottlenecked populations. Slightly deleterious variants are a transient feature of evolution in the long term, but they have substantially affected contemporary species, including our own.

Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions

International Nuclear Information System (INIS)

Nangia, Shivangi; Garrison, Barbara J.

2011-01-01

There is synergy between matrix assisted laser desorption ionization (MALDI) experiments and molecular dynamics (MD) simulations. To understand analyte ejection from the matrix, MD simulations have been employed. Prior calculations show that the ejected analyte molecules remain solvated by the matrix molecules in the ablated plume. In contrast, the experimental data show free analyte ions. The main idea of this work is that analyte molecule ejection may depend on the microscopic details of analyte interaction with the matrix. Intermolecular matrix-analyte interactions have been studied by focusing on 2,5-dihydroxybenzoic acid (DHB; matrix) and amino acids (AA; analyte) using Chemistry at HARvard Molecular Mechanics (CHARMM) force field. A series of AA molecules have been studied to analyze the DHB-AA interaction. A relative scale of AA molecule affinity towards DHB has been developed.

Evolution of circadian rhythms: from bacteria to human.

Science.gov (United States)

Bhadra, Utpal; Thakkar, Nirav; Das, Paromita; Pal Bhadra, Manika

2017-07-01

The human body persists in its rhythm as per its initial time zone, and transition always occur according to solar movements around the earth over 24 h. While traveling across different latitudes and longitudes, at the pace exceeding the earth's movement, the changes in the external cues exceed the level of toleration of the body's biological clock. This poses an alteration in our physiological activities of sleep-wake pattern, mental alertness, organ movement, and eating habits, causing them to temporarily lose the track of time. This is further re-synchronized with the physiological cues of the destination over time. The mechanism of resetting of the clocks with varying time zones and cues occur in organisms from bacteria to humans. It is the result of the evolution of different pathways and molecular mechanisms over the time. There has been evolution of numerous comprehensive mechanisms using various research tools to get a deeper insight into the rapid turnover of molecular mechanisms in various species. This review reports insights into the evolution of the circadian mechanism and its evolutionary shift which is vital and plays a major role in assisting different organisms to adapt in different zones and controls their internal biological clocks with changing external cues. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular modeling of the microstructure evolution during carbon fiber processing

Science.gov (United States)

Desai, Saaketh; Li, Chunyu; Shen, Tongtong; Strachan, Alejandro

2017-12-01

The rational design of carbon fibers with desired properties requires quantitative relationships between the processing conditions, microstructure, and resulting properties. We developed a molecular model that combines kinetic Monte Carlo and molecular dynamics techniques to predict the microstructure evolution during the processes of carbonization and graphitization of polyacrylonitrile (PAN)-based carbon fibers. The model accurately predicts the cross-sectional microstructure of the fibers with the molecular structure of the stabilized PAN fibers and physics-based chemical reaction rates as the only inputs. The resulting structures exhibit key features observed in electron microcopy studies such as curved graphitic sheets and hairpin structures. In addition, computed X-ray diffraction patterns are in good agreement with experiments. We predict the transverse moduli of the resulting fibers between 1 GPa and 5 GPa, in good agreement with experimental results for high modulus fibers and slightly lower than those of high-strength fibers. The transverse modulus is governed by sliding between graphitic sheets, and the relatively low value for the predicted microstructures can be attributed to their perfect longitudinal texture. Finally, the simulations provide insight into the relationships between chemical kinetics and the final microstructure; we observe that high reaction rates result in porous structures with lower moduli.

"Simulated molecular evolution" or computer-generated artifacts?

Science.gov (United States)

Darius, F; Rojas, R

1994-11-01

1. The authors define a function with value 1 for the positive examples and 0 for the negative ones. They fit a continuous function but do not deal at all with the error margin of the fit, which is almost as large as the function values they compute. 2. The term "quality" for the value of the fitted function gives the impression that some biological significance is associated with values of the fitted function strictly between 0 and 1, but there is no justification for this kind of interpretation and finding the point where the fit achieves its maximum does not make sense. 3. By neglecting the error margin the authors try to optimize the fitted function using differences in the second, third, fourth, and even fifth decimal place which have no statistical significance. 4. Even if such a fit could profit from more data points, the authors should first prove that the region of interest has some kind of smoothness, that is, that a continuous fit makes any sense at all. 5. "Simulated molecular evolution" is a misnomer. We are dealing here with random search. Since the margin of error is so large, the fitted function does not provide statistically significant information about the points in search space where strings with cleavage sites could be found. This implies that the method is a highly unreliable stochastic search in the space of strings, even if the neural network is capable of learning some simple correlations. 6. Classical statistical methods are for these kind of problems with so few data points clearly superior to the neural networks used as a "black box" by the authors, which in the way they are structured provide a model with an error margin as large as the numbers being computed.7. And finally, even if someone would provide us with a function which separates strings with cleavage sites from strings without them perfectly, so-called simulated molecular evolution would not be better than random selection.Since a perfect fit would only produce exactly ones or

Excipient-assisted vinpocetine nanoparticles: experiments and molecular dynamic simulations.

Science.gov (United States)

Li, Cai-Xia; Wang, Hao-Bo; Oppong, Daniel; Wang, Jie-Xin; Chen, Jian-Feng; Le, Yuan

2014-11-03

Hydrophilic excipients can be used to increase the solubility and bioavailability of poorly soluble drugs. In this work, the conventional water-soluble pharmaceutical excipients hydroxypropylmethylcellulose (HPMC), polyvinylpyrrolidone (PVP), and lactose (LAC) were used as solid supports to prevent drug nanoparticles from aggregation and enhance drug dissolution. Excipient-assisted vinpocetine (VIN) nanoparticles were prepared by reactive precipitation. The analysis results indicated that HPMC was a suitable excipient to prepare VIN nanoparticles. VIN/HPMC nanoparticles had a mean size of 130 nm within a narrow distribution. The dissolution rate of VIN nanoparticles was significantly faster than those of a physical mixture of VIN/HPMC and raw VIN. VIN/HPMC nanoparticles had a higher dissolution profile than VIN/PVP and VIN/LAC nanoparticles. Besides, molecular dynamics (MD) simulation was applied to investigate the molecular interactions between VIN and excipients. The calculated results revealed that VIN interacted with excipients by Coulomb and Lennard-Jones (LJ) interactions. Few hydrogen bonds were formed between VIN and excipients. The HPMC affording smaller particle size may be a result of the stronger interactions between VIN and HPMC (mainly LJ interaction) and the property of HPMC. These characteristics may greatly influence the adsorption behavior and may be the crucial parameter for the better performance of HPMC.

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers

Czech Academy of Sciences Publication Activity Database

Hypša, Václav

2006-01-01

Roč. 36, č. 2 (2006), s. 141-155 ISSN 0020-7519 R&D Projects: GA ČR GA206/04/0520 Institutional research plan: CEZ:AV0Z60220518 Keywords : molecular phylogeny * parasite evolution Subject RIV: EE - Microbiology, Virology Impact factor: 3.337, year: 2006

Cleavage and formation of molecular dinitrogen in a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine.

Science.gov (United States)

Miyazaki, Takamasa; Tanaka, Hiromasa; Tanabe, Yoshiaki; Yuki, Masahiro; Nakajima, Kazunari; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

2014-10-20

The N≡N bond of molecular dinitrogen bridging two molybdenum atoms in the pentamethylcyclopentadienyl molybdenum complexes that bear ferrocenyldiphosphine as an auxiliary ligand is homolytically cleaved under visible light irradiation at room temperature to afford two molar molybdenum nitride complexes. Conversely, the bridging molecular dinitrogen is reformed by the oxidation of the molybdenum nitride complex at room temperature. This result provides a successful example of the cleavage and formation of molecular dinitrogen induced by a pair of two different external stimuli using a single system assisted by molybdenum complexes bearing ferrocenyldiphosphine under ambient conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Science.gov (United States)

Eu, Byung Chan

2008-09-07

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

Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteria

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Ochman Howard

2009-09-01

Full Text Available Abstract Background Because bacteria do not have a robust fossil record, attempts to infer the timing of events in their evolutionary history requires comparisons of molecular sequences. This use of molecular clocks is based on the assumptions that substitution rates for homologous genes or sites are fairly constant through time and across taxa. Violation of these conditions can lead to erroneous inferences and result in estimates that are off by orders of magnitude. In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating. Results By examining the evolution of 16S rRNA gene in obligate endosymbionts, which can be calibrated by the fossil record of their hosts, we found that the rates are consistent within a clade but varied widely across different bacterial lineages. Genome-wide estimates of nonsynonymous and synonymous substitutions suggest that these two measures are highly variable in their rates across bacterial taxa. Genetic drift plays a fundamental role in determining the accumulation of substitutions in 16S rRNA genes and at nonsynonymous sites. Moreover, divergence estimates based on a set of universally conserved protein-coding genes also exhibit low correspondence to those based on 16S rRNA genes. Conclusion Our results document a wide range of substitution rates across genes and bacterial taxa. This high level of variation cautions against the assumption of a universal molecular clock for inferring divergence times in bacteria. However, by applying relative-rate tests to homologous genes, it is possible to derive reliable local clocks that can be used to calibrate bacterial evolution. Reviewers This article was reviewed by Adam Eyre-Walker, Simonetta Gribaldo and Tal Pupko (nominated by Dan Graur.

A methodological overview on molecular preimplantation genetic diagnosis and screening: a genomic future?

Science.gov (United States)

Vendrell, Xavier; Bautista-Llácer, Rosa

2012-12-01

The genetic diagnosis and screening of preimplantation embryos generated by assisted reproduction technology has been consolidated in the prenatal care framework. The rapid evolution of DNA technologies is tending to molecular approaches. Our intention is to present a detailed methodological view, showing different diagnostic strategies based on molecular techniques that are currently applied in preimplantation genetic diagnosis. The amount of DNA from one single, or a few cells, obtained by embryo biopsy is a limiting factor for the molecular analysis. In this sense, genetic laboratories have developed molecular protocols considering this restrictive condition. Nevertheless, the development of whole-genome amplification methods has allowed preimplantation genetic diagnosis for two or more indications simultaneously, like the selection of histocompatible embryos plus detection of monogenic diseases or aneuploidies. Moreover, molecular techniques have permitted preimplantation genetic screening to progress, by implementing microarray-based comparative genome hybridization. Finally, a future view of the embryo-genetics field based on molecular advances is proposed. The normalization, cost-effectiveness analysis, and new technological tools are the next topics for preimplantation genetic diagnosis and screening. Concomitantly, these additions to assisted reproduction technologies could have a positive effect on the schedules of preimplantation studies.

Cyan laser diode grown by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Turski, H.; Muziol, G.; Wolny, P.; Cywiński, G.; Grzanka, S.; Sawicka, M.; Perlin, P.; Skierbiszewski, C.

2014-01-01

We demonstrate AlGaN-cladding-free laser diodes (LDs), operating in continuous wave (CW) mode at 482 nm grown by plasma-assisted molecular beam epitaxy (PAMBE). The maximum CW output power was 230 mW. LDs were grown on c-plane GaN substrates obtained by hydride vapor phase epitaxy. The PAMBE process was carried out in metal-rich conditions, supplying high nitrogen flux (Φ N ) during quantum wells (QWs) growth. We found that high Φ N improves quality of high In content InGaN QWs. The role of nitrogen in the growth of InGaN on (0001) GaN surface as well as the influence of LDs design on threshold current density are discussed

Molecular evolution across the Asteraceae: micro- and macroevolutionary processes.

Science.gov (United States)

Kane, Nolan C; Barker, Michael S; Zhan, Shing H; Rieseberg, Loren H

2011-12-01

The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.

Detection of Wind Evolution and Lidar Trajectory Optimization for Lidar-Assisted Wind Turbine Control

Directory of Open Access Journals (Sweden)

David Schlipf

2015-11-01

Full Text Available Recent developments in remote sensing are offering a promising opportunity to rethink conventional control strategies of wind turbines. With technologies such as lidar, the information about the incoming wind field - the main disturbance to the system - can be made available ahead of time. Initial field testing of collective pitch feedforward control shows, that lidar measurements are only beneficial if they are filtered properly to avoid harmful control action. However, commercial lidar systems developed for site assessment are usually unable to provide a usable signal for real time control. Recent research shows, that the correlation between the measurement of rotor effective wind speed and the turbine reaction can be modeled and that the model can be used to optimize a scan pattern. This correlation depends on several criteria such as turbine size, position of the measurements, measurement volume, and how the wind evolves on its way towards the rotor. In this work the longitudinal wind evolution is identified with the line-of-sight measurements of a pulsed lidar system installed on a large commercial wind turbine. This is done by staring directly into the inflowing wind during operation of the turbine and fitting the coherence between the wind at different measurement distances to an exponential model taking into account the yaw misalignment, limitation to line-of-sight measurements and the pulse volume. The identified wind evolution is then used to optimize the scan trajectory of a scanning lidar for lidar-assisted feedforward control in order to get the best correlation possible within the constraints of the system. Further, an adaptive filer is fitted to the modeled correlation to avoid negative impact of feedforward control because of uncorrelated frequencies of the wind measurement. The main results of the presented work are a first estimate of the wind evolution in front of operating wind turbines and an approach which manufacturers of

Molecular evolution and diversification of snake toxin genes, revealed by analysis of intron sequences.

Science.gov (United States)

Fujimi, T J; Nakajyo, T; Nishimura, E; Ogura, E; Tsuchiya, T; Tamiya, T

2003-08-14

The genes encoding erabutoxin (short chain neurotoxin) isoforms (Ea, Eb, and Ec), LsIII (long chain neurotoxin) and a novel long chain neurotoxin pseudogene were cloned from a Laticauda semifasciata genomic library. Short and long chain neurotoxin genes were also cloned from the genome of Laticauda laticaudata, a closely related species of L. semifasciata, by PCR. A putative matrix attached region (MAR) sequence was found in the intron I of the LsIII gene. Comparative analysis of 11 structurally relevant snake toxin genes (three-finger-structure toxins) revealed the molecular evolution of these toxins. Three-finger-structure toxin genes diverged from a common ancestor through two types of evolutionary pathways (long and short types), early in the course of evolution. At a later stage of evolution in each gene, the accumulation of mutations in the exons, especially exon II, by accelerated evolution may have caused the increased diversification in their functions. It was also revealed that the putative MAR sequence found in the LsIII gene was integrated into the gene after the species-level divergence.

Interplay between chaperones and protein disorder promotes the evolution of protein networks.

Directory of Open Access Journals (Sweden)

Sebastian Pechmann

2014-06-01

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

The Lifetimes and Evolution of Molecular Cloud Cores

Science.gov (United States)

Vázquez-Semadeni, Enrique; Kim, Jongsoo; Shadmehri, Mohsen; Ballesteros-Paredes, Javier

2005-01-01

We discuss the lifetimes and evolution of clumps and cores formed as turbulent density fluctuations in nearly isothermal molecular clouds. In order to maintain a broad perspective, we consider both the magnetic and nonmagnetic cases. In the latter, we argue that clumps are unlikely to reach a hydrostatic state if molecular clouds can in general be described as single-phase media with an effective polytropic exponent γecriticality of their ``parent clouds'' (the numerical boxes). In subcritical boxes, magnetostatic clumps do not form. A minority of moderately gravitationally bound clumps form, which however are dispersed by the turbulence in ~1.3 Myr, suggesting that these few longer lived cores can marginally be ``captured'' by AD to increase their mass-to-flux ratio and eventually collapse, although on timescales not significantly longer than the dynamical ones. In supercritical boxes, some cores manage to become locally supercritical and collapse in typical timescales of 2 tfc (~1 Myr). In the most supercritical simulation, a few longer lived cores are observed, which last for up to ~3 Myr, but these end up re-expanding rather than collapsing, because they are sub-Jeans in spite of being supercritical. Fewer clumps and cores form in these simulations than in their nonmagnetic counterpart. Our results suggest the following: (1) not all cores observed in molecular clouds will necessarily form stars and that a class of ``failed cores'' should exist, which will eventually redisperse and which may be related to the observed starless cores; (2) cores may be out-of-equilibrium, transient structures, rather than quasi-magnetostatic configurations; (3) the magnetic field may help reduce the star formation efficiency by reducing the probability of core formation, rather than by significantly delaying the collapse of individual cores, even in magnetically supercritical clouds.

Molecular evolution of a novel family of putative calcium transporters.

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Didier Demaegd

Full Text Available The UPF0016 family is a group of uncharacterized membrane proteins, well conserved through evolution and defined by the presence of one or two copies of an E-Φ-G-D-(KR-(ST consensus motif. Our previous results have shown that two members of this family, the human TMEM165 and the budding yeast Gdt1p, are functionally related and might form a new group of cation/Ca2+ exchangers. Most members of the family are made of two homologous clusters of three transmembrane spans, separated by a central loop and assembled with an opposite orientation in the membrane. However, some bacterial members of the family have only one cluster of transmembrane domains. Among these 'single-domain membrane proteins' some cyanobacterial members were found as pairs of adjacent genes within the genome, but each gene was slightly different. We performed a bioinformatic analysis to propose the molecular evolution of the UPF0016 family and the emergence of the antiparallel topology. Our hypotheses were confirmed experimentally using functional complementation in yeast. This suggests an important and conserved function for UPF0016 proteins in a fundamental cellular process. We also show that members of the UPF0016 family share striking similarities, but no primary sequence homology, with members of the cation/Ca2+ exchangers (CaCA superfamily. Such similarities could be an example of convergent evolution, supporting the previous hypothesis that members of the UPF0016 family are cation/Ca2+ exchangers.

Molecular Evolution and Functional Divergence of Trace Amine-Associated Receptors.

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Seong-Il Eyun

Full Text Available Trace amine-associated receptors (TAARs are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey. We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian-specific in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4 have emerged earlier, generally have single-copy orthologs (very few duplication or loss, and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9 have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors.

Structural evolution of self-assisted GaAs nanowires grown on Si(111)

Energy Technology Data Exchange (ETDEWEB)

Biermanns, Andreas; Davydok, Anton; Pietsch, Ullrich [University of Siegen, Solid State Physics Group, Walter-Flex-Str. 3, 57072 Siegen (Germany); Breuer, Steffen; Geelhaar, Lutz [Paul-Drude-Institut fuer Festkoerperelektronik, Hausvogteiplatz 5-7, 10117 Berlin (Germany)

2011-04-15

GaAs nanowires are grown on Si(111) by self-assisted molecular beam epitaxy, and the ratio between wurtzite and zinc-blende phases is determined as function of nanowire length using asymmetric X-ray diffraction. We show that under the applied growth conditions, nanowires grow in both phases during the initial stage of growth, whereas the zinc-blende content increases with growth time and dominates in long nanowires. Compared to the zinc-blende units, the vertical lattice parameter of the wurtzite segments is 0.7% larger, as measured by the positions of respective diffraction peaks. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Immobilization of molecular cobalt electrocatalyst by hydrophobic interaction with hematite photoanode for highly stable oxygen evolution

KAUST Repository

Joya, Khurram

2015-07-15

A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst – hematite photoanode hybrid material showed significant onset shift and high stability for photoelectrochemical oxidation evolution reaction (OER).

Immobilization of molecular cobalt electrocatalyst by hydrophobic interaction with hematite photoanode for highly stable oxygen evolution

KAUST Repository

Joya, Khurram; Morlanes, Natalia; Maloney, Edward; Rodionov, Valentin; Takanabe, Kazuhiro

2015-01-01

A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst – hematite photoanode hybrid material showed significant onset shift and high stability for photoelectrochemical oxidation evolution reaction (OER).

Structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy

Science.gov (United States)

Kanzyuba, Vasily; Dong, Sining; Liu, Xinyu; Li, Xiang; Rouvimov, Sergei; Okuno, Hanako; Mariette, Henri; Zhang, Xueqiang; Ptasinska, Sylwia; Tracy, Brian D.; Smith, David J.; Dobrowolska, Margaret; Furdyna, Jacek K.

2017-02-01

We describe the structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy on GaAs (111) substrates, as revealed by transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. When the Mn concentration is increased, the lattice of the ternary (Sn,Mn)Se films evolves quasi-coherently from a SnSe2 two-dimensional (2D) crystal structure into a more complex quasi-2D lattice rearrangement, ultimately transforming into the magnetically concentrated antiferromagnetic MnSe 3D rock-salt structure as Mn approaches 50 at. % of this material. These structural transformations are expected to underlie the evolution of magnetic properties of this ternary system reported earlier in the literature.

Neighboring Hetero-Atom Assistance of Sacrificial Amines to Hydrogen Evolution Using Pt-Loaded TiO2-Photocatalyst

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Masahide Yasuda

2014-05-01

Full Text Available Photocatalytic H2 evolution was examined using Pt-loaded TiO2-photocatalyst in the presence of amines as sacrificial agents. In the case of amines with all of the carbon attached to the hetero-atom such as 2-aminoethanol, 1,2-diamonoethane, 2-amino-1,3-propanediol, and 3-amino-1,2-propanediol, they were completely decomposed into CO2 and water to quantitatively evolve H2. On the other hand, the amines with both hetero-atoms and one methyl group at the β-positions (neighboring carbons of amino group such as 2-amino-1-propanol and 1,2-diaminopropane were partially decomposed. Also, the photocatalytic H2 evolution using amines without the hetero-atoms at the β-positions such as ethylamine, propylamine, 1-butylamine, 1,3-diaminopropane, 2-propylamine, and 2-butylamine was inefficient. Thus, it was found that the neighboring hetero-atom strongly assisted the degradation of sacrificial amines. Moreover, rate constants for H2 evolution were compared among amines. In conclusion, the neighboring hetero-atom did not affect the rate constants but enhanced the yield of hydrogen evolution.

Molecular evolution of the polyamine oxidase gene family in Metazoa

Directory of Open Access Journals (Sweden)

Polticelli Fabio

2012-06-01

monophyletic clades including, respectively, all the SMOs and APAOs from vertebrates. The two vertebrate monophyletic clades clustered strictly mirroring the organismal phylogeny of fishes, amphibians, reptiles, birds, and mammals. Evidences from comparative genomic analysis, structural evolution and functional divergence in a phylogenetic framework across Metazoa suggested an evolutionary scenario where the ancestor PAO coding sequence, present in invertebrates as an orthologous gene, has been duplicated in the vertebrate branch to originate the paralogous SMO and APAO genes. A further genome evolution event concerns the SMO gene of placental, but not marsupial and monotremate, mammals which increased its functional variation following an alternative splicing (AS mechanism. Conclusions In this study the explicit integration in a phylogenomic framework of phylogenetic tree construction, structure prediction, and biochemical function data/prediction, allowed inferring the molecular evolutionary history of the PAO gene family and to disambiguate paralogous genes related by duplication event (SMO and APAO and orthologous genes related by speciation events (PAOs, SMOs/APAOs. Further, while in vertebrates experimental data corroborate SMO and APAO molecular function predictions, in invertebrates the finding of a supported phylogenetic clusters of insect PAOs and the co-occurrence of two PAO variants in the amphioxus urgently claim the need for future structure-function studies.

Microwave-assisted synthesis, molecular docking and antitubercular activity of 1,2,3,4-tetrahydropyrimidine-5-carbonitrile derivatives

Czech Academy of Sciences Publication Activity Database

Mohan, S. B.; Kumar, B. V. V. R.; Dinda, S. C.; Naik, D.; Seenivasan, S. P.; Kumar, V.; Rana, D. N.; Brahmkshatriya, Pathik

2012-01-01

Roč. 22, č. 24 (2012), s. 7539-7542 ISSN 0960-894X Institutional research plan: CEZ:AV0Z40550506 Keywords : antitubercular * binding interactions * luciferase reporter phage (LRP) assay * microwave-assisted * molecular docking Subject RIV: CC - Organic Chemistry Impact factor: 2.338, year: 2012

The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.

Science.gov (United States)

Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C; Paoletti, Christopher; Nowak, Martin A

2015-02-01

Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

The molecular clock of neutral evolution can be accelerated or slowed by asymmetric spatial structure.

Directory of Open Access Journals (Sweden)

Benjamin Allen

2015-02-01

Full Text Available Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a "molecular clock" to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution.

Science.gov (United States)

Melkikh, Alexey V; Khrennikov, Andrei

2017-11-01

A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics.

Science.gov (United States)

Ma, Peng-Fei; Vorontsova, Maria S; Nanjarisoa, Olinirina Prisca; Razanatsoa, Jacqueline; Guo, Zhen-Hua; Haevermans, Thomas; Li, De-Zhu

2017-12-21

Heterogeneous rates of molecular evolution are universal across the tree of life, posing challenges for phylogenetic inference. The temperate woody bamboos (tribe Arundinarieae, Poaceae) are noted for their extremely slow molecular evolutionary rates, supposedly caused by their mysterious monocarpic reproduction. However, the correlation between substitution rates and flowering cycles has not been formally tested. Here we present 15 newly sequenced plastid genomes of temperate woody bamboos, including the first genomes ever sequenced from Madagascar representatives. A data matrix of 46 plastid genomes representing all 12 lineages of Arundinarieae was assembled for phylogenetic and molecular evolutionary analyses. We conducted phylogenetic analyses using different sequences (e.g., coding and noncoding) combined with different data partitioning schemes, revealing conflicting relationships involving internodes among several lineages. A great difference in branch lengths were observed among the major lineages, and topological inconsistency could be attributed to long-branch attraction (LBA). Using clock model-fitting by maximum likelihood and Bayesian approaches, we furthermore demonstrated extensive rate variation among these major lineages. Rate accelerations mainly occurred for the isolated lineages with limited species diversification, totaling 11 rate shifts during the tribe's evolution. Using linear regression analysis, we found a negative correlation between rates of molecular evolution and flowering cycles for Arundinarieae, notwithstanding that the correlation maybe insignificant when taking the phylogenetic structure into account. Using the temperate woody bamboos as an example, we found further evidence that rate heterogeneity is universal in plants, suggesting that this will pose a challenge for phylogenetic reconstruction of bamboos. The bamboos with longer flowering cycles tend to evolve more slowly than those with shorter flowering cycles, in accordance

Bioinspired molecular co-catalysts bonded to a silicon photocathode for solar hydrogen evolution

DEFF Research Database (Denmark)

Hou, Yidong; Abrams, Billie L.; Vesborg, Peter Christian Kjærgaard

2011-01-01

The production of fuels from sunlight represents one of the main challenges in the development of a sustainable energy system. Hydrogen is the simplest fuel to produce and although platinum and other noble metals are efficient catalysts for photoelectrochemical hydrogen evolution, earth...... that harvests red photons in the solar spectrum. The current densities at the reversible potential match the requirement of a photoelectrochemical hydrogen production system with a solar-to-hydrogen efficiency in excess of 10% (ref. 16). The experimental observations are supported by density functional theory......-abundant alternatives are needed for large-scale use. We show that bioinspired molecular clusters based on molybdenum and sulphur evolve hydrogen at rates comparable to that of platinum. The incomplete cubane-like clusters (Mo3S 4) efficiently catalyse the evolution of hydrogen when coupled to a p-type Si semiconductor...

Non-sensitized selective photochemical reduction of CO2 to CO under visible light with an iron molecular catalyst.

Science.gov (United States)

Rao, Heng; Bonin, Julien; Robert, Marc

2017-03-02

A substituted tetraphenyl iron porphyrin, bearing positively charged trimethylammonio groups at the para position of each phenyl ring, demonstrates its ability as a homogeneous molecular catalyst to selectively reduce CO 2 to CO under visible light irradiation in organic media without the assistance of a sensitizer and no competitive hydrogen evolution for several days.

The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity.

Science.gov (United States)

Razeto-Barry, Pablo; Díaz, Javier; Vásquez, Rodrigo A

2012-06-01

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model

Rates and patterns of molecular evolution in freshwater versus terrestrial insects.

Science.gov (United States)

Mitterboeck, T Fatima; Fu, Jinzhong; Adamowicz, Sarah J

2016-11-01

Insect lineages have crossed between terrestrial and aquatic habitats many times, for both immature and adult life stages. We explore patterns in molecular evolutionary rates between 42 sister pairs of related terrestrial and freshwater insect clades using publicly available protein-coding DNA sequence data from the orders Coleoptera, Diptera, Lepidoptera, Hemiptera, Mecoptera, Trichoptera, and Neuroptera. We furthermore test for habitat-associated convergent molecular evolution in the cytochrome c oxidase subunit I (COI) gene in general and at a particular amino acid site previously reported to exhibit habitat-linked convergence within an aquatic beetle group. While ratios of nonsynonymous-to-synonymous substitutions across available loci were higher in terrestrial than freshwater-associated taxa in 26 of 42 lineage pairs, a stronger trend was observed (20 of 31, p binomial = 0.15, p Wilcoxon = 0.017) when examining only terrestrial-aquatic pairs including fully aquatic taxa. We did not observe any widespread changes at particular amino acid sites in COI associated with habitat shifts, although there may be general differences in selection regime linked to habitat.

Surface Functionalization of g-C 3 N 4 : Molecular-Level Design of Noble-Metal-Free Hydrogen Evolution Photocatalysts

KAUST Repository

Chen, Yin; Lin, Bin; Yu, Weili; Yang, Yong; Bashir, Shahid M.; Wang, Hong; Takanabe, Kazuhiro; Idriss, Hicham; Basset, Jean-Marie

2015-01-01

A stable noble-metal-free hydrogen evolution photocatalyst based on graphite carbon nitride (g-C3N4) was developed by a molecular-level design strategy. Surface functionalization was successfully conducted to introduce a single nickel active site

Evolution of the protists and protistan parasites from the perspective of molecular systematics.

Science.gov (United States)

Sogin, M L; Silberman, J D

1998-01-01

Unlike prokaryotes, the Protista are rich in morphological and ultrastructure information. Their amazing phenotypic diversity permits assignment of many protists to cohesive phyletic assemblages but sometimes blurs relationships between major lineages. With the advent of molecular techniques, it became possible to test evolutionary hypotheses that were originally formulated according to shared phenotypic traits. More than any other gene family, studies of rRNAs changed our understanding of protist evolution. Stramenopiles (oomycetes, chrysophytes, phaeophytes, synurophytes, diatoms, xanthophytes, bicosoecids, slime nets) and alveolates (dinoflagellates, apicomplexans, ciliates) are two novel, complex evolutionary assemblages which diverged nearly simultaneously with animals, fungi, plants, rhodophytes, haptophytes and a myriad of independent amoeboid lineages. Their separation may have occurred one billion years ago and collectively these lineages make up the "crown" of the eukaryotic tree. Deeper branches in the eukaryotic tree show 16S-like rRNA sequence variation that is much greater than that observed within the Archaea and the Bacteria. A progression of independent protist branches, some as ancient as the divergence between the two prokaryotic domains, preceded the sudden radiation of "crown" groups. Trichomonads, diplomonads and Microsporidia are basal to all other eukaryotes included in rRNA studies. Together with pelobionts, oxymonads, retortamonads and hypermastigids, these amitochondriate taxa comprise the Archaezoa. This skeletal phylogeny suggested that early branching eukaryotes lacked mitochondria, peroxisomes and typical stacked Golgi dictyosomes. However, recent studies of heat shock proteins indicate that the first eukaryotes may have had mitochondria. When evaluated in terms of evolution of ultrastructure, lifestyles and other phenotypic traits, the rRNA phylogenies provide the most consistent of molecular trees. They permit identification of the

Prediction of temperature-insensitive molecular absorption lines in laser-assisted combustion diagnostics

International Nuclear Information System (INIS)

Walewski, Joachim W.; Elmqvist, Anders

2005-01-01

In laser-assisted combustion diagnostics it is a recurring task to predict molecular transitions whose signal strength depends only weakly on variations in temperature. The signal strength is proportional to the Boltzmann fraction of the level probed and the amplitude of the absorption line profile. In the past investigations have been presented in which this task was attack by detailed numerical calculations of the temperature dependence of pertinent physical properties of the molecule. Another widely applied approach relies on an analytical formula for the Boltzmann fraction of hetero-nuclear diatomic molecules and the neglect of line shape effects. The analytical approach experiences a continuing popularity in laser-assisted combustion diagnostics, which is why we compared both approaches with each other. The objective of this comparison was to assess the accuracy of the analytical approach and to reveal its potential pitfalls. Our comparison revealed that the analytical approach suffers from mediocre accuracy, which makes it unfit for practical applications. One cause is the neglect of higher lying vibrational levels, which show a non-negligible population for typical flame temperatures. Another reason is the neglect of fine structure splitting in molecules with non-zero orbit angular momentum in the ground state. Another reason for the observed inaccuracy is the neglect of line shape effects quenching, which were found to have a significant effect on the temperature sensitivity of a line. Because of its insufficient accuracy due to both oversimplified models of the molecular energy levels and the neglect of line shape effects and quenching we discourage from applying the analytical approach and recommend the use of detailed numerical approaches that are free of the above limitations

First comparative study of primate morphological and molecular evolutionary rates including muscle data: implications for the tempo and mode of primate and human evolution

Science.gov (United States)

Diogo, Rui; Peng, Zuogang; Wood, Bernard

2013-01-01

Here we provide the first report about the rates of muscle evolution derived from Bayesian and parsimony cladistic analyses of primate higher-level phylogeny, and compare these rates with published rates of molecular evolution. It is commonly accepted that there is a ‘general molecular slow-down of hominoids’, but interestingly the rates of muscle evolution in the nodes leading and within the hominoid clade are higher than those in the vast majority of other primate clades. The rate of muscle evolution at the node leading to Homo (1.77) is higher than that at the nodes leading to Pan (0.89) and particularly to Gorilla (0.28). Notably, the rates of muscle evolution at the major euarchontan and primate nodes are different, but within each major primate clade (Strepsirrhini, Platyrrhini, Cercopithecidae and Hominoidea) the rates at the various nodes, and particularly at the nodes leading to the higher groups (i.e. including more than one genera), are strikingly similar. We explore the implications of these new data for the tempo and mode of primate and human evolution. PMID:23320764

Rapid molecular evolution of human bocavirus revealed by Bayesian coalescent inference.

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Zehender, Gianguglielmo; De Maddalena, Chiara; Canuti, Marta; Zappa, Alessandra; Amendola, Antonella; Lai, Alessia; Galli, Massimo; Tanzi, Elisabetta

2010-03-01

Human bocavirus (HBoV) is a linear single-stranded DNA virus belonging to the Parvoviridae family that has recently been isolated from the upper respiratory tract of children with acute respiratory infection. All of the strains observed so far segregate into two genotypes (1 and 2) with a low level of polymorphism. Given the recent description of the infection and the lack of epidemiological and molecular data, we estimated the virus's rates of molecular evolution and population dynamics. A dataset of forty-nine dated VP2 sequences, including also eight new isolates obtained from pharyngeal swabs of Italian patients with acute respiratory tract infections, was submitted to phylogenetic analysis. The model parameters, evolutionary rates and population dynamics were co-estimated using a Bayesian Markov Chain Monte Carlo approach, and site-specific positive and negative selection was also investigated. Recombination was investigated by seven different methods and one suspected recombinant strain was excluded from further analysis. The estimated mean evolutionary rate of HBoV was 8.6x10(-4)subs/site/year, and that of the 1st+2nd codon positions was more than 15 times less than that of the 3rd codon position. Viral population dynamics analysis revealed that the two known genotypes diverged recently (mean tMRCA: 24 years), and that the epidemic due to HBoV genotype 2 grew exponentially at a rate of 1.01year(-1). Selection analysis of the partial VP2 showed that 8.5% of sites were under significant negative pressure and the absence of positive selection. Our results show that, like other parvoviruses, HBoV is characterised by a rapid evolution. The low level of polymorphism is probably due to a relatively recent divergence between the circulating genotypes and strong purifying selection acting on viral antigens.

Hydro-chemical study of the evolution of interstellar pre-biotic molecules during the collapse of molecular clouds

International Nuclear Information System (INIS)

Majumdar, Liton; Das, Ankan; Chakrabarti, Sandip K.; Chakrabarti, Sonali

2012-01-01

One of the stumbling blocks for studying the evolution of interstellar molecules is the lack of adequate knowledge about the rate coefficients of various reactions which take place in the interstellar medium and molecular clouds. Some theoretical models of rate coefficients do exist in the literature for computing abundances of complex pre-biotic molecules. So far these have been used to study the abundances of these molecules in space. However, in order to obtain more accurate final compositions in these media, we have calculated the rate coefficients for the formation of some of the most important interstellar pre-biotic molecules by using quantum chemical theory. We use these rates inside our hydro-chemical model to examine the chemical evolution and final abundances of pre-biotic species during the collapsing phase of a proto-star. We find that a significant amount of various pre-biotic molecules could be produced during the collapse phase of a proto-star. We thoroughly study the formation of these molecules via successive neutral-neutral and radical-radical/radical-molecular reactions. We present the time evolution of the chemical species with an emphasis on how the production of these molecules varies with the depth of a cloud. We compare the formation of adenine in interstellar space using our rate-coefficients and using those obtained from existing theoretical models. Formation routes of the pre-biotic molecules are found to be highly dependent on the abundances of the reactive species and the rate coefficients involved in the reactions. The presence of grains strongly affects the abundances of the gas phase species. We also carry out a comparative study between different pathways available for the synthesis of adenine, alanine, glycine and other molecules considered in our network. Despite the huge abundances of the neutral reactive species, production of adenine is found to be strongly dominated by the radical-radical/radical-molecular reaction pathways

Molecular development of fibular reduction in birds and its evolution from dinosaurs.

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Botelho, João Francisco; Smith-Paredes, Daniel; Soto-Acuña, Sergio; O'Connor, Jingmai; Palma, Verónica; Vargas, Alexander O

2016-03-01

Birds have a distally reduced, splinter-like fibula that is shorter than the tibia. In embryonic development, both skeletal elements start out with similar lengths. We examined molecular markers of cartilage differentiation in chicken embryos. We found that the distal end of the fibula expresses Indian hedgehog (IHH), undergoing terminal cartilage differentiation, and almost no Parathyroid-related protein (PTHrP), which is required to develop a proliferative growth plate (epiphysis). Reduction of the distal fibula may be influenced earlier by its close contact with the nearby fibulare, which strongly expresses PTHrP. The epiphysis-like fibulare however then separates from the fibula, which fails to maintain a distal growth plate, and fibular reduction ensues. Experimental downregulation of IHH signaling at a postmorphogenetic stage led to a tibia and fibula of equal length: The fibula is longer than in controls and fused to the fibulare, whereas the tibia is shorter and bent. We propose that the presence of a distal fibular epiphysis may constrain greater growth in the tibia. Accordingly, many Mesozoic birds show a fibula that has lost its distal epiphysis, but remains almost as long as the tibia, suggesting that loss of the fibulare preceded and allowed subsequent evolution of great fibulo-tibial disparity. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

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

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Shen, Jian Qi; Gu, Jing

2018-04-01

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

Morphological evolution of Bi2Se3 nanocrystalline materials synthesized by microwave assisted solvothermal method

Science.gov (United States)

Bera, Sumit; Behera, P.; Mishra, A. K.; Krishnan, M.; Patidar, M. M.; Singh, D.; Gangrade, M.; Venkatesh, R.; Deshpande, U. P.; Phase, D. M.; Ganesan, V.

2018-04-01

Structural, morphological and spectroscopic properties of Bi2Se3 nanoparticles synthesized by microwave assisted solvothermal method were investigated systematically. A controlled synthesis of different morphologies by a small variation in synthesis procedure is demonstrated. Powder X-ray diffraction (XRD) confirmed the formation of single phase. Crystallite and particle size reductions were studied with XRD and AFM (Atomic Force Microscopy). Different morphologies such as hexagonal nanoflakes with cross section of around˜6µm, nanoflower and octahedral agglomerated crystals of nearly ˜60 nm size have been observed in scanning electron microscope while varying the microwave assisted synthesis procedures. A significant blue shift observed in diffuse reflectance spectroscopy evidences the energy gap tuning as a result of morphological evolution. The difference in morphology observed in this three fast, facile and scalable synthesis is advantageous for tuning the thermoelectric figure of merit and for probing the surface states of these topological insulators. Low temperature resistivity remains similar for all three variants depicting a 2D character as evidenced by a -lnT term of localization.

Molecular evolution of colorectal cancer: from multistep carcinogenesis to the big bang.

Science.gov (United States)

Amaro, Adriana; Chiara, Silvana; Pfeffer, Ulrich

2016-03-01

Colorectal cancer is characterized by exquisite genomic instability either in the form of microsatellite instability or chromosomal instability. Microsatellite instability is the result of mutation of mismatch repair genes or their silencing through promoter methylation as a consequence of the CpG island methylator phenotype. The molecular causes of chromosomal instability are less well characterized. Genomic instability and field cancerization lead to a high degree of intratumoral heterogeneity and determine the formation of cancer stem cells and epithelial-mesenchymal transition mediated by the TGF-β and APC pathways. Recent analyses using integrated genomics reveal different phases of colorectal cancer evolution. An initial phase of genomic instability that yields many clones with different mutations (big bang) is followed by an important, previously not detected phase of cancer evolution that consists in the stabilization of several clones and a relatively flat outgrowth. The big bang model can best explain the coexistence of several stable clones and is compatible with the fact that the analysis of the bulk of the primary tumor yields prognostic information.

Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants

Energy Technology Data Exchange (ETDEWEB)

Schenck, Craig A.; Holland, Cynthia K.; Schneider, Matthew R.; Men, Yusen; Lee, Soon Goo; Jez, Joseph M.; Maeda , Hiroshi A. (UW); (WU)

2017-06-26

L-Tyrosine (Tyr) is essential for protein synthesis and is a precursor of numerous specialized metabolites crucial for plant and human health. Tyr can be synthesized via two alternative routes by different key regulatory TyrA family enzymes, prephenate dehydrogenase (PDH, also known as TyrAp) or arogenate dehydrogenase (ADH, also known as TyrAa), representing a unique divergence of primary metabolic pathways. The molecular foundation underlying the evolution of these alternative Tyr pathways is currently unknown. Here we characterized recently diverged plant PDH and ADH enzymes, obtained the X-ray crystal structure of soybean PDH, and identified a single amino acid residue that defines TyrA substrate specificity and regulation. Structures of mutated PDHs co-crystallized with Tyr indicate that substitutions of Asn222 confer ADH activity and Tyr sensitivity. Reciprocal mutagenesis of the corresponding residue in divergent plant ADHs further introduced PDH activity and relaxed Tyr sensitivity, highlighting the critical role of this residue in TyrA substrate specificity that underlies the evolution of alternative Tyr biosynthetic pathways in plants.

Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster

Science.gov (United States)

Robertson, Hugh M.; Warr, Coral G.; Carlson, John R.

2003-01-01

The insect chemoreceptor superfamily in Drosophila melanogaster is predicted to consist of 62 odorant receptor (Or) and 68 gustatory receptor (Gr) proteins, encoded by families of 60 Or and 60 Gr genes through alternative splicing. We include two previously undescribed Or genes and two previously undescribed Gr genes; two previously predicted Or genes are shown to be alternative splice forms. Three polymorphic pseudogenes and one highly defective pseudogene are recognized. Phylogenetic analysis reveals deep branches connecting multiple highly divergent clades within the Gr family, and the Or family appears to be a single highly expanded lineage within the superfamily. The genes are spread throughout the Drosophila genome, with some relatively recently diverged genes still clustered in the genome. The Gr5a gene on the X chromosome, which encodes a receptor for the sugar trehalose, has transposed from one such tandem cluster of six genes at cytological location 64, as has Gr61a, and all eight of these receptors might bind sugars. Analysis of intron evolution suggests that the common ancestor consisted of a long N-terminal exon encoding transmembrane domains 1-5 followed by three exons encoding transmembrane domains 6-7. As many as 57 additional introns have been acquired idiosyncratically during the evolution of the superfamily, whereas the ancestral introns and some of the older idiosyncratic introns have been lost at least 48 times independently. Altogether, these patterns of molecular evolution suggest that this is an ancient superfamily of chemoreceptors, probably dating back at least to the origin of the arthropods. PMID:14608037

Extraordinary molecular evolution in the PRDM9 fertility gene.

Directory of Open Access Journals (Sweden)

James H Thomas

2009-12-01

Full Text Available Recent work indicates that allelic incompatibility in the mouse PRDM9 (Meisetz gene can cause hybrid male sterility, contributing to genetic isolation and potentially speciation. The only phenotype of mouse PRDM9 knockouts is a meiosis I block that causes sterility in both sexes. The PRDM9 gene encodes a protein with histone H3(K4 trimethyltransferase activity, a KRAB domain, and a DNA-binding domain consisting of multiple tandem C2H2 zinc finger (ZF domains. We have analyzed human coding polymorphism and interspecies evolutionary changes in the PRDM9 gene. The ZF domains of PRDM9 are evolving very rapidly, with compelling evidence of positive selection in primates. Positively selected amino acids are predominantly those known to make nucleotide specific contacts in C2H2 zinc fingers. These results suggest that PRDM9 is subject to recurrent selection to change DNA-binding specificity. The human PRDM9 protein is highly polymorphic in its ZF domains and nearly all polymorphisms affect the same nucleotide contact residues that are subject to positive selection. ZF domain nucleotide sequences are strongly homogenized within species, indicating that interfinger recombination contributes to their evolution. PRDM9 has previously been assumed to be a transcription factor required to induce meiosis specific genes, a role that is inconsistent with its molecular evolution. We suggest instead that PRDM9 is involved in some aspect of centromere segregation conflict and that rapidly evolving centromeric DNA drives changes in PRDM9 DNA-binding domains.

Measurement Frontiers in Molecular Biology

Science.gov (United States)

Laderman, Stephen

2009-03-01

Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

Molecular Evolution of Slow and Quick Anion Channels (SLACs and QUACs/ALMTs).

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Dreyer, Ingo; Gomez-Porras, Judith Lucia; Riaño-Pachón, Diego Mauricio; Hedrich, Rainer; Geiger, Dietmar

2012-01-01

Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant) SLAC-like and 422 (402 non-redundant) ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general.

Molecular evolution of slow and quick anion channels (SLACs and QUACs/ALMTs

Directory of Open Access Journals (Sweden)

Ingo eDreyer

2012-11-01

Full Text Available Electrophysiological analyses conducted about 25 years ago detected two types of anion channels in the plasma membrane of guard cells. One type of channel responds slowly to changes in membrane voltage while the other responds quickly. Consequently, they were named SLAC, for SLow Anion Channel, and QUAC, for QUick Anion Channel. Recently, genes SLAC1 and QUAC1/ALMT12, underlying the two different anion current components, could be identified in the model plant Arabidopsis thaliana. Expression of the gene products in Xenopus oocytes confirmed the quick and slow current kinetics. In this study we provide an overview on our current knowledge on slow and quick anion channels in plants and analyze the molecular evolution of ALMT/QUAC-like and SLAC-like channels. We discovered fingerprints that allow screening databases for these channel types and were able to identify 192 (177 non-redundant SLAC-like and 422 (402 non-redundant ALMT/QUAC-like proteins in the fully sequenced genomes of 32 plant species. Phylogenetic analyses provided new insights into the molecular evolution of these channel types. We also combined sequence alignment and clustering with predictions of protein features, leading to the identification of known conserved phosphorylation sites in SLAC1-like channels along with potential sites that have not been yet experimentally confirmed. Using a similar strategy to analyze the hydropathicity of ALMT/QUAC-like channels, we propose a modified topology with additional transmembrane regions that integrates structure and function of these membrane proteins. Our results suggest that cross-referencing phylogenetic analyses with position-specific protein properties and functional data could be a very powerful tool for genome research approaches in general.

Molecular pathways to parallel evolution: I. Gene nexuses and their morphological correlates.

Science.gov (United States)

Zuckerkandl, E

1994-12-01

Aspects of the regulatory interactions among genes are probably as old as most genes are themselves. Correspondingly, similar predispositions to changes in such interactions must have existed for long evolutionary periods. Features of the structure and the evolution of the system of gene regulation furnish the background necessary for a molecular understanding of parallel evolution. Patently "unrelated" organs, such as the fat body of a fly and the liver of a mammal, can exhibit fractional homology, a fraction expected to become subject to quantitation. This also seems to hold for different organs in the same organism, such as wings and legs of a fly. In informational macromolecules, on the other hand, homology is indeed all or none. In the quite different case of organs, analogy is expected usually to represent attenuated homology. Many instances of putative convergence are likely to turn out to be predominantly parallel evolution, presumably including the case of the vertebrate and cephalopod eyes. Homology in morphological features reflects a similarity in networks of active genes. Similar nexuses of active genes can be established in cells of different embryological origins. Thus, parallel development can be considered a counterpart to parallel evolution. Specific macromolecular interactions leading to the regulation of the c-fos gene are given as an example of a "controller node" defined as a regulatory unit. Quantitative changes in gene control are distinguished from relational changes, and frequent parallelism in quantitative changes is noted in Drosophila enzymes. Evolutionary reversions in quantitative gene expression are also expected. The evolution of relational patterns is attributed to several distinct mechanisms, notably the shuffling of protein domains. The growth of such patterns may in part be brought about by a particular process of compensation for "controller gene diseases," a process that would spontaneously tend to lead to increased regulatory

The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.

Science.gov (United States)

Diaz, Maureen H; Winchell, Jonas M

2016-01-01

Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

Genome-Wide Identification, Molecular Evolution, and Expression Profiling Analysis of Pectin Methylesterase Inhibitor Genes in Brassica campestris ssp. chinensis

Directory of Open Access Journals (Sweden)

Tingting Liu

2018-05-01

Full Text Available Pectin methylesterase inhibitor genes (PMEIs are a large multigene family and play crucial roles in cell wall modifications in plant growth and development. Here, a comprehensive analysis of the PMEI gene family in Brassica campestris, an important leaf vegetable, was performed. We identified 100 Brassica campestris PMEI genes (BcPMEIs, among which 96 BcPMEIs were unevenly distributed on 10 chromosomes and nine tandem arrays containing 20 BcPMEIs were found. We also detected 80 pairs of syntenic PMEI orthologs. These findings indicated that whole-genome triplication (WGT and tandem duplication (TD were the main mechanisms accounting for the current number of BcPMEIs. In evolution, BcPMEIs were retained preferentially and biasedly, consistent with the gene balance hypothesis and two-step theory, respectively. The molecular evolution analysis of BcPMEIs manifested that they evolved through purifying selection and the divergence time is in accordance with the WGT data of B. campestris. To obtain the functional information of BcPMEIs, the expression patterns in five tissues and the cis-elements distributed in promoter regions were investigated. This work can provide a better understanding of the molecular evolution and biological function of PMEIs in B. campestris.

The impact of treatment density and molecular weight for fractional laser-assisted drug delivery

DEFF Research Database (Denmark)

Haak, Christina S; Bhayana, Brijesh; Farinelli, William A

2012-01-01

Ablative fractional lasers (AFXL) facilitate uptake of topically applied drugs by creating narrow open micro-channels into the skin, but there is limited information on optimal laser settings for delivery of specific molecules. The objective of this study was to investigate the impact of laser...... treatment density (% of skin occupied by channels) and molecular weight (MW) for fractional CO(2) laser-assisted drug delivery. AFXL substantially increased intra- and transcutaneous delivery of polyethylene glycols (PEGs) in a MW range from 240 to 4300 Da (Nuclear Magnetic Resonance, p...

Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple-protein-encoding P gene.

Science.gov (United States)

Jordan, I K; Sutter, B A; McClure, M A

2000-01-01

Presented here is an analysis of the molecular evolutionary dynamics of the P gene among 76 representative sequences of the Paramyxoviridae and Rhabdoviridae RNA virus families. In a number of Paramyxoviridae taxa, as well as in vesicular stomatitis viruses of the Rhabdoviridae, the P gene encodes multiple proteins from a single genomic RNA sequence. These products include the phosphoprotein (P), as well as the C and V proteins. The complexity of the P gene makes it an intriguing locus to study from an evolutionary perspective. Amino acid sequence alignments of the proteins encoded at the P and N loci were used in independent phylogenetic reconstructions of the Paramyxoviridae and Rhabdoviridae families. P-gene-coding capacities were mapped onto the Paramyxoviridae phylogeny, and the most parsimonious path of multiple-coding-capacity evolution was determined. Levels of amino acid variation for Paramyxoviridae and Rhabdoviridae P-gene-encoded products were also analyzed. Proteins encoded in overlapping reading frames from the same nucleotides have different levels of amino acid variation. The nucleotide architecture that underlies the amino acid variation was determined in order to evaluate the role of selection in the evolution of the P gene overlapping reading frames. In every case, the evolution of one of the proteins encoded in the overlapping reading frames has been constrained by negative selection while the other has evolved more rapidly. The integrity of the overlapping reading frame that represents a derived state is generally maintained at the expense of the ancestral reading frame encoded by the same nucleotides. The evolution of such multicoding sequences is likely a response by RNA viruses to selective pressure to maximize genomic information content while maintaining small genome size. The ability to evolve such a complex genomic strategy is intimately related to the dynamics of the viral quasispecies, which allow enhanced exploration of the adaptive

Sex speeds adaptation by altering the dynamics of molecular evolution.

Science.gov (United States)

McDonald, Michael J; Rice, Daniel P; Desai, Michael M

2016-03-10

Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations.

Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

Energy Technology Data Exchange (ETDEWEB)

Lang, Lin [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China); Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Tian, Zean; Xiao, Shifang [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Deng, Huiqiu, E-mail: hqdeng@hnu.edu.cn [Department of Applied Physics, School of Physics and Electronics, Hunan University, Changsha 410082 (China); Ao, Bingyun [Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang 621907 (China); Chen, Piheng, E-mail: chenpiheng@caep.cn [Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang 621907 (China); Hu, Wangyu [College of Materials Science and Engineering, Hunan University, Changsha 410082 (China)

2017-02-15

Highlights: • The structural evolution of Cu{sub 64.5}Zr{sub 35.5} MG under irradiation was studied. • The structure clusters were analyzed using the LSCA method. • Most of these radiation damages have been self-recovered quickly. - Abstract: Molecular dynamics simulations have been performed to investigate the structural evolution of Cu{sub 64.5}Zr{sub 35.5} metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

A review of the evolution of viviparity in squamate reptiles: the past, present and future role of molecular biology and genomics.

Science.gov (United States)

Murphy, Bridget F; Thompson, Michael B

2011-07-01

Squamate reptiles (lizards and snakes) offer a unique model system for testing hypotheses about the evolutionary transition from oviparity (egg-laying) to viviparity (live-bearing) in amniote vertebrates. The evolution of squamate viviparity has occurred remarkably frequently (>108 times) and has resulted in major changes in reproductive physiology. Such frequent changes in reproductive strategy pose two questions: (1) what are the molecular mechanisms responsible for the evolution of squamate viviparity? (2) Are these molecular mechanisms the same for separate origins of viviparity? Molecular approaches, such as RT-PCR, in situ hybridisation, Western blotting and immunofluorescence, have been invaluable for identifying genes and proteins that are involved in squamate placental development, materno-foetal immunotolerance, placental transport, placental angiogenesis, hormone synthesis and hormone receptor expression. However, the candidate-gene or -protein approach that has been used until now does not allow for de novo gene/protein discovery; results to date suggest that the reproductive physiologies of mammals and squamate reptiles are very similar, but this conclusion may simply be due to a limited capacity to study the subset of genes and proteins that are unique to reptiles. Progress has also been slowed by the lack of appropriate molecular and genomic resources for squamate reptiles. The advent of next-generation sequencing provides a relatively inexpensive way to conduct rapid high-throughput sequencing of genomes and transcriptomes. We discuss the potential use of next-generation sequencing technologies to analyse differences in gene expression between oviparous and viviparous squamates, provide important sequence information for reptiles, and generate testable hypotheses for the evolution of viviparity.

Patterns of molecular evolution of an avian neo-sex chromosome.

Science.gov (United States)

Pala, Irene; Hasselquist, Dennis; Bensch, Staffan; Hansson, Bengt

2012-12-01

Newer parts of sex chromosomes, neo-sex chromosomes, offer unique possibilities for studying gene degeneration and sequence evolution in response to loss of recombination and population size decrease. We have recently described a neo-sex chromosome system in Sylvioidea passerines that has resulted from a fusion between the first half (10 Mb) of chromosome 4a and the ancestral sex chromosomes. In this study, we report the results of molecular analyses of neo-Z and neo-W gametologs and intronic parts of neo-Z and autosomal genes on the second half of chromosome 4a in three species within different Sylvioidea lineages (Acrocephalidea, Timaliidae, and Alaudidae). In line with hypotheses of neo-sex chromosome evolution, we observe 1) lower genetic diversity of neo-Z genes compared with autosomal genes, 2) moderate synonymous and weak nonsynonymous sequence divergence between neo-Z and neo-W gametologs, and 3) lower GC content on neo-W than neo-Z gametologs. Phylogenetic reconstruction of eight neo-Z and neo-W gametologs suggests that recombination continued after the split of Alaudidae from the rest of the Sylvioidea lineages (i.e., after ~42.2 Ma) and with some exceptions also after the split of Acrocephalidea and Timaliidae (i.e., after ~39.4 Ma). The Sylvioidea neo-sex chromosome shares classical evolutionary features with the ancestral sex chromosomes but, as expected from its more recent origin, shows weaker divergence between gametologs.

THE GLOBAL EVOLUTION OF GIANT MOLECULAR CLOUDS. II. THE ROLE OF ACCRETION

International Nuclear Information System (INIS)

Goldbaum, Nathan J.; Krumholz, Mark R.; Matzner, Christopher D.; McKee, Christopher F.

2011-01-01

We present virial models for the global evolution of giant molecular clouds (GMCs). Focusing on the presence of an accretion flow and accounting for the amount of mass, momentum, and energy supplied by accretion and star formation feedback, we are able to follow the growth, evolution, and dispersal of individual GMCs. Our model clouds reproduce the scaling relations observed in both galactic and extragalactic clouds. We find that accretion and star formation contribute roughly equal amounts of turbulent kinetic energy over the lifetime of the cloud. Clouds attain virial equilibrium and grow in such a way as to maintain roughly constant surface densities, with typical surface densities of order 50-200 M sun pc -2 , in good agreement with observations of GMCs in the Milky Way and nearby external galaxies. We find that as clouds grow, their velocity dispersion and radius must also increase, implying that the linewidth-size relation constitutes an age sequence. Lastly, we compare our models to observations of GMCs and associated young star clusters in the Large Magellanic Cloud and find good agreement between our model clouds and the observed relationship between H II regions, young star clusters, and GMCs.

Molecular evolution and thermal adaptation

Science.gov (United States)

Chen, Peiqiu

2011-12-01

In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

The evolution of advanced molecular diagnostics for the detection and characterization of Mycoplasma pneumoniae

Directory of Open Access Journals (Sweden)

Maureen H. Diaz

2016-03-01

Full Text Available Over the past several years there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis and sequencing typing (MLVA and MLST, respectively, matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS, single nucleotide polymorphism (SNP typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

Molecular musings in microbial ecology and evolution.

Science.gov (United States)

Case, Rebecca J; Boucher, Yan

2011-11-10

A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies

Si Incorporation in InP Nanowires Grown by Au-Assisted Molecular Beam Epitaxy

Directory of Open Access Journals (Sweden)

Lorenzo Rigutti

2009-01-01

Full Text Available We report on the growth, structural characterization, and conductivity studies of Si-doped InP nanowires grown by Au-assisted molecular beam epitaxy. It is shown that Si doping reduces the mean diffusion length of adatoms on the lateral nanowire surface and consequently reduces the nanowire growth rate and promotes lateral growth. A resistivity as low as 5.1±0.3×10−5 Ω⋅cm is measured for highly doped nanowires. Two dopant incorporation mechanisms are discussed: incorporation via catalyst particle and direct incorporation on the nanowire sidewalls. The first mechanism is shown to be less efficient than the second one, resulting in inhomogeneous radial dopant distribution.

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.

Science.gov (United States)

Pazos, Florencio; Chagoyen, Monica

2018-01-16

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Phase evolution and mechanical behavior of 0.36 wt% C high strength TRIP-assisted steel

Energy Technology Data Exchange (ETDEWEB)

Ghosh, Swarup Kumar; Chattopadhyay, Partha Protim [Department of Metallurgy and Materials Engineering, Bengal Engineering and Science University, Shibpur, Howrah 711 103 (India)

2012-12-15

Phase evolution in a 0.36 wt% C steel has been studied by thermodynamic calculation and dilatometric analysis with an aim to achieve high strength TRIP-assisted steel with bainitic microstructure. The equilibrium phase fraction calculated as the function of temperature indicated the formation of {delta}-ferrite ({approx}98%) at 1417 C. In contrast, similar calculation under para-equilibrium condition exhibited transformation of {delta}-ferrite to austenite at the temperature below 1300 C. During further cooling two-phase ({alpha}+{gamma}) microstructure has been found to be stable at the intercritical temperature range. The experimentally determined CCT diagram has revealed that adequate hardenability is achievable in the steel under continuous cooling condition at cooling rate >5 C s{sup -1}. In view of the aforesaid results, the steel has been hot rolled and subjected to different process schedule conducive to the evolution of bainitic microstructure. The hot rolled steel has exhibited reasonably good tensile properties. However, cold deformation of the hot rolled sample followed by intercritical annealing and subsequent isothermal bainitic transformation has resulted in high strength (>1000 MPa) with attractive elongation due to the favorable work hardening condition during plastic deformation offered by the multiphase microstructure. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Growth of thin films of low molecular weight proteins by matrix assisted pulsed laser evaporation (MAPLE)

DEFF Research Database (Denmark)

Matei, Andreea; Schou, Jørgen; Constantinescu, C.

2011-01-01

Thin films of lysozyme and myoglobin grown by matrix assisted pulsed laser evaporation (MAPLE) from a water ice matrix have been investigated. The deposition rate of these two low molecular weight proteins (lysozyme: 14307 amu and myoglobin: 17083 amu) exhibits a maximum of about 1–2 ng/cm2 per....... The results for lysozyme demonstrate that the fragmentation rate of the proteins during the MAPLE process is not influenced by the pH of the water solution prior to freezing....

Laser-assisted fabrication of materials

CERN Document Server

Manna, Indranil

2013-01-01

Laser assisted fabrication involves shaping of materials using laser as a source of heat. It can be achieved by removal of materials (laser assisted cutting, drilling, etc.), deformation (bending, extrusion), joining (welding, soldering) and addition of materials (surface cladding or direct laser cladding). This book on ´Laser assisted Fabrication’ is aimed at developing in-depth engineering concepts on various laser assisted macro and micro-fabrication techniques with the focus on application and a review of the engineering background of different micro/macro-fabrication techniques, thermal history of the treated zone and microstructural development and evolution of properties of the treated zone.

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

Science.gov (United States)

Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

2011-07-01

Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Science.gov (United States)

Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

2011-01-01

Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing. PMID:21646336

Surface Functionalization of g-C 3 N 4 : Molecular-Level Design of Noble-Metal-Free Hydrogen Evolution Photocatalysts

KAUST Repository

Chen, Yin

2015-06-12

A stable noble-metal-free hydrogen evolution photocatalyst based on graphite carbon nitride (g-C3N4) was developed by a molecular-level design strategy. Surface functionalization was successfully conducted to introduce a single nickel active site onto the surface of the semiconducting g-C3N4. This catalyst family (with less than 0.1 wt% of Ni) has been found to produce hydrogen with a rate near to the value obtained by using 3 wt% platinum as co-catalyst. This new catalyst also exhibits very good stability under hydrogen evolution conditions, without any evidence of deactivation after 24h. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clinical application of a microfluidic chip for immunocapture and quantification of circulating exosomes to assist breast cancer diagnosis and molecular classification.

Science.gov (United States)

Fang, Shimeng; Tian, Hongzhu; Li, Xiancheng; Jin, Dong; Li, Xiaojie; Kong, Jing; Yang, Chun; Yang, Xuesong; Lu, Yao; Luo, Yong; Lin, Bingcheng; Niu, Weidong; Liu, Tingjiao

2017-01-01

Increasing attention has been attracted by exosomes in blood-based diagnosis because cancer cells release more exosomes in serum than normal cells and these exosomes overexpress a certain number of cancer-related biomarkers. However, capture and biomarker analysis of exosomes for clinical application are technically challenging. In this study, we developed a microfluidic chip for immunocapture and quantification of circulating exosomes from small sample volume and applied this device in clinical study. Circulating EpCAM-positive exosomes were measured in 6 cases breast cancer patients and 3 healthy controls to assist diagnosis. A significant increase in the EpCAM-positive exosome level in these patients was detected, compared to healthy controls. Furthermore, we quantified circulating HER2-positive exosomes in 19 cases of breast cancer patients for molecular classification. We demonstrated that the exosomal HER2 expression levels were almost consistent with that in tumor tissues assessed by immunohistochemical staining. The microfluidic chip might provide a new platform to assist breast cancer diagnosis and molecular classification.

Mechanochemical Ring-Opening Polymerization of Lactide: Liquid-Assisted Grinding for the Green Synthesis of Poly(lactic acid) with High Molecular Weight.

Science.gov (United States)

Ohn, Nuri; Shin, Jihoon; Kim, Sung Sik; Kim, Jeung Gon

2017-09-22

Mechanochemical polymerization of lactide is carried out by using ball milling. Mechanical energy from collisions between the balls and the vessel efficiently promotes an organic-base-mediated metal- and solvent-free solid-state polymerization. Investigation of the parameters of the ball-milling synthesis revealed that the degree of lactide ring-opening polymerization could be modulated by the ball-milling time, vibration frequency, mass of the ball media, and liquid-assisted grinding. Liquid-assisted grinding was found to be an especially important factor for achieving a high degree of mechanochemical polymerization. Although polymer-chain scission from the strong collision energy prevented mechanical-force-driven high-molecular-weight polymer synthesis, the addition of only a small amount of liquid enabled sufficient energy dissipation and poly(lactic acid) was thereby obtained with a molecular weight of over 1×10 5  g mol -1 . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Instant Update: Considering the Molecular Mechanisms of Mutation & Natural Selection

Science.gov (United States)

Hubler, Tina; Adams, Patti; Scammell, Jonathan

2015-01-01

The molecular basis of evolution is an important concept to understand but one that students and teachers often find challenging. This article provides training and guidance for teachers on how to present molecular evolution concepts so that students will associate molecular changes with the evolution of form and function in organisms. Included…

Robotic instrumentation: Evolution and microsurgical applications

Directory of Open Access Journals (Sweden)

Sijo J Parekattil

2010-01-01

Full Text Available This article presents a review of the history and evolution of robotic instrumentation and its applications in urology. A timeline for the evolution of robotic instrumentation is presented to better facilitate an understanding of our current-day applications. Some new directions including robotic microsurgical applications (robotic assisted denervation of the spermatic cord for chronic orchialgia and robotic assisted vasectomy reversal are presented. There is a paucity of prospective comparative effectiveness studies for a number of robotic applications. However, right or wrong, human nature has always led to our infatuation with the concept of using tools to meet our needs. This chapter is a brief tribute to where we have come from and where we may be potentially heading in the field of robotic assisted urologic surgery.

Molecular evolution of the reactive oxygen-generating NADPH oxidase (Nox/Duox family of enzymes

Directory of Open Access Journals (Sweden)

Lambeth J David

2007-07-01

Full Text Available Abstract Background NADPH-oxidases (Nox and the related Dual oxidases (Duox play varied biological and pathological roles via regulated generation of reactive oxygen species (ROS. Members of the Nox/Duox family have been identified in a wide variety of organisms, including mammals, nematodes, fruit fly, green plants, fungi, and slime molds; however, little is known about the molecular evolutionary history of these enzymes. Results We assembled and analyzed the deduced amino acid sequences of 101 Nox/Duox orthologs from 25 species, including vertebrates, urochordates, echinoderms, insects, nematodes, fungi, slime mold amoeba, alga and plants. In contrast to ROS defense enzymes, such as superoxide dismutase and catalase that are present in prokaryotes, ROS-generating Nox/Duox orthologs only appeared later in evolution. Molecular taxonomy revealed seven distinct subfamilies of Noxes and Duoxes. The calcium-regulated orthologs representing 4 subfamilies diverged early and are the most widely distributed in biology. Subunit-regulated Noxes represent a second major subdivision, and appeared first in fungi and amoeba. Nox5 was lost in rodents, and Nox3, which functions in the inner ear in gravity perception, emerged the most recently, corresponding to full-time adaptation of vertebrates to land. The sea urchin Strongylocentrotus purpuratus possesses the earliest Nox2 co-ortholog of vertebrate Nox1, 2, and 3, while Nox4 first appeared somewhat later in urochordates. Comparison of evolutionary substitution rates demonstrates that Nox2, the regulatory subunits p47phox and p67phox, and Duox are more stringently conserved in vertebrates than other Noxes and Nox regulatory subunits. Amino acid sequence comparisons identified key catalytic or regulatory regions, as 68 residues were highly conserved among all Nox/Duox orthologs, and 14 of these were identical with those mutated in Nox2 in variants of X-linked chronic granulomatous disease. In addition to

Peptidylation for the determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Science.gov (United States)

Tang, Feng; Cen, Si-Ying; He, Huan; Liu, Yi; Yuan, Bi-Feng; Feng, Yu-Qi

2016-05-23

Determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been a great challenge in the analytical research field. Here we developed a universal peptide-based derivatization (peptidylation) strategy for the sensitive analysis of low-molecular-weight compounds by MALDI-TOF-MS. Upon peptidylation, the molecular weights of target analytes increase, thus avoiding serious matrix ion interference in the low-molecular-weight region in MALDI-TOF-MS. Since peptides typically exhibit good signal response during MALDI-TOF-MS analysis, peptidylation endows high detection sensitivities of low-molecular-weight analytes. As a proof-of-concept, we analyzed low-molecular-weight compounds of aldehydes and thiols by the developed peptidylation strategy. Our results showed that aldehydes and thiols can be readily determined upon peptidylation, thus realizing the sensitive and efficient determination of low-molecular-weight compounds by MALDI-TOF-MS. Moreover, target analytes also can be unambiguously detected in biological samples using the peptidylation strategy. The established peptidylation strategy is a universal strategy and can be extended to the sensitive analysis of various low-molecular-weight compounds by MALDI-TOF-MS, which may be potentially used in areas such as metabolomics.

Phylogenomic Insights into Animal Evolution.

Science.gov (United States)

Telford, Maximilian J; Budd, Graham E; Philippe, Hervé

2015-10-05

Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage point as members of the animal kingdom, the evolution of the bewildering diversity of animal forms is endlessly fascinating. In the century following the publication of Darwin's Origin of Species, hypotheses regarding the evolution of the major branches of the animal kingdom - their relationships to each other and the evolution of their body plans - was based on a consideration of the morphological and developmental characteristics of the different animal groups. This morphology-based approach had many successes but important aspects of the evolutionary tree remained disputed. In the past three decades, molecular data, most obviously primary sequences of DNA and proteins, have provided an estimate of animal phylogeny largely independent of the morphological evolution we would ultimately like to understand. The molecular tree that has evolved over the past three decades has drastically altered our view of animal phylogeny and many aspects of the tree are no longer contentious. The focus of molecular studies on relationships between animal groups means, however, that the discipline has become somewhat divorced from the underlying biology and from the morphological characteristics whose evolution we aim to understand. Here, we consider what we currently know of animal phylogeny; what aspects we are still uncertain about and what our improved understanding of animal phylogeny can tell us about the evolution of the great diversity of animal life. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular basis for convergent evolution of glutamate recognition by pentameric ligand-gated ion channels

DEFF Research Database (Denmark)

Lynagh, Timothy; Beech, Robin N.; Lalande, Maryline J.

2015-01-01

that glutamate recognition requires an arginine residue in the base of the binding site, which originated at least three distinct times according to phylogenetic analysis. Most remarkably, the arginine emerged on the principal face of the binding site in the Lophotrochozoan lineage, but 65 amino acids upstream......Glutamate is an indispensable neurotransmitter, triggering postsynaptic signals upon recognition by postsynaptic receptors. We questioned the phylogenetic position and the molecular details of when and where glutamate recognition arose in the glutamate-gated chloride channels. Experiments revealed......, on the complementary face, in the Ecdysozoan lineage. This combined experimental and computational approach throws new light on the evolution of synaptic signalling....

Evolution of complex organic molecules in hot molecular cores. Synthetic spectra at (sub-)mm wavebands

Science.gov (United States)

Choudhury, R.; Schilke, P.; Stéphan, G.; Bergin, E.; Möller, T.; Schmiedeke, A.; Zernickel, A.

2015-03-01

Context. Hot molecular cores (HMCs) are intermediate stages of high-mass star formation and are also known for their rich chemical reservoirs and emission line spectra at (sub-)mm wavebands. Complex organic molecules (COMs) such as methanol (CH3OH), ethanol (C2H5OH), dimethyl ether (CH3OCH3), and methyl formate (HCOOCH3) produce most of these observed lines. The observed spectral feature of HMCs such as total number of emission lines and associated line intensities are also found to vary with evolutionary stages. Aims: We aim to investigate the spectral evolution of these COMs to explore the initial evolutionary stages of high-mass star formation including HMCs. Methods: We developed various 3D models for HMCs guided by the evolutionary scenarios proposed by recent empirical and modeling studies. We then investigated the spatio-temporal variation of temperature and molecular abundances in HMCs by consistently coupling gas-grain chemical evolution with radiative transfer calculations. We explored the effects of varying physical conditions on molecular abundances including density distribution and luminosity evolution of the central protostar(s) among other parameters. Finally, we simulated the synthetic spectra for these models at different evolutionary timescales to compare with observations. Results: Temperature has a profound effect on the formation of COMs through the depletion and diffusion on grain surface to desorption and further gas-phase processing. The time-dependent temperature structure of the hot core models provides a realistic framework for investigating the spatial variation of ice mantle evaporation as a function of evolutionary timescales. We find that a slightly higher value (15 K) than the canonical dark cloud temperature (10 K) provides a more productive environment for COM formation on grain surface. With increasing protostellar luminosity, the water ice evaporation font (~100 K) expands and the spatial distribution of gas phase abundances of

Evolution of the outflow activity of protostars

International Nuclear Information System (INIS)

Bontemps, Sylvain

1996-01-01

After a first part describing the formation of low-mass stars (sites of stellar formation, protostellar evolution) and matter outflows from young objects (molecular flows and their origin, optical and radio jets, outflow mechanisms), this research thesis discusses the evolution of molecular flows by reprinting a published article (Evolution of outflow activity around low-mass embedded young stellar objects), and by outlining some remaining issues (differences between clouds of stellar formation, morphological evolution of molecular flows). The author then discusses the continuous radio centimetre emission: origin, systematic search for Class 0 objects by using the VLA (Very Large Array radio interferometer), presentation of a new Class 0 protostar (HH24MMS). The author reports the study of H_2 emission in the infrared: generalities on protostellar shocks, infrared jet by HH24MMS, H_2 emission at 10 microns by using the ISOCAM camera [fr

Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi

Directory of Open Access Journals (Sweden)

LaMunyon Craig W

2009-01-01

Full Text Available Abstract Background As exemplified by the famously successful model organism Caenorhabditis elegans, nematodes offer outstanding animal systems for investigating diverse biological phenomena due to their small genome sizes, short generation times and ease of laboratory maintenance. Nematodes in the genus Panagrolaimus have served in comparative development and anhydrobiosis studies, and the Antarctic species P. davidi offers a powerful paradigm for understanding the biological mechanisms of extreme cold tolerance. Panagrolaimus nematodes are also unique in that examples of gonochoristic, hermaphroditic and parthenogenetic reproductive modes have been reported for members of this genus. The evolutionary origins of these varying reproductive modes and the Antarctic species P. davidi, however, remain enigmatic. Results We collected nuclear ribosomal RNA gene and mitochondrial protein-coding gene sequences from diverse Panagrolaimus species and strains, including newly discovered isolates from Oregon, to investigate phylogenetic relationships in this nematode genus. Nuclear phylogenies showed that the species and strains historically identified as members of Panagrolaimus constitute a paraphyletic group, suggesting that taxonomic revision is required for Panagrolaimus and related nematode lineages. Strain-specific reproductive modes were mapped onto the molecular phylogeny to show a single origin of parthenogenesis from a presumably gonochoristic ancestor. The hermaphroditic strains were all placed outside a major monophyletic clade that contained the majority of other Panagrolaimus nematodes. Phylogenetic analyses of mitochondrial sequences showed that substantial molecular and geographic diversity exists within the clade of parthenogenetic strains. The Antarctic species P. davidi was found to be very closely related to two Panagrolaimus strains from southern California. Phylogenetic and molecular clock analyses suggested that P. davidi and the

Molecular Evolution of the Infrared Sensory Gene TRPA1 in Snakes and Implications for Functional Studies

Science.gov (United States)

Jiang, Ke; Zhang, Peng

2011-01-01

TRPA1 is a calcium ion channel protein recently identified as the infrared receptor in pit organ-containing snakes. Therefore, understanding the molecular evolution of TRPA1 may help to illuminate the origin of “heat vision” in snakes and reveal the molecular mechanism of infrared sensitivity for TRPA1. To this end, we sequenced the infrared sensory gene TRPA1 in 24 snake species, representing nine snake families and multiple non-snake outgroups. We found that TRPA1 is under strong positive selection in the pit-bearing snakes studied, but not in other non-pit snakes and non-snake vertebrates. As a comparison, TRPV1, a gene closely related to TRPA1, was found to be under strong purifying selection in all the species studied, with no difference in the strength of selection between pit-bearing snakes and non-pit snakes. This finding demonstrates that the adaptive evolution of TRPA1 specifically occurred within the pit-bearing snakes and may be related to the functional modification for detecting infrared radiation. In addition, by comparing the TRPA1 protein sequences, we identified 11 amino acid sites that were diverged in pit-bearing snakes but conserved in non-pit snakes and other vertebrates, 21 sites that were diverged only within pit-vipers but conserved in the remaining snakes. These specific amino acid substitutions may be potentially functional important for infrared sensing. PMID:22163322

Evolutionary molecular medicine.

Science.gov (United States)

Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

2012-05-01

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

ALMA SPECTROSCOPIC SURVEY IN THE HUBBLE ULTRA DEEP FIELD: CO LUMINOSITY FUNCTIONS AND THE EVOLUTION OF THE COSMIC DENSITY OF MOLECULAR GAS

Energy Technology Data Exchange (ETDEWEB)

Decarli, Roberto; Walter, Fabian [Max-Planck Institut für Astronomie, Königstuhl 17, D-69117, Heidelberg (Germany); Aravena, Manuel; Assef, Roberto J. [Núcleo de Astronomía, Facultad de Ingeniería, Universidad Diego Portales, Av. Ejército 441, Santiago (Chile); Carilli, Chris [National Radio Astronomy Observatory, Pete V. Domenici Array Science Center, P.O. Box O, Socorro, NM 87801 (United States); Bouwens, Rychard [Leiden Observatory, Leiden University, P.O. Box 9513, NL2300 RA Leiden (Netherlands); Da Cunha, Elisabete [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, Victoria 3122 (Australia); Daddi, Emanuele [Laboratoire AIM, CEA/DSM-CNRS-Université Paris Diderot, Irfu/Service d’Astrophysique, CEA Saclay, Orme des Merisiers, F-91191 Gif-sur-Yvette cedex (France); Ivison, R. J.; Popping, Gergö [European Southern Observatory, Karl-Schwarzschild-Strasse 2, D-85748, Garching (Germany); Riechers, Dominik [Cornell University, 220 Space Sciences Building, Ithaca, NY 14853 (United States); Smail, Ian R. [6 Centre for Extragalactic Astronomy, Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Swinbank, Mark [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-053121 Bonn (Germany); Weiss, Axel; Anguita, Timo, E-mail: decarli@mpia.de [Departamento de Ciencias Físicas, Universidad Andres Bello, Fernandez Concha 700, Las Condes, Santiago (Chile); and others

2016-12-10

In this paper we use ASPECS, the ALMA Spectroscopic Survey in the Hubble Ultra Deep Field in band 3 and band 6, to place blind constraints on the CO luminosity function and the evolution of the cosmic molecular gas density as a function of redshift up to z  ∼ 4.5. This study is based on galaxies that have been selected solely through their CO emission and not through any other property. In all of the redshift bins the ASPECS measurements reach the predicted “knee” of the CO luminosity function (around 5 × 10{sup 9} K km s{sup −1} pc{sup 2}). We find clear evidence of an evolution in the CO luminosity function with respect to z  ∼ 0, with more CO-luminous galaxies present at z  ∼ 2. The observed galaxies at z  ∼ 2 also appear more gas-rich than predicted by recent semi-analytical models. The comoving cosmic molecular gas density within galaxies as a function of redshift shows a drop by a factor of 3–10 from z  ∼ 2 to z  ∼ 0 (with significant error bars), and possibly a decline at z  > 3. This trend is similar to the observed evolution of the cosmic star formation rate density. The latter therefore appears to be at least partly driven by the increased availability of molecular gas reservoirs at the peak of cosmic star formation ( z  ∼ 2).

Galaxy evolution in extreme environments: Molecular gas content star formation and AGN in isolated void galaxies

Science.gov (United States)

Das, Mousumi; Iono, Daisuke; Saito, Toshiki; Subramanian, Smitha

Since the early redshift surveys of the large scale structure of our universe, it has become clear that galaxies cluster along walls, sheet and filaments leaving large, empty regions called voids between them. Although voids represent the most under dense parts of our universe, they do contain a sparse but significant population of isolated galaxies that are generally low luminosity, late type disk galaxies. Recent studies show that most void galaxies have ongoing star formation and are in an early stage of evolution. We present radio, optical studies of the molecular gas content and star formation in a sample of void galaxies. Using SDSS data, we find that AGN are rare in these systems and are found only in the Bootes void; their black hole masses and radio properties are similar to bright spirals galaxies. Our studies suggest that close galaxy interactions and gas accretion are the main drivers of galaxy evolution in these systems despite their location in the underdense environment of the voids.

Star formation in evolving molecular clouds

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Völschow, M.; Banerjee, R.; Körtgen, B.

2017-09-01

Molecular clouds are the principle stellar nurseries of our universe; they thus remain a focus of both observational and theoretical studies. From observations, some of the key properties of molecular clouds are well known but many questions regarding their evolution and star formation activity remain open. While numerical simulations feature a large number and complexity of involved physical processes, this plethora of effects may hide the fundamentals that determine the evolution of molecular clouds and enable the formation of stars. Purely analytical models, on the other hand, tend to suffer from rough approximations or a lack of completeness, limiting their predictive power. In this paper, we present a model that incorporates central concepts of astrophysics as well as reliable results from recent simulations of molecular clouds and their evolutionary paths. Based on that, we construct a self-consistent semi-analytical framework that describes the formation, evolution, and star formation activity of molecular clouds, including a number of feedback effects to account for the complex processes inside those objects. The final equation system is solved numerically but at much lower computational expense than, for example, hydrodynamical descriptions of comparable systems. The model presented in this paper agrees well with a broad range of observational results, showing that molecular cloud evolution can be understood as an interplay between accretion, global collapse, star formation, and stellar feedback.

Molecular corridors and parameterizations of volatility in the chemical evolution of organic aerosols

Directory of Open Access Journals (Sweden)

Y. Li

2016-03-01

Full Text Available The formation and aging of organic aerosols (OA proceed through multiple steps of chemical reaction and mass transport in the gas and particle phases, which is challenging for the interpretation of field measurements and laboratory experiments as well as accurate representation of OA evolution in atmospheric aerosol models. Based on data from over 30 000 compounds, we show that organic compounds with a wide variety of functional groups fall into molecular corridors, characterized by a tight inverse correlation between molar mass and volatility. We developed parameterizations to predict the saturation mass concentration of organic compounds containing oxygen, nitrogen, and sulfur from the elemental composition that can be measured by soft-ionization high-resolution mass spectrometry. Field measurement data from new particle formation events, biomass burning, cloud/fog processing, and indoor environments were mapped into molecular corridors to characterize the chemical nature of the observed OA components. We found that less-oxidized indoor OA are constrained to a corridor of low molar mass and high volatility, whereas highly oxygenated compounds in atmospheric water extend to high molar mass and low volatility. Among the nitrogen- and sulfur-containing compounds identified in atmospheric aerosols, amines tend to exhibit low molar mass and high volatility, whereas organonitrates and organosulfates follow high O : C corridors extending to high molar mass and low volatility. We suggest that the consideration of molar mass and molecular corridors can help to constrain volatility and particle-phase state in the modeling of OA particularly for nitrogen- and sulfur-containing compounds.

Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO2-H2O systems.

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Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang

2014-01-28

In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π(*) orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2 (-) oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n](-) systems. Interestingly, hydration occurs not only on the O atoms of the core CO2 (-) through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2 (-) anion in the first hydration shell is about 4∼7. No dimer-core (C2O4 (-)) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.

Ga-assisted catalyst-free growth mechanism of GaAs nanowires by molecular beam epitaxy

International Nuclear Information System (INIS)

Colombo, C.; Spirkoska, D.; Frimmer, M.; Abstreiter, G.; Fontcuberta i Morral, A.

2008-01-01

The mechanisms of Ga-assisted GaAs nanowires grown by molecular beam epitaxy are addressed. The axial and radial growth rates as a function of the Ga rate and As pressure indicate that on the opposite of what is observed in thin film epitaxy, the growth rate of the nanowires is arsenic limited. As a consequence, the axial growth rate of the wires can be controlled by the As 4 pressure. Additionally, due to the small As 4 pressure leading to nanowire growth, the deposition on the facets is very slow, leading to a much lower radial growth rate. Finally, we present a model that is able to accurately describe the presented observations and predicts a maximum length of nontapered nanowires of 40 μm

Molecular beam epitaxy of GaAs nanowires and their sustainability for optoelectronic applications. Comparing Au- and self-assisted growth methods

Energy Technology Data Exchange (ETDEWEB)

Breuer, Steffen

2011-09-28

In this work the synthesis of GaAs nanowires by molecular beam epitaxy (MBE) using the vapour-liquid-solid (VLS) mechanism is investigated. A comparison between Au- and self-assisted VLS growth is at the centre of this thesis. While the Au-assisted method is established as a versatile tool for nanowire growth, the recently developed self-assisted variation results from the exchange of Au by Ga droplets and thus eliminates any possibility of Au incorporation. By both methods, we achieve nanowires with epitaxial alignment to the Si(111) substrates. Caused by differences during nanowire nucleation, a parasitic planar layer grows between the nanowires by the Au-assisted method, but can be avoided by the self-assisted method. Au-assisted nanowires grow predominantly in the metastable wurtzite crystal structure, while their self-assisted counterparts have the zincblende structure. All GaAs nanowires are fully relaxed and the strain arising from the lattice mismatch between GaAs and Si of 4.1 % is accommodated by misfit dislocations at the interface. Self-assisted GaAs nanowires are generally found to have vertical and non-polar side facets, while tilted and polar nanofacets were described for Au-assisted GaAs nanowires. We employ VLS nucleation theory to understand the effect of the droplet material on the lateral facets. Optoelectronic applications require long minority carrier lifetimes at room temperature. We fabricate GaAs/(Al,Ga)As core-shell nanowires and analyse them by transient photoluminescence (PL) spectroscopy. The results are 2.5 ns for the self-assisted nanowires as well as 9 ps for the Au-assisted nanowires. By temperature-dependent PL measurements we find a characteristic activation energy of 77 meV that is present only in the Au-assisted nanowires. We conclude that most likely Au is incorporated from the droplets into the GaAs nanowires and acts as a deep, non-radiative recombination centre.

Green's function-stochastic methods framework for probing nonlinear evolution problems: Burger's equation, the nonlinear Schroedinger's equation, and hydrodynamic organization of near-molecular-scale vorticity

International Nuclear Information System (INIS)

Keanini, R.G.

2011-01-01

Research highlights: → Systematic approach for physically probing nonlinear and random evolution problems. → Evolution of vortex sheets corresponds to evolution of an Ornstein-Uhlenbeck process. → Organization of near-molecular scale vorticity mediated by hydrodynamic modes. → Framework allows calculation of vorticity evolution within random strain fields. - Abstract: A framework which combines Green's function (GF) methods and techniques from the theory of stochastic processes is proposed for tackling nonlinear evolution problems. The framework, established by a series of easy-to-derive equivalences between Green's function and stochastic representative solutions of linear drift-diffusion problems, provides a flexible structure within which nonlinear evolution problems can be analyzed and physically probed. As a preliminary test bed, two canonical, nonlinear evolution problems - Burgers' equation and the nonlinear Schroedinger's equation - are first treated. In the first case, the framework provides a rigorous, probabilistic derivation of the well known Cole-Hopf ansatz. Likewise, in the second, the machinery allows systematic recovery of a known soliton solution. The framework is then applied to a fairly extensive exploration of physical features underlying evolution of randomly stretched and advected Burger's vortex sheets. Here, the governing vorticity equation corresponds to the Fokker-Planck equation of an Ornstein-Uhlenbeck process, a correspondence that motivates an investigation of sub-sheet vorticity evolution and organization. Under the assumption that weak hydrodynamic fluctuations organize disordered, near-molecular-scale, sub-sheet vorticity, it is shown that these modes consist of two weakly damped counter-propagating cross-sheet acoustic modes, a diffusive cross-sheet shear mode, and a diffusive cross-sheet entropy mode. Once a consistent picture of in-sheet vorticity evolution is established, a number of analytical results, describing the

Evolution of Vision

Science.gov (United States)

Ostrovsky, Mikhail

The evolution of photoreception, giving rise to eye, offers a kaleidoscopic view on selection acting at both the organ and molecular levels. The molecular level is mainly considered in the lecture. The greatest progress to date has been made in relation to the opsin visual pigments. Opsins appeared before eyes did. Two- and three-dimensional organization for rhodopsin in the rod outer segment disk membrane, as well as molecular mechanisms of visual pigments spectral tuning, photoisomerization and also opsin as a G-protein coupled receptor are considered. Molecular mechanisms of visual pigments spectral tuning, namely switching of chromophore (physiological time scale) and amino acid changes in the chromophore site of opsin (evolutionary time scale) is considered in the lecture. Photoisomerization of rhodopsin chromophore, 11-cis retinal is the only photochemical reaction in vision. The reaction is extemely fast (less that 200 fs) and high efficient (. is 0.65). The rhodopsin photolysis and kinetics of the earlier products appearance, photo- and bathorhodopsin, is considered. It is known that light is not only a carrier of information, but also a risk factor of damage to the eye. This photobiological paradox of vision is mainly due to the nature of rhodopsin chromophore. Photooxidation is the base of the paradox. All factors present in the phototrceptor cells to initiate free-radical photooxidation: photosensitizers, oxygen and substrates of oxidation: lipids and proteins (opsin). That is why photoprotective system of the eye structures appeared in the course of evolution. Three lines of protective system to prevent light damage to the retina and retina pigment epithelium is known: permanent renewal of rod and cone outer segment, powerful antioxidant system and optical media as cut-off filters where the lens is a key component. The molecular mechanisms of light damage to the eye and photoprotective system of the eye is considered in the lecture. The molecular

Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae).

Science.gov (United States)

Ritz, C M; Reiker, J; Charles, G; Hoxey, P; Hunt, D; Lowry, M; Stuppy, W; Taylor, N

2012-11-01

The cacti of tribe Tephrocacteae (Cactaceae-Opuntioideae) are adapted to diverse climatic conditions over a wide area of the southern Andes and adjacent lowlands. They exhibit a range of life forms from geophytes and cushion-plants to dwarf shrubs, shrubs or small trees. To confirm or challenge previous morphology-based classifications and molecular phylogenies, we sampled DNA sequences from the chloroplast trnK/matK region and the nuclear low copy gene phyC and compared the resulting phylogenies with previous data gathered from nuclear ribosomal DNA sequences. The here presented chloroplast and nuclear low copy gene phylogenies were mutually congruent and broadly coincident with the classification based on gross morphology and seed micro-morphology and anatomy. Reconstruction of hypothetical ancestral character states suggested that geophytes and cushion-forming species probably evolved several times from dwarf shrubby precursors. We also traced an increase of embryo size at the expense of the nucellus-derived storage tissue during the evolution of the Tephrocacteae, which is thought to be an evolutionary advantage because nutrients are then more rapidly accessible for the germinating embryo. In contrast to these highly concordant phylogenies, nuclear ribosomal DNA data sampled by a previous study yielded conflicting phylogenetic signals. Secondary structure predictions of ribosomal transcribed spacers suggested that this phylogeny is strongly influenced by the inclusion of paralogous sequence probably arisen by genome duplication during the evolution of this plant group. Copyright © 2012 Elsevier Inc. All rights reserved.

Stochastic evolution of refractory interstellar dust during the chemical evolution of a two-phase interstellar medium

International Nuclear Information System (INIS)

Liffman, K.; Clayton, D.D.

1989-01-01

The evolution course of refractory interstellar dust during the chemical evolution of a two-phase interstellar medium (ISM) is studied using a simple model of the chemical evolution of ISM. It is assumed that, in this medium, the stars are born in molecular clouds, but new nucleosynthesis products and stellar return are entered into a complementary diffuse medium; the well-mixed matter of each interstellar phase is repeatedly cycled stochastically through the complementary phase and back. The dust is studied on a particle-by-particle bases as it is sputtered by shock waves in the diffuse medium, accretes an amorphous mantle of gaseous refractory atoms while its local medium joins the molecular cloud medium, and encounters the possibility of astration within molecular clouds. Results are presented relevant to the size spectrum of accreted mantles, its age spectrum and the distinction among its several lifetimes, depletion factors of refractory atoms in the diffuse gas, and isotopic anomalies. 26 refs

Tin-Assisted Synthesis of ɛ -Ga2O3 by Molecular Beam Epitaxy

Science.gov (United States)

Kracht, M.; Karg, A.; Schörmann, J.; Weinhold, M.; Zink, D.; Michel, F.; Rohnke, M.; Schowalter, M.; Gerken, B.; Rosenauer, A.; Klar, P. J.; Janek, J.; Eickhoff, M.

2017-11-01

The synthesis of ɛ -Ga2O3 and β -Ga2O3 by plasma-assisted molecular beam epitaxy on (001 )Al2O3 substrates is studied. The growth window of β -Ga2O3 in the Ga-rich regime, usually limited by the formation of volatile gallium suboxide, is expanded due to the presence of tin during the growth process, which stabilizes the formation of gallium oxides. X-ray diffraction, transmission electron microscopy, time-of-flight secondary-ion mass spectrometry, Raman spectroscopy, and atomic force microscopy are used to analyze the influence of tin on the layer formation. We demonstrate that it allows the synthesis of phase-pure ɛ -Ga2O3 . A growth model based on the oxidation of gallium suboxide by reduction of an intermediate sacrificial tin oxide is suggested.

MOLECULAR CLOUD EVOLUTION. III. ACCRETION VERSUS STELLAR FEEDBACK

International Nuclear Information System (INIS)

Vazquez-Semadeni, Enrique; ColIn, Pedro; Gomez, Gilberto C.; Ballesteros-Paredes, Javier; Watson, Alan W.

2010-01-01

We numerically investigate the effect of feedback from the ionization heating from massive stars on the evolution of giant molecular clouds (GMCs) and their star formation efficiency (SFE), which we treat as an instantaneous, time-dependent quantity. We follow the GMCs' evolution from their formation to advanced star-forming stages. After an initial period of contraction, the collapsing clouds begin forming stars, whose feedback evaporates part of the clouds' mass, opposing the continuing accretion from the infalling gas. Our results are as follows: (1) in the presence of feedback, the clouds attain levels of the SFE that are consistent at all times with observational determinations for regions of comparable star formation rates. (2) However, the dense gas mass is larger in general in the presence of feedback, while the total mass (dense gas + stars) is nearly insensitive to the presence of feedback, suggesting that it is determined mainly by the accretion, while the feedback inhibits mainly the conversion of dense gas to stars, because it acts directly to reheat and disperse the gas that is directly on its way to forming stars. (3) The factor by which the SFE is reduced upon the inclusion of feedback is a decreasing function of the cloud's mass, for clouds of size ∼10 pc. This naturally explains the larger observed SFEs of massive-star-forming regions. (4) The clouds may attain a pseudo-virialized state, with a value of the virial mass very similar to the actual cloud mass. However, this state differs from true virialization in that the clouds, rather than being equilibrium entities, are the centers of a larger-scale collapse, in which accretion replenishes the mass consumed by star formation. (5) The higher-density regions within the clouds are in a similar situation, accreting gas infalling from the less-dense, more extended regions of the clouds. (6) The density probability density functions of the regions containing the clouds in general exhibit a shape

Protein Based Molecular Markers Provide Reliable Means to Understand Prokaryotic Phylogeny and Support Darwinian Mode of Evolution

Directory of Open Access Journals (Sweden)

Vaibhav eBhandari

2012-07-01

Full Text Available The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning whether the Darwinian model of evolution is applicable to the prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs and conserved signature proteins (CSPs for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical

Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.

Science.gov (United States)

Bhandari, Vaibhav; Naushad, Hafiz S; Gupta, Radhey S

2012-01-01

The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.

Molecular evolution of a chordate specific family of G protein-coupled receptors

Directory of Open Access Journals (Sweden)

Leese Florian

2011-08-01

Full Text Available Abstract Background Chordate evolution is a history of innovations that is marked by physical and behavioral specializations, which led to the development of a variety of forms from a single ancestral group. Among other important characteristics, vertebrates obtained a well developed brain, anterior sensory structures, a closed circulatory system and gills or lungs as blood oxygenation systems. The duplication of pre-existing genes had profound evolutionary implications for the developmental complexity in vertebrates, since mutations modifying the function of a duplicated protein can lead to novel functions, improving the evolutionary success. Results We analyzed here the evolution of the GPRC5 family of G protein-coupled receptors by comprehensive similarity searches and found that the receptors are only present in chordates and that the size of the receptor family expanded, likely due to genome duplication events in the early history of vertebrate evolution. We propose that a single GPRC5 receptor coding gene originated in a stem chordate ancestor and gave rise by duplication events to a gene family comprising three receptor types (GPRC5A-C in vertebrates, and a fourth homologue present only in mammals (GPRC5D. Additional duplications of GPRC5B and GPRC5C sequences occurred in teleost fishes. The finding that the expression patterns of the receptors are evolutionarily conserved indicates an important biological function of these receptors. Moreover, we found that expression of GPRC5B is regulated by vitamin A in vivo, confirming previous findings that linked receptor expression to retinoic acid levels in tumor cell lines and strengthening the link between the receptor expression and the development of a complex nervous system in chordates, known to be dependent on retinoic acid signaling. Conclusions GPRC5 receptors, a class of G protein-coupled receptors with unique sequence characteristics, may represent a molecular novelty that helped non

Molecular evolution of a Y chromosome to autosome gene duplication in Drosophila.

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Dyer, Kelly A; White, Brooke E; Bray, Michael J; Piqué, Daniel G; Betancourt, Andrea J

2011-03-01

In contrast to the rest of the genome, the Y chromosome is restricted to males and lacks recombination. As a result, Y chromosomes are unable to respond efficiently to selection, and newly formed Y chromosomes degenerate until few genes remain. The rapid loss of genes from newly formed Y chromosomes has been well studied, but gene loss from highly degenerate Y chromosomes has only recently received attention. Here, we identify and characterize a Y to autosome duplication of the male fertility gene kl-5 that occurred during the evolution of the testacea group species of Drosophila. The duplication was likely DNA based, as other Y-linked genes remain on the Y chromosome, the locations of introns are conserved, and expression analyses suggest that regulatory elements remain linked. Genetic mapping reveals that the autosomal copy of kl-5 resides on the dot chromosome, a tiny autosome with strongly suppressed recombination. Molecular evolutionary analyses show that autosomal copies of kl-5 have reduced polymorphism and little recombination. Importantly, the rate of protein evolution of kl-5 has increased significantly in lineages where it is on the dot versus Y linked. Further analyses suggest this pattern is a consequence of relaxed purifying selection, rather than adaptive evolution. Thus, although the initial fixation of the kl-5 duplication may have been advantageous, slightly deleterious mutations have accumulated in the dot-linked copies of kl-5 faster than in the Y-linked copies. Because the dot chromosome contains seven times more genes than the Y and is exposed to selection in both males and females, these results suggest that the dot suffers the deleterious effects of genetic linkage to more selective targets compared with the Y chromosome. Thus, a highly degenerate Y chromosome may not be the worst environment in the genome, as is generally thought, but may in fact be protected from the accumulation of deleterious mutations relative to other nonrecombining

Evolution and variation of multigene families

CERN Document Server

Ohta, Tomoko

1980-01-01

During the last decade and a half, studies of evolution and variation have been revolutionized by the introduction of the methods and concepts of molecular genetics. We can now construct reliable phylogenetic trees, even when fossil records are missing, by compara­ tive studies of protein or mRNA sequences. If, in addition, paleon­ tological information is available, we can estimate the rate at which genes are substituted in the species in the course of evolution. Through the application of electrophoretic methods, it has become possible to study intraspecific variation in molecular terms. We now know that an immense genetic variability exists in a sexually repro­ ducing species, and our human species is no exception. The mathematical theory of population genetics (particularly its stochastic aspects) in conjunction with these new developments led us to formulate the "neutral theory" of molecular evolution, pointing out that chance, in the form of random gene frequency drift, is playing a much more importa...

Molecular evolution of flavonoid dioxygenases in the family Apiaceae.

Science.gov (United States)

Gebhardt, Yvonne; Witte, Simone; Forkmann, Gert; Lukacin, Richard; Matern, Ulrich; Martens, Stefan

2005-06-01

Plant species of the family Apiaceae are known to accumulate flavonoids mainly in the form of flavones and flavonols. Three 2-oxoglutarate-dependent dioxygenases, flavone synthase or flavanone 3 beta-hydroxylase and flavonol synthase are involved in the biosynthesis of these secondary metabolites. The corresponding genes were cloned recently from parsley (Petroselinum crispum) leaves. Flavone synthase I appears to be confined to the Apiaceae, and the unique occurrence as well as its high sequence similarity to flavanone 3beta-hydroxylase laid the basis for evolutionary studies. In order to examine the relationship of these two enzymes throughout the Apiaceae, RT-PCR based cloning and functional identification of flavone synthases I or flavanone 3beta-hydroxylases were accomplished from Ammi majus, Anethum graveolens, Apium graveolens, Pimpinella anisum, Conium maculatum and Daucus carota, yielding three additional synthase and three additional hydroxylase cDNAs. Molecular and phylogenetic analyses of these sequences were compatible with the phylogeny based on morphological characteristics and suggested that flavone synthase I most likely resulted from gene duplication of flavanone 3beta-hydroxylase, and functional diversification at some point during the development of the apiaceae subfamilies. Furthermore, the genomic sequences from Petroselinum crispum and Daucus carota revealed two introns in each of the synthases and a lack of introns in the hydroxylases. These results might be explained by intron losses from the hydroxylases occurring at a later stage of evolution.

Evolution of dynamic susceptibility in molecular glass formers-a critical assessment

International Nuclear Information System (INIS)

Brodin, A; Gainaru, C; Porokhonskyy, V; Roessler, E A

2007-01-01

Dielectric, depolarized light scattering (LS) and optical Kerr effect (OKE) data are critically discussed in an attempt to achieve a common interpretation of the evolution of dynamic susceptibility in molecular glass formers at temperatures down to the glass transition T g . The so-called intermediate power-law, observed in OKE data below a certain temperature T x , is identified with the excess wing, long since known from dielectric spectroscopy, with a temperature-independent exponent. This is in contrast with several recent analyses that concluded a considerable temperature dependence of spectral shapes. We introduce a new approach to disentangle α-peak and excess wing contributions in the dielectric spectra, which allows for frequency-temperature superposition (FTS) of the α-process at all temperatures above T g . From the LS spectra we conclude, in particular, that FTS holds even at temperatures well above the melting point, i.e. in normal equilibrium liquids. Attempting to correlate the fragility and stretching, our conclusions are opposite to those made previously. Specifically, we observe that a high fragility is associated with a less stretched relaxation function

Molecular Epidemiology and Evolution of European Bat Lyssavirus 2

Science.gov (United States)

McElhinney, Lorraine M.; Zanoni, Reto; Kooi, Engbert A.; Neubauer-Juric, Antonie; Nokireki, Tiina; Müller, Thomas; Fooks, Anthony R.

2018-01-01

Bat rabies cases in Europe are mainly attributed to two lyssaviruses, namely European Bat Lyssavirus 1 (EBLV-1) and European Bat Lyssavirus 2 (EBLV-2). Prior to the death of a bat worker in Finland in 1985, very few bat rabies cases were reported. Enhanced surveillance in the two subsequent years (1986–1987) identified 263 cases (more than a fifth of all reported cases to date). Between 1977 and 2016, 1183 cases of bat rabies were reported, with the vast majority (>97%) being attributed to EBLV-1. In contrast, there have been only 39 suspected cases of EBLV-2, of which 34 have been confirmed by virus typing and presently restricted to just two bat species; Myotis daubentonii and Myotis dasycneme. The limited number of EBLV-2 cases in Europe prompted the establishment of a network of European reference laboratories to collate all available viruses and data. Despite the relatively low number of EBLV-2 cases, a large amount of anomalous data has been published in the scientific literature, which we have here reviewed and clarified. In this review, 29 EBLV-2 full genome sequences have been analysed to further our understanding of the diversity and molecular evolution of EBLV-2 in Europe. Analysis of the 29 complete EBLV-2 genome sequences clearly corroborated geographical relationships with all EBLV-2 sequences clustering at the country level irrespective of the gene studied. Further geographical clustering was also observed at a local level. There are high levels of homogeneity within the EBLV-2 species with nucleotide identities ranging from 95.5–100% and amino acid identities between 98.7% and 100%, despite the widespread distribution of the isolates both geographically and chronologically. The mean substitution rate for EBLV-2 across the five concatenated genes was 1.65 × 10−5, and evolutionary clock analysis confirms the slow evolution of EBLV-2 both between and within countries in Europe. This is further supported by the first detailed EBLV-2 intra

Molecular Epidemiology and Evolution of European Bat Lyssavirus 2

Directory of Open Access Journals (Sweden)

Lorraine M. McElhinney

2018-01-01

Full Text Available Bat rabies cases in Europe are mainly attributed to two lyssaviruses, namely European Bat Lyssavirus 1 (EBLV-1 and European Bat Lyssavirus 2 (EBLV-2. Prior to the death of a bat worker in Finland in 1985, very few bat rabies cases were reported. Enhanced surveillance in the two subsequent years (1986–1987 identified 263 cases (more than a fifth of all reported cases to date. Between 1977 and 2016, 1183 cases of bat rabies were reported, with the vast majority (>97% being attributed to EBLV-1. In contrast, there have been only 39 suspected cases of EBLV-2, of which 34 have been confirmed by virus typing and presently restricted to just two bat species; Myotis daubentonii and Myotis dasycneme. The limited number of EBLV-2 cases in Europe prompted the establishment of a network of European reference laboratories to collate all available viruses and data. Despite the relatively low number of EBLV-2 cases, a large amount of anomalous data has been published in the scientific literature, which we have here reviewed and clarified. In this review, 29 EBLV-2 full genome sequences have been analysed to further our understanding of the diversity and molecular evolution of EBLV-2 in Europe. Analysis of the 29 complete EBLV-2 genome sequences clearly corroborated geographical relationships with all EBLV-2 sequences clustering at the country level irrespective of the gene studied. Further geographical clustering was also observed at a local level. There are high levels of homogeneity within the EBLV-2 species with nucleotide identities ranging from 95.5–100% and amino acid identities between 98.7% and 100%, despite the widespread distribution of the isolates both geographically and chronologically. The mean substitution rate for EBLV-2 across the five concatenated genes was 1.65 × 10−5, and evolutionary clock analysis confirms the slow evolution of EBLV-2 both between and within countries in Europe. This is further supported by the first detailed EBLV

Molecular Epidemiology and Evolution of European Bat Lyssavirus 2.

Science.gov (United States)

McElhinney, Lorraine M; Marston, Denise A; Wise, Emma L; Freuling, Conrad M; Bourhy, Hervé; Zanoni, Reto; Moldal, Torfinn; Kooi, Engbert A; Neubauer-Juric, Antonie; Nokireki, Tiina; Müller, Thomas; Fooks, Anthony R

2018-01-05

Bat rabies cases in Europe are mainly attributed to two lyssaviruses, namely European Bat Lyssavirus 1 (EBLV-1) and European Bat Lyssavirus 2 (EBLV-2). Prior to the death of a bat worker in Finland in 1985, very few bat rabies cases were reported. Enhanced surveillance in the two subsequent years (1986-1987) identified 263 cases (more than a fifth of all reported cases to date). Between 1977 and 2016, 1183 cases of bat rabies were reported, with the vast majority (>97%) being attributed to EBLV-1. In contrast, there have been only 39 suspected cases of EBLV-2, of which 34 have been confirmed by virus typing and presently restricted to just two bat species; Myotis daubentonii and Myotis dasycneme . The limited number of EBLV-2 cases in Europe prompted the establishment of a network of European reference laboratories to collate all available viruses and data. Despite the relatively low number of EBLV-2 cases, a large amount of anomalous data has been published in the scientific literature, which we have here reviewed and clarified. In this review, 29 EBLV-2 full genome sequences have been analysed to further our understanding of the diversity and molecular evolution of EBLV-2 in Europe. Analysis of the 29 complete EBLV-2 genome sequences clearly corroborated geographical relationships with all EBLV-2 sequences clustering at the country level irrespective of the gene studied. Further geographical clustering was also observed at a local level. There are high levels of homogeneity within the EBLV-2 species with nucleotide identities ranging from 95.5-100% and amino acid identities between 98.7% and 100%, despite the widespread distribution of the isolates both geographically and chronologically. The mean substitution rate for EBLV-2 across the five concatenated genes was 1.65 × 10 -5 , and evolutionary clock analysis confirms the slow evolution of EBLV-2 both between and within countries in Europe. This is further supported by the first detailed EBLV-2 intra

Real time spectroscopic ellipsometry investigation of homoepitaxial GaN grown by plasma assisted molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Kim, Tong-Ho; Choi, Soojeong; Wu, Pae; Brown, April [Department of Electrical and Computer Engineering, Duke University, 128 Hudson Hall, Durham, NC (United States); Losurdo, Maria; Giangregorio, Maria M.; Bruno, Giovanni [Institute of Inorganic Methodologies and of Plasmas, IMIP-CNR and INSTM UdR Bari, via Orabona, 4, 70126 Bari (Italy); Moto, Akihiro [Innovation Core SEI, Inc., 3235 Kifer Road, Santa Clara, CA 95051 (United States)

2006-06-15

The growth of GaN by plasma assisted molecular beam epitaxy on GaN template substrates (GaN on sapphire) is investigated with in-situ multi-channel spectroscopic ellipsometry. Growth is performed under various Ga/N flux ratios at growth temperatures in the range 710-780 C. The thermal roughening of the GaN template caused by decomposition of the surface is investigated through the temporal variation of the GaN pseudodielectric function over the temperature range of 650 C to 850 C. The structural, morphological, and optical properties are also discussed. (copyright 2006 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Evolution of man in the light of molecular genetics: a review. Part I. Our evolutionary history and genomics.

Science.gov (United States)

Portin, Petter

2007-07-01

The discovery in the mid 1970s of efficient methods of DNA sequencing and their subsequent development into more and more rapid procedures followed by sequencing the genomes of many species, including man in 2001, revolutionised the whole of biology. Remarkably, new light could be cast on the evolutionary relations of different species, and the tempo and mode of evolution within a given species, notably man, could quantitatively be illuminated including ongoing evolution possibly involving also the size of the brains. This review is a short summary of the results of the molecular genetic investigations of human evolution including the time and place of the formation of our species, our evolutionary relation to the closest living species relatives as well as extinct forms of the genus Homo. The nature and amount of genetic polymorphism in man is also considered with special emphasis on the causes of this variation, and the role of natural selection in human evolution. A consensus about the mosaic nature of our genome and the rather dynamic structure of our ancestral population is gradually emerging. The modern gene pool has most likely been contributed to several different ancestral demes either before or after the emergence of the anatomically modern human phenotype in the extent that even the nature of the evolutionary lineage leading to the anatomically modern man as a distinct biological species is disputable. Regulation of the function of genes, as well as the evolution of brains will be dealt with in the second part of this review.

Explaining the luminosity spread in young clusters: proto and pre-main sequence stellar evolution in a molecular cloud environment

Science.gov (United States)

Jensen, Sigurd S.; Haugbølle, Troels

2018-02-01

Hertzsprung-Russell diagrams of star-forming regions show a large luminosity spread. This is incompatible with well-defined isochrones based on classic non-accreting protostellar evolution models. Protostars do not evolve in isolation of their environment, but grow through accretion of gas. In addition, while an age can be defined for a star-forming region, the ages of individual stars in the region will vary. We show how the combined effect of a protostellar age spread, a consequence of sustained star formation in the molecular cloud, and time-varying protostellar accretion for individual protostars can explain the observed luminosity spread. We use a global magnetohydrodynamic simulation including a sub-scale sink particle model of a star-forming region to follow the accretion process of each star. The accretion profiles are used to compute stellar evolution models for each star, incorporating a model of how the accretion energy is distributed to the disc, radiated away at the accretion shock, or incorporated into the outer layers of the protostar. Using a modelled cluster age of 5 Myr, we naturally reproduce the luminosity spread and find good agreement with observations of the Collinder 69 cluster, and the Orion Nebular Cluster. It is shown how stars in binary and multiple systems can be externally forced creating recurrent episodic accretion events. We find that in a realistic global molecular cloud model massive stars build up mass over relatively long time-scales. This leads to an important conceptual change compared to the classic picture of non-accreting stellar evolution segmented into low-mass Hayashi tracks and high-mass Henyey tracks.

Molecular and morphological systematics of the Ellisellidae (Coelenterata: Octocorallia): Parallel evolution in a globally distributed family of octocorals

KAUST Repository

Bilewitch, Jaret P.

2014-04-01

The octocorals of the Ellisellidae constitute a diverse and widely distributed family with subdivisions into genera based on colonial growth forms. Branching patterns are repeated in several genera and congeners often display region-specific variations in a given growth form. We examined the systematic patterns of ellisellid genera and the evolution of branching form diversity using molecular phylogenetic and ancestral morphological reconstructions. Six of eight included genera were found to be polyphyletic due to biogeographical incompatibility with current taxonomic assignments and the creation of at least six new genera plus several reassignments among existing genera is necessary. Phylogenetic patterns of diversification of colony branching morphology displayed a similar transformation order in each of the two primary ellisellid clades, with a sea fan form estimated as the most-probable common ancestor with likely origins in the Indo-Pacific region. The observed parallelism in evolution indicates the existence of a constraint on the genetic elements determining ellisellid colonial morphology. However, the lack of correspondence between levels of genetic divergence and morphological diversity among genera suggests that future octocoral studies should focus on the role of changes in gene regulation in the evolution of branching patterns. © 2014 Elsevier Inc.

Molecular and morphological systematics of the Ellisellidae (Coelenterata: Octocorallia): Parallel evolution in a globally distributed family of octocorals

KAUST Repository

Bilewitch, Jaret P.; Ekins, Merrick; Hooper, John; Degnan, Sandie M.

2014-01-01

The octocorals of the Ellisellidae constitute a diverse and widely distributed family with subdivisions into genera based on colonial growth forms. Branching patterns are repeated in several genera and congeners often display region-specific variations in a given growth form. We examined the systematic patterns of ellisellid genera and the evolution of branching form diversity using molecular phylogenetic and ancestral morphological reconstructions. Six of eight included genera were found to be polyphyletic due to biogeographical incompatibility with current taxonomic assignments and the creation of at least six new genera plus several reassignments among existing genera is necessary. Phylogenetic patterns of diversification of colony branching morphology displayed a similar transformation order in each of the two primary ellisellid clades, with a sea fan form estimated as the most-probable common ancestor with likely origins in the Indo-Pacific region. The observed parallelism in evolution indicates the existence of a constraint on the genetic elements determining ellisellid colonial morphology. However, the lack of correspondence between levels of genetic divergence and morphological diversity among genera suggests that future octocoral studies should focus on the role of changes in gene regulation in the evolution of branching patterns. © 2014 Elsevier Inc.

Molecular Population Genetics.

Science.gov (United States)

Casillas, Sònia; Barbadilla, Antonio

2017-03-01

Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

Science.gov (United States)

Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

2012-01-01

Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

Evolution. Teacher's Guide.

Science.gov (United States)

Bershad, Carol

This teacher's guide was developed to assist teachers in the use of multimedia resources for the Public Broadcasting System (PBS) program, "Evolution." Each unit uses an inquiry-based approach to meet the National Science Education Standards. Units include: (1) "What is the Nature of Science?"; (2) "Who Was Charles Darwin?"; (3) "What is the…

EVOLUTIONARY FOUNDATIONS FOR MOLECULAR MEDICINE

Science.gov (United States)

Nesse, Randolph M.; Ganten, Detlev; Gregory, T. Ryan; Omenn, Gilbert S.

2015-01-01

Evolution has long provided a foundation for population genetics, but many major advances in evolutionary biology from the 20th century are only now being applied in molecular medicine. They include the distinction between proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are further transforming evolutionary biology and creating yet more opportunities for progress at the interface of evolution with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and others to speed the development of evolutionary molecular medicine. PMID:22544168

Assisted stellar suicide: the wind-driven evolution of the recurrent nova T Pyxidis

Science.gov (United States)

Knigge, Ch.; King, A. R.; Patterson, J.

2000-12-01

We show that the extremely high luminosity of the short-period recurrent nova T Pyx in quiescence can be understood if this system is a wind-driven supersoft x-ray source (SSS). In this scenario, a strong, radiation-induced wind is excited from the secondary star and accelerates the binary evolution. The accretion rate is therefore much higher than in an ordinary cataclysmic binary at the same orbital period, as is the luminosity of the white dwarf primary. In the steady state, the enhanced luminosity is just sufficient to maintain the wind from the secondary. The accretion rate and luminosity predicted by the wind-driven model for T Pyx are in good agreement with the observational evidence. X-ray observations with Chandra or XMM may be able to confirm T Pyx's status as a SSS. T Pyx's lifetime in the wind-driven state is on the order of a million years. Its ultimate fate is not certain, but the system may very well end up destroying itself, either via the complete evaporation of the secondary star, or in a Type Ia supernova if the white dwarf reaches the Chandrasekhar limit. Thus either the primary, the secondary, or both may currently be committing assisted stellar suicide.

Genetic diversity and molecular evolution of Ornithogalum mosaic virus based on the coat protein gene sequence

Directory of Open Access Journals (Sweden)

Fangluan Gao

2018-03-01

Full Text Available Ornithogalum mosaic virus (OrMV has a wide host range and affects the production of a variety of ornamentals. In this study, the coat protein (CP gene of OrMVwas used to investigate the molecular mechanisms underlying the evolution of this virus. The 36 OrMV isolates fell into two groups which have significant subpopulation differentiation with an FST value of 0.470. One isolate was identified as a recombinant and the other 35 recombination-free isolates could be divided into two major clades under different evolutionary constraints with dN/dS values of 0.055 and 0.028, respectively, indicating a role of purifying selection in the differentiation of OrMV. In addition, the results from analysis of molecular variance (AMOVA indicated that the effect of host species on the genetic divergence of OrMV is greater than that of geography. Furthermore, OrMV isolates from the genera Ornithogalum, Lachenalia and Diuri tended to group together, indicating that OrMV diversification was maintained, in part, by host-driven adaptation.

Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process

OpenAIRE

Kishimoto, Toshihiko; Ying, Bei-Wen; Tsuru, Saburo; Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya

2015-01-01

The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution e...

Molecular Evolution at a Meiosis Gene Mediates Species Differences in the Rate and Patterning of Recombination.

Science.gov (United States)

Brand, Cara L; Cattani, M Victoria; Kingan, Sarah B; Landeen, Emily L; Presgraves, Daven C

2018-04-23

Crossing over between homologous chromosomes during meiosis repairs programmed DNA double-strand breaks, ensures proper segregation at meiosis I [1], shapes the genomic distribution of nucleotide variability in populations, and enhances the efficacy of natural selection among genetically linked sites [2]. Between closely related Drosophila species, large differences exist in the rate and chromosomal distribution of crossing over. Little, however, is known about the molecular genetic changes or population genetic forces that mediate evolved differences in recombination between species [3, 4]. Here, we show that a meiosis gene with a history of rapid evolution acts as a trans-acting modifier of species differences in crossing over. In transgenic flies, the dicistronic gene, mei-217/mei-218, recapitulates a large part of the species differences in the rate and chromosomal distribution of crossing over. These phenotypic differences appear to result from changes in protein sequence not gene expression. Our population genetics analyses show that the protein-coding sequence of mei-218, but not mei-217, has a history of recurrent positive natural selection. By modulating the intensity of centromeric and telomeric suppression of crossing over, evolution at mei-217/-218 has incidentally shaped gross differences in the chromosomal distribution of nucleotide variability between species. We speculate that recurrent bouts of adaptive evolution at mei-217/-218 might reflect a history of coevolution with selfish genetic elements. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evolution of the genus Aristolochia - Systematics, Molecular Evolution and Ecology

OpenAIRE

Wanke, Stefan

2007-01-01

Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (excep...

Molecular Evolution of Two Distinct dmrt1 Promoters for Germ and Somatic Cells in Vertebrate Gonads.

Science.gov (United States)

Mawaribuchi, Shuuji; Musashijima, Masato; Wada, Mikako; Izutsu, Yumi; Kurakata, Erina; Park, Min Kyun; Takamatsu, Nobuhiko; Ito, Michihiko

2017-03-01

The transcription factor DMRT1 has important functions in two distinct processes, somatic-cell masculinization and germ-cell development in mammals. However, it is unknown whether the functions are conserved during evolution, and what mechanism underlies its expression in the two cell lineages. Our analysis of the Xenopus laevis and Silurana tropicalis dmrt1 genes indicated the presence of two distinct promoters: one upstream of the noncoding first exon (ncEx1), and one within the first intron. In contrast, only the ncEx1-upstream promoter was detected in the dmrt1 gene of the agnathan sand lamprey, which expressed dmrt1 exclusively in the germ cells. In X. laevis, the ncEx1- and exon 2-upstream promoters were predominantly used for germ-cell and somatic-cell transcription, respectively. Importantly, knockdown of the ncEx1-containing transcript led to reduced germ-cell numbers in X. laevis gonads. Intriguingly, two genetically female individuals carrying the knockdown construct developed testicles. Analysis of the reptilian leopard gecko dmrt1 revealed the absence of ncEx1. We propose that dmrt1 regulated germ-cell development in the vertebrate ancestor, then acquired another promoter in its first intron to regulate somatic-cell masculinization during gnathostome evolution. In the common ancestor of reptiles and mammals, only one promoter got function for both the two cell lineages, accompanied with the loss of ncEx1. In addition, we found a conserved noncoding sequence (CNS) in the dmrt1 5'-flanking regions only among amniote species, and two CNSs in the introns among most vertebrates except for agnathans. Finally, we discuss relationships between these CNSs and the promoters of dmrt1 during vertebrate evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Second Symposium on Chemical Evolution and the Origin of Life

International Nuclear Information System (INIS)

Devincenzi, D.L.; Dufour, P.A.

1986-05-01

Recent findings by NASA Exobiology investigators are reported. Scientific papers are 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 and molecular epidemiology of classical swine fever virus during a multi-annual outbreak amongst European wild boar.

Science.gov (United States)

Goller, Katja V; Gabriel, Claudia; Dimna, Mireille Le; Le Potier, Marie-Frédérique; Rossi, Sophie; Staubach, Christoph; Merboth, Matthias; Beer, Martin; Blome, Sandra

2016-03-01

Classical swine fever is a viral disease of pigs that carries tremendous socio-economic impact. In outbreak situations, genetic typing is carried out for the purpose of molecular epidemiology in both domestic pigs and wild boar. These analyses are usually based on harmonized partial sequences. However, for high-resolution analyses towards the understanding of genetic variability and virus evolution, full-genome sequences are more appropriate. In this study, a unique set of representative virus strains was investigated that was collected during an outbreak in French free-ranging wild boar in the Vosges-du-Nord mountains between 2003 and 2007. Comparative sequence and evolutionary analyses of the nearly full-length sequences showed only slow evolution of classical swine fever virus strains over the years and no impact of vaccination on mutation rates. However, substitution rates varied amongst protein genes; furthermore, a spatial and temporal pattern could be observed whereby two separate clusters were formed that coincided with physical barriers.

Molecular evolution of rbcL in three gymnosperm families: identifying adaptive and coevolutionary patterns

LENUS (Irish Health Repository)

Sen, Lin

2011-06-03

mutations put forward the conclusion that this evolutionary scenario has been possible through a complex interplay between adaptive mutations, often structurally destabilizing, and compensatory mutations. Our results unearth patterns of evolution that have likely optimized the Rubisco activity and uncover mutational dynamics useful in the molecular engineering of enzymatic activities. Reviewers This article was reviewed by Prof. Christian Blouin (nominated by Dr W Ford Doolittle), Dr Endre Barta (nominated by Dr Sandor Pongor), and Dr Nicolas Galtier.

Molecular size evolution of oligomers in organic aerosols collected in urban atmospheres and generated in a smog chamber.

Science.gov (United States)

Kalberer, Markus; Sax, Mirjam; Samburova, Vera

2006-10-01

Only a minor fraction of the total organic aerosol mass can be resolved on a molecular level. High molecular weight compounds in organic aerosols have recently gained much attention because this class of compound potentially explains a major fraction of the unexplained organic aerosol mass. These compounds have been identified with different mass spectrometric methods, and compounds with molecular masses up to 1000 Da are found in secondary organic aerosols (SOA) generated from aromatic and terpene precursors in smog chamber experiments. Here, we apply matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to SOA particles from two biogenic precursors, alpha-pinene and isoprene. Similar oligomer patterns are found in these two SOA systems, but also in SOA from trimethylbenzene, an anthropogenic SOA precursor. However, different maxima molecular sizes were measured for these three SOA systems. While oligomers in alpha-pinene and isoprene have sizes mostly below 600-700 Da, they grow up to about 1000 Da in trimethylbenzene-SOA. The final molecular size of the oligomers is reached early during the particle aging process, whereas other particle properties related to aging, such as the overall acid concentration or the oligomer concentration, increase continuously over a much longer time scale. This kinetic behavior of the oligomer molecular size growth can be explained by a chain growth kinetic regime. Similar oligomer mass patterns were measured in aqueous extracts of ambient aerosol samples (measured with the same technique). Distinct differences between summer and winter were observed. In summer a few single mass peaks were measured with much higher intensity than in winter, pointing to a possible difference in the formation processes of these compounds in winter and summer.

Epitaxial growth of M-plane GaN on ZnO micro-rods by plasma-assisted molecular beam epitaxy

Directory of Open Access Journals (Sweden)

Shuo-Ting You

2015-12-01

Full Text Available We have studied the GaN grown on ZnO micro-rods by plasma-assisted molecular beam epitaxy. From the analyses of GaN microstructure grown on non-polar M-plane ZnO surface ( 10 1 ̄ 0 by scanning transmission electron microscope, we found that the ZnGa2O4 compound was formed at the M-plane hetero-interface, which was confirmed by polarization-dependent photoluminescence. We demonstrated that the M-plane ZnO micro-rod surface can be used as an alternative substrate to grow high quality M-plane GaN epi-layers.

Molecular HIV screening.

Science.gov (United States)

Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

2013-09-01

Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

GaN Schottky diodes with single-crystal aluminum barriers grown by plasma-assisted molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Tseng, H. Y.; Yang, W. C.; Lee, P. Y.; Lin, C. W.; Cheng, Kai-Yuan; Hsieh, K. C.; Cheng, K. Y., E-mail: kycheng@ee.nthu.edu.tw [Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Hsu, C.-H. [Division of Scientific Research, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan (China)

2016-08-22

GaN-based Schottky barrier diodes (SBDs) with single-crystal Al barriers grown by plasma-assisted molecular beam epitaxy are fabricated. Examined using in-situ reflection high-energy electron diffractions, ex-situ high-resolution x-ray diffractions, and high-resolution transmission electron microscopy, it is determined that epitaxial Al grows with its [111] axis coincident with the [0001] axis of the GaN substrate without rotation. In fabricated SBDs, a 0.2 V barrier height enhancement and 2 orders of magnitude reduction in leakage current are observed in single crystal Al/GaN SBDs compared to conventional thermal deposited Al/GaN SBDs. The strain induced piezoelectric field is determined to be the major source of the observed device performance enhancements.

Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L.

Science.gov (United States)

Yu, Guoqin; Olsen, Kenneth M; Schaal, Barbara A

2011-01-01

The evolution of metabolic pathways is a fundamental but poorly understood aspect of evolutionary change. One approach for understanding the complexity of pathway evolution is to examine the molecular evolution of genes that together comprise an integrated metabolic pathway. The rice endosperm starch biosynthetic pathway is one of the most thoroughly characterized metabolic pathways in plants, and starch is a trait that has evolved in response to strong selection during rice domestication. In this study, we have examined six key genes (AGPL2, AGPS2b, SSIIa, SBEIIb, GBSSI, ISA1) in the rice endosperm starch biosynthesis pathway to investigate the evolution of these genes before and after rice domestication. Genome-wide sequence tagged sites data were used as a neutral reference to overcome the problems of detecting selection in species with complex demographic histories such as rice. Five variety groups of Oryza sativa (aus, indica, tropical japonica, temperate japonica, aromatic) and its wild ancestor (O. rufipogon) were sampled. Our results showed evidence of purifying selection at AGPL2 in O. rufipogon and strong evidence of positive selection at GBSSI in temperate japonica and tropical japonica varieties and at GBSSI and SBEIIb in aromatic varieties. All the other genes showed a pattern consistent with neutral evolution in both cultivated rice and its wild ancestor. These results indicate the important role of positive selection in the evolution of starch genes during rice domestication. We discuss the role of SBEIIb and GBSSI in the evolution of starch quality during rice domestication and the power and limitation of detecting selection using genome-wide data as a neutral reference.

Structural Approaches to Sequence Evolution Molecules, Networks, Populations

CERN Document Server

Bastolla, Ugo; Roman, H. Eduardo; Vendruscolo, Michele

2007-01-01

Structural requirements constrain the evolution of biological entities at all levels, from macromolecules to their networks, right up to populations of biological organisms. Classical models of molecular evolution, however, are focused at the level of the symbols - the biological sequence - rather than that of their resulting structure. Now recent advances in understanding the thermodynamics of macromolecules, the topological properties of gene networks, the organization and mutation capabilities of genomes, and the structure of populations make it possible to incorporate these key elements into a broader and deeply interdisciplinary view of molecular evolution. This book gives an account of such a new approach, through clear tutorial contributions by leading scientists specializing in the different fields involved.

Molecular phylogenetic analysis of Commiphora (Burseraceae) yields insight on the evolution and historical biogeography of an "impossible" genus.

Science.gov (United States)

Weeks, Andrea; Simpson, Beryl B

2007-01-01

Expansion of the arid zone of sub-Saharan tropical Africa during the Miocene is posited as a significant contributing factor in the evolution of contemporary African flora. Nevertheless, few molecular phylogenetic studies have tested this hypothesis using reconstructed historical biogeographies of plants within this zone. Here, we present a molecular phylogeny of Commiphora, a predominantly tropical African, arid-adapted tree genus, in order to test the monophyly of its taxonomic sections and identify clades that will help direct future study of this species-rich and geographically widespread taxon. We then use multiple fossil calibrations of Commiphora phylogeny to determine the timing of well-supported diversification events within the genus and interpret these age estimates to determine the relative contribution of vicariance and dispersal in the expansion of Commiphora's geographic range. We find that Commiphora is sister to Vietnamese Bursera tonkinensis and that its crown group radiation corresponds with the onset of the Miocene.

Phylogenetic estimates of diversification rate are affected by molecular rate variation.

Science.gov (United States)

Duchêne, D A; Hua, X; Bromham, L

2017-10-01

Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Molecular evolution of the Li/li chemical defence polymorphism in white clover (Trifolium repens L.).

Science.gov (United States)

Olsen, K M; Sutherland, B L; Small, L L

2007-10-01

White clover (Trifolium repens) is naturally polymorphic for cyanogenesis (hydrogen cyanide release following tissue damage). The ecological factors favouring cyanogenic and acyanogenic plants have been examined in numerous studies over the last half century, making this one of the best-documented examples of an adaptive polymorphism in plants. White clover cyanogenesis is controlled by two, independently segregating Mendelian genes: Ac/ac controls the presence/absence of cyanogenic glucosides; and Li/li controls the presence/absence of their hydrolysing enzyme, linamarase. In this study, we examine the molecular evolution and population genetics of Li as it relates to the cyanogenesis polymorphism. We report here that Li exists as a single-copy gene in plants possessing linamarase activity, and that the absence of enzyme activity in li/li plants is correlated with the absence of much or all of the gene from the white clover genome. Consistent with this finding, we confirm by reverse transcription-polymerase chain reaction that Li gene expression is absent in plants lacking enzyme activity. In a molecular population genetic analysis of Li and three unlinked genes using a worldwide sample of clover plants, we find an absence of nucleotide variation and statistically significant deviations from neutrality at Li; these findings are consistent with recent positive directional selection at this cyanogenesis locus.

Molecular evolution of myoglobin in the Tibetan Plateau endemic schizothoracine fish (Cyprinidae, Teleostei) and tissue-specific expression changes under hypoxia.

Science.gov (United States)

Qi, Delin; Chao, Yan; Zhao, Yongli; Xia, Mingzhe; Wu, Rongrong

2018-04-01

Myoglobin (Mb) is an oxygen-binding hemoprotein that was once thought to be exclusively expressed in oxidative myocytes of skeletal and cardiac muscle where it serves in oxygen storage and facilitates intracellular oxygen diffusion. In this study, we cloned the coding sequence of the Mb gene from four species, representing three groups, of the schizothoracine fish endemic to the Qinghai-Tibetan Plateau (QTP), then conducted molecular evolution analyses. We also investigated tissue expression patterns of Mb and the expression response to moderate and severe hypoxia at the mRNA and protein levels in a representative of the highly specialized schizothoracine fish species, Schizopygopsis pylzovi. Molecular evolution analyses showed that Mb from the highly specialized schizothoracine fish have undergone positive selection and one positively selected residue (81L) was identified, which is located in the F helix, close to or in contact with the heme. We present tentative evidence that the Mb duplication event occurred in the ancestor of the schizothoracine and Cyprininae fish (common carp and goldfish), and that the Mb2 paralog was subsequently lost in the schizothoracine fish. In S. pylzovi, Mb mRNA is expressed in various tissues with the exception of the intestine and gill, but all such tissues, including the liver, muscle, kidney, brain, eye, and skin, expressed very low levels of Mb mRNA (Tibetan Plateau fish.

Molecular dynamics study of the effect of substrate temperature and Ar ion assisted deposition on the deposition of amorphous TiO_2 films

International Nuclear Information System (INIS)

Chen, Xian; Zhang, Jing; Zhao, Yu-Qing

2017-01-01

Highlights: • The surface roughness of a-TiO_2 films is decreased with the increment of the Ar ion assisted energy. • The surface roughness of a-TiO_2 films is decreased with higher substrate temperature when the substrate has an island structure. • The assisted Ar ion has power of making a flat surface and increasing the local temperature. • The assisted Ar ion will influence the growth mode with the change of surface atom mobility. • The Volmer-Weber (island) growth mode is inhibited with a high assisted Ar ion energy. - Abstract: This paper has investigated the impact of the substrate temperature and Ar ion assisted deposition on the surface structure formation mechanism and the film properties during the amorphous TiO_2 thin film deposition process with the molecular dynamics simulation method. The results show that the reduction of the surface roughness happen when the energy of Ar ions assisted is increased or the substrate temperature rises, and also the film density on surface is changed with the increasing of Ar ions energy and substrate temperature. It is also found that the Volmer-Weber (island) growth mode of films is promoted by the lower Ar ion energy and higher substrate temperature when the substrate has an island structure. The assisted Ar ion has power of making a flat surface and increasing the local temperature. Besides, it will influence the growth mode with the change of surface atom mobility. With a high assisted Ar ion energy the Volmer-Weber (island) growth mode is inhibited, which will be conducive to the formation of more smooth film surface.

Molecular dynamics simulation of gold cluster growth during sputter deposition

Energy Technology Data Exchange (ETDEWEB)

Abraham, J. W., E-mail: abraham@theo-physik.uni-kiel.de; Bonitz, M., E-mail: bonitz@theo-physik.uni-kiel.de [Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, Leibnizstraße 15, D-24098 Kiel (Germany); Strunskus, T.; Faupel, F. [Institut für Materialwissenschaft, Lehrstuhl für Materialverbunde, Christian-Albrechts-Universität zu Kiel, Kaiserstraße 2, D-24143 Kiel (Germany)

2016-05-14

We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.

Science.gov (United States)

Liu, Xiaofeng; Bai, Fang; Ouyang, Sisheng; Wang, Xicheng; Li, Honglin; Jiang, Hualiang

2009-03-31

Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105-112). Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 A to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 +/- 0.18 seconds per molecule) renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms other four multiple conformer generators in the case of

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation

Directory of Open Access Journals (Sweden)

Li Honglin

2009-03-01

Full Text Available Abstract Background Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. Results The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105–112. Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 Å to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 ± 0.18 seconds per molecule renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. Conclusion On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms

Chloroplast DNA analysis of Tunisian cork oak populations (Quercus suber L.): sequence variations and molecular evolution of the trnL (UAA)-trnF (GAA) region.

Science.gov (United States)

Abdessamad, A; Baraket, G; Sakka, H; Ammari, Y; Ksontini, M; Hannachi, A Salhi

2016-10-24

Sequences of the trnL-trnF spacer and combined trnL-trnF region in chloroplast DNA of cork oak (Quercus suber L.) were analyzed to detect polymorphisms and to elucidate molecular evolution and demographic history. The aligned sequences varied in length and nucleotide composition. The overall ratio of transition/transversion (ti/tv) of 0.724 for the intergenic spacer and 0.258 for the pooled sequences were estimated, and indicated that transversions are more frequent than transitions. The molecular evolution and demographic history of Q. suber were investigated. Neutrality tests (Tajima's D and Fu and Li) ruled out the null hypothesis of a strictly neutral model, and Fu's Fs and Ramos-Onsins and Rozas' R2 confirmed the recent expansion of cork oak trees, validating its persistency in North Africa since the last glaciation during the Quaternary. The observed uni-modal mismatch distribution and the Harpending's raggedness index confirmed the demographic history model for cork oak. A phylogenetic dendrogram showed that the distribution of Q. suber trees occurs independently of geographical origin, the relief of the population site, and the bioclimatic stages. The molecular history and cytoplasmic diversity suggest that in situ and ex situ conservation strategies can be recommended for preserving landscape value and facing predictable future climatic changes.

Evolution of Robot-assisted ultrasound-guided breast biopsy systems

Directory of Open Access Journals (Sweden)

Mustafa Z. Mahmoud

2018-01-01

Full Text Available Robot-assisted ultrasound-guided breast biopsy combines ultrasound (US imaging with a robotic system for medical interventions. This study was designed to provide a literature review of a robotic US-guided breast biopsy system to delineate its efficacious impact on current medical practice. In addition, the strengths and limitations of this approach were also addressed. Articles published in the English language between 2000 and 2016 were appraised in this review. A wide range of systems that bind robotics with US imaging and guided breast biopsy were examined in this article. The fundamental safety and real-time imaging capabilities of US, together with the accuracy and maneuverability of robotic devices, is clearly an effective association with unmatched capabilities. Numerous experimental systems have obvious benefits over old-fashioned techniques, and the future of robot-assisted US-guided breast biopsy will be characterized by increasing levels of automation, and they hold tremendous possibility to impact doctor achievement, patient recovery, and clinical management.

Molecular dynamics study on the evolution of interfacial dislocation network and mechanical properties of Ni-based single crystal superalloys

Science.gov (United States)

Li, Nan-Lin; Wu, Wen-Ping; Nie, Kai

2018-05-01

The evolution of misfit dislocation network at γ /γ‧ phase interface and tensile mechanical properties of Ni-based single crystal superalloys at various temperatures and strain rates are studied by using molecular dynamics (MD) simulations. From the simulations, it is found that with the increase of loading, the dislocation network effectively inhibits dislocations emitted in the γ matrix cutting into the γ‧ phase and absorbs the matrix dislocations to strengthen itself which increases the stability of structure. Under the influence of the temperature, the initial mosaic structure of dislocation network gradually becomes irregular, and the initial misfit stress and the elastic modulus slowly decline as temperature increasing. On the other hand, with the increase of the strain rate, it almost has no effect on the elastic modulus and the way of evolution of dislocation network, but contributes to the increases of the yield stress and tensile strength. Moreover, tension-compression asymmetry of Ni-based single crystal superalloys is also presented based on MD simulations.

Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes.

Science.gov (United States)

Carlson, David E; Hedin, Marshal

2017-01-01

Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.

The evolution, morphology and development of fern leaves

Directory of Open Access Journals (Sweden)

Alejandra eVasco

2013-09-01

Full Text Available Leaves are lateral determinate structures formed in a predictable sequence (phyllotaxy on the flanks of an indeterminate shoot apical meristem. The origin and evolution of leaves in vascular plants has been widely debated. Being the main conspicuous organ of nearl all vascular plants and often easy to recognize as such, it seems surprising that leaves have had multiple origins. For decades, morphologists, anatomists, paleobotanists, and systematists have contributed data to this debate. More recently, molecular genetic studies have provided insight into leaf evolution and development mainly within angiosperms and, to a lesser extent, lycophytes. There has been recent interest in extending leaf evolutionary developmental studies to other species and lineages, particularly in lycophytes and ferns. Therefore, a review of fern leaf morphology, evolution and development is timely. Here we discuss the theories of leaf evolution in ferns, morphology and diversity of fern leaves, and experimental results of fern leaf development. We summarize what is known about the molecular genetics of fern leaf development and what future studies might tell us about the evolution of fern leaf development.

Mg doping of GaN grown by plasma-assisted molecular beam epitaxy under nitrogen-rich conditions

International Nuclear Information System (INIS)

Zhang Meng; Bhattacharya, Pallab; Guo Wei; Banerjee, Animesh

2010-01-01

Acceptor doping of GaN with Mg during plasma-assisted molecular beam epitaxy, under N-rich conditions and a relatively high growth temperature of 740 deg. C, was investigated. The p-doping level steadily increases with increasing Mg flux. The highest doping level achieved, determined from Hall measurements, is 2.1x10 18 cm -3 . The corresponding doping efficiency and hole mobility are ∼4.9% and 3.7 cm 2 /V s at room temperature. Cross-sectional transmission electron microscopy and photoluminescence measurements confirm good crystalline and optical quality of the Mg-doped layers. An InGaN/GaN quantum dot light emitting diode (λ peak =529 nm) with p-GaN contact layers grown under N-rich condition exhibits a low series resistance of 9.8 Ω.

Molecular Cochaperones: Tumor Growth and Cancer Treatment

Directory of Open Access Journals (Sweden)

Stuart K. Calderwood

2013-01-01

Full Text Available Molecular chaperones play important roles in all cellular organisms by maintaining the proteome in an optimally folded state. They appear to be at a premium in cancer cells whose evolution along the malignant pathways requires the fostering of cohorts of mutant proteins that are employed to overcome tumor suppressive regulation. To function at significant rates in cells, HSPs interact with cochaperones, proteins that assist in catalyzing individual steps in molecular chaperoning as well as in posttranslational modification and intracellular localization. We review current knowledge regarding the roles of chaperones such as heat shock protein 90 (Hsp90 and Hsp70 and their cochaperones in cancer. Cochaperones are potential targets for cancer therapy in themselves and can be used to assess the likely prognosis of individual malignancies. Hsp70 cochaperones Bag1, Bag3, and Hop play significant roles in the etiology of some cancers as do Hsp90 cochaperones Aha1, p23, Cdc37, and FKBP1. Others such as the J domain protein family, HspBP1, TTC4, and FKBPL appear to be associated with more benign tumor phenotypes. The key importance of cochaperones for many pathways of protein folding in cancer suggests high promise for the future development of novel pharmaceutical agents.

Solvent-vapor-assisted imprint lithography

NARCIS (Netherlands)

Voicu, Nicoleta E.; Ludwigs, Sabine; Crossland, Edward J. W.; Andrew, Piers; Steiner, Ullrich

2007-01-01

Sub-micrometer features are replicated into high-molecular-weight polymer resists by using solvent-assisted nanoimprint lithography (see figure). By swelling the polymer in a controlled solvent-vapor atmosphere, millibar pressures and ambient temperatures are sufficient to achieve high-fidelity

Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

Science.gov (United States)

Macelroy, R. D.; Pohorille, A.

1986-01-01

The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

Methylome evolution in plants

NARCIS (Netherlands)

Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank

2016-01-01

Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over

Cyanobacterial evolution during the Precambrian

Science.gov (United States)

Schirrmeister, Bettina E.; Sanchez-Baracaldo, Patricia; Wacey, David

2016-07-01

Life on Earth has existed for at least 3.5 billion years. Yet, relatively little is known of its evolution during the first two billion years, due to the scarceness and generally poor preservation of fossilized biological material. Cyanobacteria, formerly known as blue green algae were among the first crown Eubacteria to evolve and for more than 2.5 billion years they have strongly influenced Earth's biosphere. Being the only organism where oxygenic photosynthesis has originated, they have oxygenated Earth's atmosphere and hydrosphere, triggered the evolution of plants -being ancestral to chloroplasts- and enabled the evolution of complex life based on aerobic respiration. Having such a strong impact on early life, one might expect that the evolutionary success of this group may also have triggered further biosphere changes during early Earth history. However, very little is known about the early evolution of this phylum and ongoing debates about cyanobacterial fossils, biomarkers and molecular clock analyses highlight the difficulties in this field of research. Although phylogenomic analyses have provided promising glimpses into the early evolution of cyanobacteria, estimated divergence ages are often very uncertain, because of vague and insufficient tree-calibrations. Results of molecular clock analyses are intrinsically tied to these prior calibration points, hence improving calibrations will enable more precise divergence time estimations. Here we provide a review of previously described Precambrian microfossils, biomarkers and geochemical markers that inform upon the early evolution of cyanobacteria. Future research in micropalaeontology will require novel analyses and imaging techniques to improve taxonomic affiliation of many Precambrian microfossils. Consequently, a better understanding of early cyanobacterial evolution will not only allow for a more specific calibration of cyanobacterial and eubacterial phylogenies, but also provide new dates for the tree

Molecular Evolution and Expansion Analysis of the NAC Transcription Factor in Zea mays

Science.gov (United States)

Fan, Kai; Wang, Ming; Miao, Ying; Ni, Mi; Bibi, Noreen; Yuan, Shuna; Li, Feng; Wang, Xuede

2014-01-01

NAC (NAM, ATAF1, 2 and CUC2) family is a plant-specific transcription factor and it controls various plant developmental processes. In the current study, 124 NAC members were identified in Zea mays and were phylogenetically clustered into 13 distinct subfamilies. The whole genome duplication (WGD), especially an additional WGD event, may lead to expanding ZmNAC members. Different subfamily has different expansion rate, and NAC subfamily preference was found during the expansion in maize. Moreover, the duplication events might occur after the divergence of the lineages of Z. mays and S. italica, and segmental duplication seemed to be the dominant pattern for the gene duplication in maize. Furthermore, the expansion of ZmNAC members may be also related to gain and loss of introns. Besides, the restriction of functional divergence was discovered after most of the gene duplication events. These results could provide novel insights into molecular evolution and expansion analysis of NAC family in maize, and advance the NAC researches in other plants, especially polyploid plants. PMID:25369196

Molecular dynamics study of the effect of substrate temperature and Ar ion assisted deposition on the deposition of amorphous TiO{sub 2} films

Energy Technology Data Exchange (ETDEWEB)

Chen, Xian, E-mail: mus_c@qq.com [Science and Technology on Analog Integrated Circuit Laboratory, ChongQing, 401332 (China); Zhang, Jing [Science and Technology on Analog Integrated Circuit Laboratory, ChongQing, 401332 (China); Zhao, Yu-Qing [Key Laboratory for Physical Electronics and Devices of the Ministry of Education, Xi' an Jiaotong University, Xi’AN, 710049 (China)

2017-05-15

Highlights: • The surface roughness of a-TiO{sub 2} films is decreased with the increment of the Ar ion assisted energy. • The surface roughness of a-TiO{sub 2} films is decreased with higher substrate temperature when the substrate has an island structure. • The assisted Ar ion has power of making a flat surface and increasing the local temperature. • The assisted Ar ion will influence the growth mode with the change of surface atom mobility. • The Volmer-Weber (island) growth mode is inhibited with a high assisted Ar ion energy. - Abstract: This paper has investigated the impact of the substrate temperature and Ar ion assisted deposition on the surface structure formation mechanism and the film properties during the amorphous TiO{sub 2} thin film deposition process with the molecular dynamics simulation method. The results show that the reduction of the surface roughness happen when the energy of Ar ions assisted is increased or the substrate temperature rises, and also the film density on surface is changed with the increasing of Ar ions energy and substrate temperature. It is also found that the Volmer-Weber (island) growth mode of films is promoted by the lower Ar ion energy and higher substrate temperature when the substrate has an island structure. The assisted Ar ion has power of making a flat surface and increasing the local temperature. Besides, it will influence the growth mode with the change of surface atom mobility. With a high assisted Ar ion energy the Volmer-Weber (island) growth mode is inhibited, which will be conducive to the formation of more smooth film surface.

The role of macromolecular crowding in the evolution of lens crystallins with high molecular refractive index

International Nuclear Information System (INIS)

Zhao, Huaying; Magone, M Teresa; Schuck, Peter

2011-01-01

Crystallins are present in the lens at extremely high concentrations in order to provide transparency and generate a high refractive power of the lens. The crystallin families prevalent in the highest density lens tissues are γ-crystallins in vertebrates and S-crystallins in cephalopods. As shown elsewhere, in parallel evolution, both have evolved molecular refractive index increments 5–10% above those of most proteins. Although this is a small increase, it is statistically very significant and can be achieved only by very unusual amino acid compositions. In contrast, such a molecular adaptation to aid in the refractive function of the lens did not occur in crystallins that are preferentially located in lower density lens tissues, such as vertebrate α-crystallin and taxon-specific crystallins. In the current work, we apply a model of non-interacting hard spheres to examine the thermodynamic contributions of volume exclusion at lenticular protein concentrations. We show that the small concentration decrease afforded by the higher molecular refractive index increment of crystallins can amplify nonlinearly to produce order of magnitude differences in chemical activities, and lead to reduced osmotic pressure and the reduced propensity for protein aggregation. Quantitatively, this amplification sets in only at protein concentrations as high as those found in hard lenses or the nucleus of soft lenses, in good correspondence to the observed crystallin properties in different tissues and different species. This suggests that volume exclusion effects provide the evolutionary driving force for the unusual refractive properties and the unusual amino acid compositions of γ-crystallins and S-crystallins

Robot-assisted general surgery.

Science.gov (United States)

Hazey, Jeffrey W; Melvin, W Scott

2004-06-01

With the initiation of laparoscopic techniques in general surgery, we have seen a significant expansion of minimally invasive techniques in the last 16 years. More recently, robotic-assisted laparoscopy has moved into the general surgeon's armamentarium to address some of the shortcomings of laparoscopic surgery. AESOP (Computer Motion, Goleta, CA) addressed the issue of visualization as a robotic camera holder. With the introduction of the ZEUS robotic surgical system (Computer Motion), the ability to remotely operate laparoscopic instruments became a reality. US Food and Drug Administration approval in July 2000 of the da Vinci robotic surgical system (Intuitive Surgical, Sunnyvale, CA) further defined the ability of a robotic-assist device to address limitations in laparoscopy. This includes a significant improvement in instrument dexterity, dampening of natural hand tremors, three-dimensional visualization, ergonomics, and camera stability. As experience with robotic technology increased and its applications to advanced laparoscopic procedures have become more understood, more procedures have been performed with robotic assistance. Numerous studies have shown equivalent or improved patient outcomes when robotic-assist devices are used. Initially, robotic-assisted laparoscopic cholecystectomy was deemed safe, and now robotics has been shown to be safe in foregut procedures, including Nissen fundoplication, Heller myotomy, gastric banding procedures, and Roux-en-Y gastric bypass. These techniques have been extrapolated to solid-organ procedures (splenectomy, adrenalectomy, and pancreatic surgery) as well as robotic-assisted laparoscopic colectomy. In this chapter, we review the evolution of robotic technology and its applications in general surgical procedures.

Characterization of GaN P-N Junction Grown on Si (111) Substrate by Plasma-assisted Molecular Beam Epitaxy

International Nuclear Information System (INIS)

Rosfariza Radzali; Rosfariza Radzali; Mohd Anas Ahmad; Zainuriah Hassan; Norzaini Zainal; Kwong, Y.F.; Woei, C.C.; Mohd Zaki Mohd Yusoff; Mohd Zaki Mohd Yusoff

2011-01-01

In this report, the growth of GaN pn junction on Si (111) substrate by plasma assisted molecular beam epitaxy (PAMBE) is presented. Doping of GaN p-n junction has been carried out using Si and Mg as n-type dopant and p-type dopants, respectively. The sample had been characterized by PL, Raman spectroscopy, HR-XRD and SEM. PL spectrum showed strong band edge emission of GaN at ∼364 nm, indicating good quality of the sample. The image of SEM cross section of the sample showed sharp interfaces. The presence of peak ∼657 cm -1 in Raman measurement exhibited successful doping of Mg in the sample. (author)

Star formation induced by cloud-cloud collisions and galactic giant molecular cloud evolution

Science.gov (United States)

Kobayashi, Masato I. N.; Kobayashi, Hiroshi; Inutsuka, Shu-ichiro; Fukui, Yasuo

2018-05-01

Recent millimeter/submillimeter observations towards nearby galaxies have started to map the whole disk and to identify giant molecular clouds (GMCs) even in the regions between galactic spiral structures. Observed variations of GMC mass functions in different galactic environments indicates that massive GMCs preferentially reside along galactic spiral structures whereas inter-arm regions have many small GMCs. Based on the phase transition dynamics from magnetized warm neutral medium to molecular clouds, Kobayashi et al. (2017, ApJ, 836, 175) proposes a semi-analytical evolutionary description for GMC mass functions including a cloud-cloud collision (CCC) process. Their results show that CCC is less dominant in shaping the mass function of GMCs than the accretion of dense H I gas driven by the propagation of supersonic shock waves. However, their formulation does not take into account the possible enhancement of star formation by CCC. Millimeter/submillimeter observations within the Milky Way indicate the importance of CCC in the formation of star clusters and massive stars. In this article, we reformulate the time-evolution equation largely modified from Kobayashi et al. (2017, ApJ, 836, 175) so that we additionally compute star formation subsequently taking place in CCC clouds. Our results suggest that, although CCC events between smaller clouds are more frequent than the ones between massive GMCs, CCC-driven star formation is mostly driven by massive GMCs ≳ 10^{5.5} M_{⊙} (where M⊙ is the solar mass). The resultant cumulative CCC-driven star formation may amount to a few 10 percent of the total star formation in the Milky Way and nearby galaxies.

Polypeptides Based Molecular Electronics

National Research Council Canada - National Science Library

Lam, Yeng M; Mhaisalkar, Subodh; Li, Lain-Jong; Dravid, Vinayak P; Shekhawat, Gajendra S; Suri, Raman

2008-01-01

... the formation of molecular devices such as transistors, diodes, and sensors. We have designed the peptides, arranged them on substrates using self-assembly, Dip-PEN nanolithography, and also e-beam assisted lithography...

P-type doping of semipolar GaN(11 anti 22) by plasma-assisted molecular-beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Das, A.; Lahourcade, L. [Equipe Mixte CEA-CNRS, Nanophysique et Semiconducteurs, CEA-Grenoble, INAC/SP2M, Grenoble (France); Pernot, J. [Institut Neel, CNRS et Universite Joseph Fourier, Grenoble (France); Valdueza-Felip, S. [Equipe Mixte CEA-CNRS, Nanophysique et Semiconducteurs, CEA-Grenoble, INAC/SP2M, Grenoble (France); Dept. Electronica, Escuela Politecnica, Universidad de Alcala, Alcala de Henares, Madrid (Spain); Ruterana, P. [CIMAP, UMR6252, CNRS-ENSICAEN-CEA-UCBN, Caen (France); Laufer, A.; Eickhoff, M. [I. Physikalisches Institut, Justus-Liebig-Universitaet Giessen (Germany); Monroy, E.

2010-07-15

We report the effect of Mg doping on the growth kinetics of semipolar GaN(11-22) synthesized by plasma-assisted molecular-beam epitaxy. Mg tends to segregate on the surface, inhibiting the formation of the self-regulated Ga film which is used as a surfactant for the growth of undoped and Si-doped GaN(11-22). As a result, the growth widow is reduced for Mg doped layers, and we observe a certain deterioration of the surface morphology. In spite of this difficulties, homogenous Mg incorporation is achieved and layers display p -type conductivity for Mg atomic concentration higher than 7 x 10{sup 18} cm{sup -3}. Microscopy studies show no evidence of the pyramidal defects or polarity inversion domains found in Mg-doped GaN(0001). (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

The growth of III-V nitrides heterostructure on Si substrate by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Beh, K.P.; Yam, F.K.; Chin, C.W.; Tneh, S.S.; Hassan, Z.

2010-01-01

This paper reports the growth of InGaN/GaN/AlN epitaxial layer on Si(1 1 1) substrate by utilizing plasma-assisted molecular beam epitaxy (PA-MBE) system. The as-grown film was characterized using high-resolution X-ray diffraction (HR-XRD) and photoluminescence (PL). High work function metals, iridium and gold were deposited on the film as metal contacts and their electrical characteristics at pre- and post-annealing were studied. The structural quality of this film is comparative to the values reported in the literature, and the indium molar fraction is 0.57 by employing Vegard's law. The relatively low yellow band emission signifies the grown film is of high quality. For metal contact studies it was found that the post-annealed sample for 5 min shows good conductivity as compared to the other samples.

The rhabdoviruses: biodiversity, phylogenetics, and evolution.

Science.gov (United States)

Kuzmin, I V; Novella, I S; Dietzgen, R G; Padhi, A; Rupprecht, C E

2009-07-01

Rhabdoviruses (family Rhabdoviridae) include a diversity of important pathogens of animals and plants. They share morphology and genome organization. The understanding of rhabdovirus phylogeny, ecology and evolution has progressed greatly during the last 30 years, due to enhanced surveillance and improved methodologies of molecular characterization. Along with six established genera, several phylogenetic groups at different levels were described within the Rhabdoviridae. However, comparative relationships between viral phylogeny and taxonomy remains incomplete, with multiple representatives awaiting further genetic characterization. The same is true for rhabdovirus evolution. To date, rather simplistic molecular clock models only partially describe the evolutionary dynamics of postulated viral lineages. Ongoing progress in viral evolutionary and ecological investigations will provide the platform for future studies of this diverse family.

Protein consensus-based surface engineering (ProCoS): a computer-assisted method for directed protein evolution.

Science.gov (United States)

Shivange, Amol V; Hoeffken, Hans Wolfgang; Haefner, Stefan; Schwaneberg, Ulrich

2016-12-01

Protein consensus-based surface engineering (ProCoS) is a simple and efficient method for directed protein evolution combining computational analysis and molecular biology tools to engineer protein surfaces. ProCoS is based on the hypothesis that conserved residues originated from a common ancestor and that these residues are crucial for the function of a protein, whereas highly variable regions (situated on the surface of a protein) can be targeted for surface engineering to maximize performance. ProCoS comprises four main steps: ( i ) identification of conserved and highly variable regions; ( ii ) protein sequence design by substituting residues in the highly variable regions, and gene synthesis; ( iii ) in vitro DNA recombination of synthetic genes; and ( iv ) screening for active variants. ProCoS is a simple method for surface mutagenesis in which multiple sequence alignment is used for selection of surface residues based on a structural model. To demonstrate the technique's utility for directed evolution, the surface of a phytase enzyme from Yersinia mollaretii (Ymphytase) was subjected to ProCoS. Screening just 1050 clones from ProCoS engineering-guided mutant libraries yielded an enzyme with 34 amino acid substitutions. The surface-engineered Ymphytase exhibited 3.8-fold higher pH stability (at pH 2.8 for 3 h) and retained 40% of the enzyme's specific activity (400 U/mg) compared with the wild-type Ymphytase. The pH stability might be attributed to a significantly increased (20 percentage points; from 9% to 29%) number of negatively charged amino acids on the surface of the engineered phytase.

Self-assembly growth of alloyed NiPt nanocrystals with holothuria-like shape for oxygen evolution reaction with enhanced catalytic activity

Directory of Open Access Journals (Sweden)

Tao Ding

2016-01-01

Full Text Available Self-assembly growth of alloyed NiPt nanocrystals with holothuria-like wire shape has been achieved via a facile and moderate hydrothermal process at 120 °C for 1 h from the reaction of nickel nitrate and chloroplatinic acid in alkaline solution in the presence of ethanediamine and hydrazine hydrate. The holothuria-like alloyed NiPt wires are Ni-rich in composition (Ni23.6Pt and uniform in diameter with many tiny tips outstretched from the wires surface. The holothuria-like wires are assembled from granular subunits with the assistance of capping molecular of ethanediamine and the wires display an improved oxygen evolution reaction catalytic activity.

The Evolution of Darwinism.

Science.gov (United States)

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)

Nitridation effects of Si(1 1 1) substrate surface on InN nanorods grown by plasma-assisted molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Feng, Shan [Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074 (China); Tan, Jin, E-mail: jintan_cug@163.com [Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074 (China); Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan 430074 (China); Li, Bin; Song, Hao; Wu, Zhengbo; Chen, Xin [Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074 (China)

2015-02-05

Graphical abstract: The morphology evolution of InN nanorods in samples (g)–(i). The alignment of InN nanorods is improved and the deviation angle distribution narrows down with increase in nitriding time. It suggests that extending the nitriding time can enhance the vertical orientation of InN nanorods. - Highlights: • InN nanorods were grown on surface nitrided Si(1 1 1) substrate using PAMBE system. • Nitridation of substrate surface has a strong effect on morphology of InN nanorods. • InN nanorods cannot be formed with 1 min nitridation of Si(1 1 1) substrate. • Increasing nitriding time will increase optimum growth temperature of InN nanorods. • Increasing nitriding time can enhance vertical orientation of InN nanorods. - Abstract: The InN nanorods were grown on Si(1 1 1) substrate by plasma-assisted molecular beam epitaxy (PAMBE) system, with a substrate nitridation process. The effect of nitriding time of Si(1 1 1) substrate on morphology, orientation and growth temperature of InN nanorods was characterized via scanning electron microscopy (SEM) and X-ray diffraction (XRD). The deviation angle of InN nanorods was measured to evaluate the alignment of arrays. The results showed that InN nanorods could not be formed with 1 min nitridation of Si(1 1 1) substrate, but they could be obtained again when the nitriding time was increased to more than 10 min. In order to get aligned InN nanorods, the growth temperature needed to increase with longer nitriding time. The vertical orientation of InN nanorods could be enhanced with increase in nitriding time. The influence of the substrate nitridation on the photoluminescence (PL) spectra of InN nanorods has been investigated.

Extracellular Matrix Molecular Remodeling in Human Liver Fibrosis Evolution.

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Andrea Baiocchini

Full Text Available Chronic liver damage leads to pathological accumulation of ECM proteins (liver fibrosis. Comprehensive characterization of the human ECM molecular composition is essential for gaining insights into the mechanisms of liver disease. To date, studies of ECM remodeling in human liver diseases have been hampered by the unavailability of purified ECM. Here, we developed a decellularization method to purify ECM scaffolds from human liver tissues. Histological and electron microscopy analyses demonstrated that the ECM scaffolds, devoid of plasma and cellular components, preserved the three-dimensional ECM structure and zonal distribution of ECM components. This method has been then applied on 57 liver biopsies of HCV-infected patients at different stages of liver fibrosis according to METAVIR classification. Label-free nLC-MS/MS proteomics and computation biology were performed to analyze the ECM molecular composition in liver fibrosis progression, thus unveiling protein expression signatures specific for the HCV-related liver fibrotic stages. In particular, the ECM molecular composition of liver fibrosis was found to involve dynamic changes in matrix stiffness, flexibility and density related to the dysregulation of predominant collagen, elastic fibers and minor components with both structural and signaling properties. This study contributes to the understanding of the molecular bases underlying ECM remodeling in liver fibrosis and suggests new molecular targets for fibrolytic strategies.

STAR FORMATION IN DISK GALAXIES. I. FORMATION AND EVOLUTION OF GIANT MOLECULAR CLOUDS VIA GRAVITATIONAL INSTABILITY AND CLOUD COLLISIONS

International Nuclear Information System (INIS)

Tasker, Elizabeth J.; Tan, Jonathan C.

2009-01-01

We investigate the formation and evolution of giant molecular clouds (GMCs) in a Milky-Way-like disk galaxy with a flat rotation curve. We perform a series of three-dimensional adaptive mesh refinement numerical simulations that follow both the global evolution on scales of ∼20 kpc and resolve down to scales ∼ H ≥ 100 cm -3 and track the evolution of individual clouds as they orbit through the galaxy from their birth to their eventual destruction via merger or via destructive collision with another cloud. After ∼140 Myr a large fraction of the gas in the disk has fragmented into clouds with masses ∼10 6 M sun and a mass spectrum similar to that of Galactic GMCs. The disk settles into a quasi-steady-state in which gravitational scattering of clouds keeps the disk near the threshold of global gravitational instability. The cloud collision time is found to be a small fraction, ∼1/5, of the orbital time, and this is an efficient mechanism to inject turbulence into the clouds. This helps to keep clouds only moderately gravitationally bound, with virial parameters of order unity. Many other observed GMC properties, such as mass surface density, angular momentum, velocity dispersion, and vertical distribution, can be accounted for in this simple model with no stellar feedback.

Deceptive desmas: molecular phylogenetics suggests a new classification and uncovers convergent evolution of lithistid demosponges.

Directory of Open Access Journals (Sweden)

Astrid Schuster

Full Text Available Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera. 'Lithistida', a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of 'lithistid' demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous 'order Lithistida'. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences, we show that 8 out of 13 'Lithistida' families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae--we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different 'lithistid' taxa, and

Ab initio molecular dynamics simulations reveal localization and time evolution dynamics of an excess electron in heterogeneous CO{sub 2}–H{sub 2}O systems

Energy Technology Data Exchange (ETDEWEB)

Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang, E-mail: byx@sdu.edu.cn [School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100 (China)

2014-01-28

In view of the important implications of excess electrons (EEs) interacting with CO{sub 2}–H{sub 2}O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO{sub 2}–H{sub 2}O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO{sub 2} molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO{sub 2}, an EE can stably reside in the empty, low-lying π{sup *} orbital of a CO{sub 2} molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO{sub 2}{sup −} oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO{sub 2}-bound solvated EE in [CO{sub 2}(H{sub 2}O){sub n}]{sup −} systems. Interestingly, hydration occurs not only on the O atoms of the core CO{sub 2}{sup −} through formation of O⋯H–O H–bond(s), but also on the C atom, through formation of a C⋯H–O H–bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H–O H–bonds, and vice versa. The number of water molecules associated with the CO{sub 2}{sup −} anion in the first hydration shell is about 4∼7. No dimer-core (C{sub 2}O{sub 4}{sup −}) and core-switching were observed in the double CO{sub 2} aqueous media. This work provides molecular dynamics

Reduction of buffer layer conduction near plasma-assisted molecular-beam epitaxy grown GaN/AlN interfaces by beryllium doping

International Nuclear Information System (INIS)

Storm, D.F.; Katzer, D.S.; Binari, S.C.; Glaser, E.R.; Shanabrook, B.V.; Roussos, J.A.

2002-01-01

Beryllium doping of epitaxial GaN layers is used to reduce leakage currents through interfacial or buffer conducting layers grown by plasma-assisted molecular-beam epitaxy on SiC. Capacitance-voltage measurements of Schottky barrier test structures and dc pinch-off characteristics of unintentionally doped GaN high-electron-mobility transistors indicate that these leakage currents are localized near the GaN/AlN interface of our AlGaN/GaN/AlN device structures. Insertion of a 2000 Aa Be:GaN layer at the interface reduces these currents by three orders of magnitude

Molecular imaging of banknote and questioned document using solvent-free gold nanoparticle-assisted laser desorption/ionization imaging mass spectrometry.

Science.gov (United States)

Tang, Ho-Wai; Wong, Melody Yee-Man; Chan, Sharon Lai-Fung; Che, Chi-Ming; Ng, Kwan-Ming

2011-01-01

Direct chemical analysis and molecular imaging of questioned documents in a non/minimal-destructive manner is important in forensic science. Here, we demonstrate that solvent-free gold-nanoparticle-assisted laser desorption/ionization mass spectrometry is a sensitive and minimal destructive method for direct detection and imaging of ink and visible and/or fluorescent dyes printed on banknotes or written on questioned documents. Argon ion sputtering of a gold foil allows homogeneous coating of a thin layer of gold nanoparticles on banknotes and checks in a dry state without delocalizing spatial distributions of the analytes. Upon N(2) laser irradiation of the gold nanoparticle-coated banknotes or checks, abundant ions are desorbed and detected. Recording the spatial distributions of the ions can reveal the molecular images of visible and fluorescent ink printed on banknotes and determine the printing order of different ink which may be useful in differentiating real banknotes from fakes. The method can also be applied to identify forged parts in questioned documents, such as number/writing alteration on a check, by tracing different writing patterns that come from different pens.

n-type dopants in (001) β-Ga2O3 grown on (001) β-Ga2O3 substrates by plasma-assisted molecular beam epitaxy

Science.gov (United States)

Han, Sang-Heon; Mauze, Akhil; Ahmadi, Elaheh; Mates, Tom; Oshima, Yuichi; Speck, James S.

2018-04-01

Ge and Sn as n-type dopants in (001) β-Ga2O3 films were investigated using plasma-assisted molecular beam epitaxy. The Ge concentration showed a strong dependence on the growth temperature, whereas the Sn concentration remains independent of the growth temperature. The maximum growth temperature at which a wide range of Ge concentrations (from 1017 to 1020 cm-3) could be achieved was 675 °C while the same range of Sn concentration could be achieved at growth temperature of 750 °C. Atomic force microscopy results revealed that higher growth temperature shows better surface morphology. Therefore, our study reveals a tradeoff between higher Ge doping concentration and high quality surface morphology on (001) β-Ga2O3 films grown by plasma-assisted molecular beam epitaxy. The Ge doped films had an electron mobility of 26.3 cm2 V-1 s-1 at the electron concentration of 6.7 × 1017 cm-3 whereas the Sn doped films had an electron mobility of 25.3 cm2 V-1 s-1 at the electron concentration of 1.1 × 1018 cm-3.

[Mobile genetic elements in plant sex evolution].

Science.gov (United States)

Gerashchenkov, G A; Rozhnova, N A

2010-11-01

The most significant theories of the appearance and maintenance of sex are presented. However, in the overwhelming majority of existing theories, the problem of sex, which is the central problem of evolutionary biology, is considered primarily through the prism of reproductive features of living organisms, whereas the issue of molecular driving forces of sexual reproduction id restricted to the possible role of mobile genetic elements (MGEs) in the appearance of sexual reproduction. The structural and functional significance of MGEs in the genomic organization of plants is illustrated. It is shown that MGEs could act as important molecular drivers of sex evolution in plants. The involvement of MGEs in the formation of sex chromosomes and possible participation in seeds-without-sex reproduction (apomixis) is discussed. Thus, the hypothesis on the active MGE participation in sex evolution is in good agreement with the modern views on pathways and directions of sex evolution in plants.

Decoherence assisting a measurement-driven quantum evolution process

International Nuclear Information System (INIS)

Roa, Luis; Olivares-Renteria, G. A.

2006-01-01

We study the problem of driving an unknown initial mixed quantum state onto a known pure state without using unitary transformations. This can be achieved, in an efficient manner, with the help of sequential measurements on at least two unbiased bases. However here we found that, when the system is affected by a decoherence mechanism, only one observable is required in order to achieve the same goal. In this way the decoherence can assist the process. We show that, depending on the sort of decoherence, the process can converge faster or slower than the method implemented by means of two complementary observables

Evolution of heteromorphic sex chromosomes in the order Aulopiformes.

Science.gov (United States)

Ota, K; Kobayashi, T; Ueno, K; Gojobori, T

2000-12-23

The fish order Aulopiformes contains both synchronously hermaphroditic and gonochoristic species. From the cytogenetic viewpoint, few reports show that gonochoristic Aulopiformes have heteromorphic sex chromosomes. Because fish in this order give us a unique opportunity to elucidate the evolution of sex chromosomes, it is important to examine a phylogenetic relationship in Aulopiformes by both molecular evolutionary and cytogenetic methods. Thus, we conducted molecular phylogenetic and cytogenetic studies of six Aulopiform species. Our results suggested that hermaphroditic species were evolutionarily derived from gonochoristic species. It follows that the hermaphroditic species might have lost the heteromorphic sex chromosomes during evolution. Here, we suggest a possibility that heteromorphic sex chromosomes can disappear from the genome, even if they have appeared once in evolution. Taking into account Ohno's hypothesis that heteromorphic sex chromosomes might have emerged from autosomes, we propose the hypothesis that heteromorphic sex chromosomes may have undergone repeated events of appearance and disappearance during the course of fish evolution.

Influences of triple junctions on stress-assisted grain boundary motion in nanocrystalline materials

International Nuclear Information System (INIS)

Aramfard, Mohammad; Deng, Chuang

2014-01-01

Stress-assisted grain boundary motion is among the most studied modes of microstructural evolution in crystalline materials. In this study, molecular dynamics simulations were used to systematically investigate the influences of triple junctions on the stress-assisted motion of symmetric tilt grain boundaries in Cu by considering a honeycomb nanocrystalline model. It was found that the grain boundary motion in nanocrystalline models was highly sensitive to the loading mode, and a strong coupling effect which was prevalent in bicrystal models was only observed when simple shear was applied. In addition, the coupling factor extracted from the honeycomb model was found to be larger and more sensitive to temperature change than that from bicrystal models for the same type of grain boundary under the same loading conditions. Furthermore, the triple junctions seemed to exhibit unusual asymmetric pinning effects to the migrating grain boundary and the constraints by the triple junctions and neighboring grains led to remarkable non-linear grain boundary motion in directions both parallel and normal to the applied shear, which was in stark contrast to that observed in bicrystal models. In addition, dislocation nucleation and propagation, which were absent in the bicrystal model, were found to play an important role on shear-induced grain boundary motion when triple junctions were present. In the end, a generalized model for shear-assisted grain boundary motion was proposed based on the findings from this research. (paper)

Morphology of self-catalyzed GaN nanowires and chronology of their formation by molecular beam epitaxy

International Nuclear Information System (INIS)

Galopin, E; Largeau, L; Patriarche, G; Travers, L; Glas, F; Harmand, J C

2011-01-01

GaN nanowires are synthesized by plasma-assisted molecular beam epitaxy on Si(111) substrates. The strong impact of the cell orientation relative to the substrate on the nanowire morphology is shown. To study the kinetics of growth, thin AlN markers are introduced periodically during NW growth. These markers are observed in single nanowires by transmission electron microscopy, giving access to the chronology of the nanowire formation and to the time evolution of the nanowire morphology. A long delay precedes the beginning of nanowire formation. Then, their elongation proceeds at a constant rate. Later, shells develop on the side-wall facets by ascending growth of layer bunches which first agglomerate at the nanowire foot.

Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.

Science.gov (United States)

Kishimoto, Toshihiko; Ying, Bei-Wen; Tsuru, Saburo; Iijima, Leo; Suzuki, Shingo; Hashimoto, Tomomi; Oyake, Ayana; Kobayashi, Hisaka; Someya, Yuki; Narisawa, Dai; Yomo, Tetsuya

2015-07-01

The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution.

Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process.

Directory of Open Access Journals (Sweden)

Toshihiko Kishimoto

2015-07-01

Full Text Available The molecular clock of neutral mutations, which represents linear mutation fixation over generations, is theoretically explained by genetic drift in fitness-steady evolution or hitchhiking in adaptive evolution. The present study is the first experimental demonstration for the molecular clock of neutral mutations in a fitness-increasing evolutionary process. The dynamics of genome mutation fixation in the thermal adaptive evolution of Escherichia coli were evaluated in a prolonged evolution experiment in duplicated lineages. The cells from the continuously fitness-increasing evolutionary process were subjected to genome sequencing and analyzed at both the population and single-colony levels. Although the dynamics of genome mutation fixation were complicated by the combination of the stochastic appearance of adaptive mutations and clonal interference, the mutation fixation in the population was simply linear over generations. Each genome in the population accumulated 1.6 synonymous and 3.1 non-synonymous neutral mutations, on average, by the spontaneous mutation accumulation rate, while only a single genome in the population occasionally acquired an adaptive mutation. The neutral mutations that preexisted on the single genome hitchhiked on the domination of the adaptive mutation. The successive fixation processes of the 128 mutations demonstrated that hitchhiking and not genetic drift were responsible for the coincidence of the spontaneous mutation accumulation rate in the genome with the fixation rate of neutral mutations in the population. The molecular clock of neutral mutations to the fitness-increasing evolution suggests that the numerous neutral mutations observed in molecular phylogenetic trees may not always have been fixed in fitness-steady evolution but in adaptive evolution.

Molecular Evolution of the CYP2D Subfamily in Primates: Purifying Selection on Substrate Recognition Sites without the Frequent or Long-Tract Gene Conversion

Science.gov (United States)

Yasukochi, Yoshiki; Satta, Yoko

2015-01-01

The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. PMID:25808902

Methylome evolution in plants.

Science.gov (United States)

Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank

2016-12-20

Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.

UVB-emitting InAlGaN multiple quantum well synthesized using plasma-assisted molecular beam epitaxy

Directory of Open Access Journals (Sweden)

W. Kong

2017-03-01

Full Text Available A high Al-content (y > 0.4 multi-quantum-well (MQW structure with a quaternary InxAlyGa(1-x-yN active layer was synthesized using plasma-assisted molecular beam epitaxy. The MQW structure exhibits strong carrier confinement and room temperature ultraviolet-B (UVB photoluminescence an order of magnitude stronger than that of a reference InxAlyGa(1-x-yN thin film with comparable composition and thickness. The samples were characterized using spectroscopic ellipsometry, atomic force microscopy, and high-resolution X-ray diffraction. Numerical simulations suggest that the UVB emission efficiency is limited by dislocation-related non-radiative recombination centers in the MQW and at the MQW - buffer interface. Emission efficiency can be significantly improved by reducing the dislocation density from 109cm−2 to 107cm−2 and by optimizing the width and depth of the quantum wells.

Room temperature Ultraviolet B emission from InAlGaN films synthesized by plasma-assisted molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Kong, W., E-mail: wei.kong@duke.edu; Jiao, W. Y.; Kim, T. H.; Brown, A. S. [Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina 27708 (United States); Roberts, A. T. [Charles Bowden Laboratory, Army Aviation and Missile RD& E Center, Redstone Arsenal, Alabama 35898 (United States); Fournelle, J. [Department of Geoscience, University of Wisconsin, Madison, Wisconsin 53706 (United States); Losurdo, M. [CNR-NANOTEC, Istituto di Nanotecnologia, via Orabona, 4-70126 Bari (Italy); Everitt, H. O. [Charles Bowden Laboratory, Army Aviation and Missile RD& E Center, Redstone Arsenal, Alabama 35898 (United States); Department of Physics, Duke University, Durham, North Carolina 27708 (United States)

2015-09-28

Thin films of the wide bandgap quaternary semiconductor In{sub x}Al{sub y}Ga{sub (1−x−y)}N with low In (x = 0.01–0.05) and high Al composition (y = 0.40–0.49) were synthesized on GaN templates by plasma-assisted molecular beam epitaxy. High-resolution X-ray diffraction was used to correlate the strain accommodation of the films to composition. Room temperature ultraviolet B (280 nm–320 nm) photoluminescence intensity increased with increasing In composition, while the Stokes shift remained relatively constant. The data suggest a competition between radiative and non-radiative recombination occurs for carriers, respectively, localized at centers produced by In incorporation and at dislocations produced by strain relaxation.

Evolution and molecular control of hybrid incompatibility in plants

Directory of Open Access Journals (Sweden)

Chen Chen

2016-08-01

Full Text Available Postzygotic reproductive isolation (RI plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with parasitic selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities.

Evolution de la frequence et des problemes lies aux evacuations

African Journals Online (AJOL)

EVOLUTION OF THE FREQUENCY AND PROBLEMS ASSOCIATED WITH ... peripheral health facility, inappropriate transportation and the initial management by midwife assistants and .... qualité au Centre Hospitalier Yalgado Ouagadougou.

Molecular characterization and volatility evolution of α-pinene ozonolysis SOA during isothermal evaporations

Science.gov (United States)

D'Ambro, E.; Schobesberger, S.; Lopez-Hilfiker, F.; Shilling, J. E.; Lee, B. H.; Thornton, J. A.

2017-12-01

α-Pinene (C10H16), the most abundantly emitted monoterpene, is a large contributor to global biogenic secondary organic aerosol (SOA) budgets due to its high SOA yields upon oxidation. We probe the volatility and evaporation behavior upon dilution of α-pinene SOA to further our understanding of the nascent volatility distribution, viscosity, and how these evolve in time absent photochemical oxidation. We present molecular composition measurements of the gas and particle phases of α-pinene ozonolysis SOA formed at 0% and 50% relative humidity (RH), followed by room-temperature evaporation in ultra-high purity N2 humidified to 20-90% RH. Experiments were performed in the Pacific Northwest National Laboratory 10.6 m3 and the University of Washington 0.7 m3 environmental chambers utilizing a Filter Inlet for Gases and AEROsols (FIGAERO) coupled to a high-resolution time of flight chemical ionization mass spectrometer utilizing iodide adduct ionization. We present novel insights into the total mass that evaporates as a function of time from 10 min to 24 hours without heating, the molecular speciation of the evaporate, as well as the effective volatility and composition of the SOA mass remaining. Consistent with previous studies, we find two stages of evaporation: a rapid loss of a large portion of the total signal over the course of ≤3 hours, followed by a stage of much slower evaporation over the proceeding 21 hours. Varying the RH of formation effects evaporation rate on timescales ≤3 hours, however the mass fraction remaining after 24 hours converges to 30-50% under all formation and evaporation RHs. We simulate the evaporation behavior and remaining fractions desorbed via temperature programmed thermal desorption to derive effective saturation vapor concentrations, mass accommodation coefficients, and rates of chemical evolution producing both higher and lower volatility components during the evaporation time period.

LGI1, CASPR2 and related antibodies: a molecular evolution of the phenotypes

Science.gov (United States)

Binks, Sophie N M; Klein, Christopher J; Waters, Patrick; Pittock, Sean J; Irani, Sarosh R

2018-01-01

Recent biochemical observations have helped redefine antigenic components within the voltage-gated potassium channel (VGKC) complex. The related autoantibodies may be now divided into likely pathogenic entities, which target the extracellular domains of leucine-rich glioma-inactivated 1 (LGI1) and contactin-associated protein-like 2 (CASPR2), and species that target intracellular neuronal components and are likely non-pathogenic. This distinction has enhanced clinical practice as direct determination of LGI1 and CASPR2 antibodies offers optimal sensitivity and specificity. In this review, we describe and compare the clinical features associated with pathogenic LGI1 and CASPR2 antibodies, illustrate emerging laboratory techniques for antibody determination and describe the immunological mechanisms that may mediate antibody-induced pathology. We highlight marked clinical overlaps between patients with either LGI1 or CASPR2 antibodies that include frequent focal seizures, prominent amnesia, dysautonomia, neuromyotonia and neuropathic pain. Although occurring at differing rates, these commonalities are striking and only faciobrachial dystonic seizures reliably differentiate these two conditions. Furthermore, the coexistence of both LGI1 and CASPR2 antibodies in an individual occurs surprisingly frequently. Patients with either antibody respond well to immunotherapies, although systematic studies are required to determine the magnitude of the effect beyond placebo. Finally, data have suggested that CASPR2 and LGI1 modulation via genetic or autoimmune mechanisms may share common intermediate molecules. Taken together, the biochemical distinction of antigenic targets has led to important clinical advances for patient care. However, the striking syndrome similarities, coexistence of two otherwise rare antibodies and molecular insights suggest the VGKC complex may yet be a common functional effector of antibody action. Hence, we argue for a molecular evolution alongside a

Cascades of convergent evolution: The corresponding evolutionary histories of euglenozoans and dinoflagellates

Czech Academy of Sciences Publication Activity Database

Lukeš, Julius; Leander, B. S.; Keeling, P. J.

2009-01-01

Roč. 106, č. 1 (2009), s. 9963-9970 ISSN 0027-8424 R&D Projects: GA ČR GA204/09/1667; GA MŠk LC07032; GA MŠk 2B06129 Institutional research plan: CEZ:AV0Z60220518 Keywords : comparative genomics * convergent evolution * dinoflagellates * Euglenozoa * mitochondria * molecular evolution * plastids * RNA editing * RNA editing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.432, year: 2009

Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution

KAUST Repository

Yu, Weili

2014-08-19

A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tethering metal ions to photocatalyst particulate surfaces by bifunctional molecular linkers for efficient hydrogen evolution

KAUST Repository

Yu, Weili; Isimjan, Tayirjan T.; Del Gobbo, Silvano; Anjum, Dalaver Hussain; Abdel-Azeim, Safwat; Cavallo, Luigi; Garcia Esparza, Angel T.; Domen, Kazunari; Xu, Wei; Takanabe, Kazuhiro

2014-01-01

A simple and versatile method for the preparation of photocatalyst particulates modified with effective cocatalysts is presented; the method involves the sequential soaking of photocatalyst particulates in solutions containing bifunctional organic linkers and metal ions. The modification of the particulate surfaces is a universal and reproducible method because the molecular linkers utilize strong covalent bonds, which in turn result in modified monolayer with a small but controlled quantity of metals. The photocatalysis results indicated that the CdS with likely photochemically reduced Pd and Ni, which were initially immobilized via ethanedithiol (EDT) as a linker, were highly efficient for photocatalytic hydrogen evolution from Na2S-Na2SO3-containing aqueous solutions. The method developed in this study opens a new synthesis route for the preparation of effective photocatalysts with various combinations of bifunctional linkers, metals, and photocatalyst particulate materials. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Convergent evolution of the genomes of marine mammals

Science.gov (United States)

Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

2015-01-01

Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

Advantageous Microwave-Assisted Suzuki Polycondensation for the Synthesis of Aniline-Fluorene Alternate Copolymers as Molecular Model with Solvent Sensing Properties

Directory of Open Access Journals (Sweden)

Rebeca Vázquez-Guilló

2018-02-01

Full Text Available Polymerization via Suzuki coupling under microwave (µW irradiation has been studied for the synthesis of poly{1,4-(2/3-aminobenzene-alt-2,7-(9,9-dihexylfluorene} (PAF, chosen as molecular model. Briefly, µW-assisted procedures accelerated by two orders of magnitude the time required when using classical polymerization processes, and the production yield was increased (>95%. In contrast, although the sizes of the polymers that were obtained by non-conventional heating reactions were reproducible and adequate for most applications, with this methodology the molecular weight of final polymers were not increased with respect to conventional heating. Asymmetric orientation of the amine group within the monomer and the assignments of each dyad or regioregularity, whose values ranged from 38% to 95% with this molecule, were analysed using common NMR spectroscopic data. Additionally, the synthesis of a new cationic polyelectrolyte, poly{1,4-(2/3-aminobenzene-co-alt-2,7-[9,9´-bis(6’’-N,N,N-trimethylammonium-hexylfluorene]} dibromide (PAFAm, from poly{1,4-(2/3-aminobenzene-co-alt-2,7-[9,9´-bis(6’’-bromohexylfluorene]} (PAFBr by using previously optimized conditions for µW-assisted heating procedures was reported. Finally, the characterization of the final products from these batches showed unkown interesting solvatochromic properties of the PAF molecule. The study of the solvatochromism phenomena, which was investigated as a function of the polarity of the solvents, showed a well-defined Lippert correlation, indicating that the emission shift observed in PAF might be due to its interaction with surrounding environment. Proven high sensitivity to changes of its environment makes PAF a promising candidate of sensing applications.

Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions

Directory of Open Access Journals (Sweden)

Afonnikov Dmitry A

2009-12-01

Full Text Available Abstract Background Prokaryotic microorganisms are able to survive and proliferate in severe environmental conditions. The increasing number of complete sequences of prokaryotic genomes has provided the basis for studying the molecular mechanisms of their adaptation at the genomic level. We apply here a computer-based approach to compare the genomes and proteomes from P. furiosus, P. horikoshii, and P. abyssi to identify features of their molecular evolution related to adaptation strategy to diverse environmental conditions. Results Phylogenetic analysis of rRNA genes from 26 Pyrococcus strains suggested that the divergence of P. furiosus, P. horikoshii and P. abyssi might have occurred from ancestral deep-sea organisms. It was demonstrated that the function of genes that have been subject to positive Darwinian selection is closely related to abiotic and biotic conditions to which archaea managed to become adapted. Divergence of the P. furiosus archaea might have been due to loss of some genes involved in cell motility or signal transduction, and/or to evolution under positive selection of the genes for translation machinery. In the course of P. horikoshii divergence, positive selection was found to operate mainly on the transcription machinery; divergence of P. abyssi was related with positive selection for the genes mainly involved in inorganic ion transport. Analysis of radical amino acid replacement rate in evolving P. furiosus, P. horikoshii and P. abyssi showed that the fixation rate was higher for radical substitutions relative to the volume of amino acid side-chain. Conclusions The current results give due credit to the important role of hydrostatic pressure as a cause of variability in the P. furiosus, P. horikoshii and P. abyssi genomes evolving in different habitats. Nevertheless, adaptation to pressure does not appear to be the sole factor ensuring adaptation to environment. For example, at the stage of the divergence of P

Topology evolution in macromolecular networks

NARCIS (Netherlands)

Kryven, I.

2014-01-01

Governed by various intermolecular forces, molecular networks tend to evolve from simple to very complex formations that have random structure. This randomness in the connectivity of the basic units can still be captured employing distributional description of the state of the system; the evolution

The Relation between Recombination Rate and Patterns of Molecular Evolution and Variation in Drosophila melanogaster

Science.gov (United States)

Campos, José L.; Halligan, Daniel L.; Haddrill, Penelope R.; Charlesworth, Brian

2014-01-01

Genetic recombination associated with sexual reproduction increases the efficiency of natural selection by reducing the strength of Hill–Robertson interference. Such interference can be caused either by selective sweeps of positively selected alleles or by background selection (BGS) against deleterious mutations. Its consequences can be studied by comparing patterns of molecular evolution and variation in genomic regions with different rates of crossing over. We carried out a comprehensive study of the benefits of recombination in Drosophila melanogaster, both by contrasting five independent genomic regions that lack crossing over with the rest of the genome and by comparing regions with different rates of crossing over, using data on DNA sequence polymorphisms from an African population that is geographically close to the putatively ancestral population for the species, and on sequence divergence from a related species. We observed reductions in sequence diversity in noncrossover (NC) regions that are inconsistent with the effects of hard selective sweeps in the absence of recombination. Overall, the observed patterns suggest that the recombination rate experienced by a gene is positively related to an increase in the efficiency of both positive and purifying selection. The results are consistent with a BGS model with interference among selected sites in NC regions, and joint effects of BGS, selective sweeps, and a past population expansion on variability in regions of the genome that experience crossing over. In such crossover regions, the X chromosome exhibits a higher rate of adaptive protein sequence evolution than the autosomes, implying a Faster-X effect. PMID:24489114

Quasi-molecular states in sd-shell nuclei

International Nuclear Information System (INIS)

Kubono, S.; Ikeda, N.; Nomura, T.

1988-08-01

Quasi-molecular states near and below the threshold of the molecular configuration in sd-shell nuclei are discussed using recent experimental data with particle-gamma coincidence method and particle-particle coincidence method. Possible quasi-molecular states have been identified in 24 Mg as well as in 28 Si and 32 S. The important role of quasi-molecular states are discussed, specifically for the shape evolution of nuclei as a function of excitation energy and angular momentum. (author)

Society for Assisted Reproductive Technology and assisted reproductive technology in the United States: a 2016 update.

Science.gov (United States)

Toner, James P; Coddington, Charles C; Doody, Kevin; Van Voorhis, Brad; Seifer, David B; Ball, G David; Luke, Barbara; Wantman, Ethan

2016-09-01

The Society for Assisted Reproductive Technology (SART) was established within a few years of assisted reproductive technology (ART) in the United States, and has not only reported on the evolution of infertility care, but also guided it toward improved success and safety. Moving beyond its initial role as a registry, SART has expanded its role to include quality assurance, data validation, practice and advertising guidelines, research, patient education and advocacy, and membership support. The success of ART in this country has greatly benefited from SART's role, as highlighted by a series of graphs. SART continues to set the standard and lead the way. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Molecular phylogeny and character evolution of the chthamaloid barnacles (Cirripedia:Thoracica)

DEFF Research Database (Denmark)

Pérez-Losada, Marcos; Høeg, Jens Thorvald; Crandall, Keith A.

2012-01-01

surrounded by whorls of small imbricating plates; but this hypothesis has never been subjected to a rigorous phylogenetic test. Here we used multilocus sequence data and extensive taxon sampling to build a comprehensive phylogeny of the Chthamaloidea as a basis for understanding their morphological evolution......The Chthamaloidea (Balanomorpha) present the most plesiomorphic characters in shell plates and cirri, mouthparts, and oral cone within the acorn barnacles (Thoracica: Sessilia). Due to their importance in understanding both the origin and diversification of the Balanomorpha, the evolution...... of the Chthamaloidea has been debated since Darwin's seminal monographs. Theories of morphological and ontogenetic evolution suggest that the group could have evolved multiple times from pedunculated relatives and that shell plate number diminished gradually (8¿6¿4) from an ancestral state with eight wall plates...

Evolution of robotic nephrectomy for living donation: from hand-assisted to totally robotic technique.

Science.gov (United States)

Giacomoni, Alessandro; Di Sandro, Stefano; Lauterio, Andrea; Concone, Giacomo; Mangoni, Iacopo; Mihaylov, Plamen; Tripepi, Matteo; De Carlis, Luciano

2014-09-01

The application of robotic-assisted surgery offers EndoWrist instruments and 3-D visualization of the operative field, which are improvements over traditional laparoscopy. The results of the few studies published so far have shown that living donor nephrectomy using the robot-assisted technique is safe, feasible, and offers advantages to patients. Since November 2009, 16 patients have undergone robotic-assisted living donor nephrectomy at our Institute. Patients were divided into two groups according to the surgical technique adopted for the procedure: Group A, hand-assisted robotic nephrectomy (eight patients); Group B, totally robotic nephrectomy (eight patients). Intra-operative bleeding was similar in the two groups (90 vs 100 mL for Group A and B, respectively). Median warm ischemia time was significantly shorter in Group A (2.3 vs 5.1 min for Group A and B, respectively, P-value = 0.05). Switching to the open procedure was never required. Median operative time was not significantly longer in Group A than Group B (275 min vs 250 min, respectively). Robotic assisted living kidney recovery is a safe and effective procedure. Considering the overall technical, clinical, and feasibility aspects of living kidney donation, we believe that the robotic assisted technique is the method of choice for surgeon's comfort and donors' safety. Copyright © 2014 John Wiley & Sons, Ltd.

Molecular Epidemiology and Genomics of Group A Streptococcus

Science.gov (United States)

Bessen, Debra E.; McShan, W. Michael; Nguyen, Scott V.; Shetty, Amol; Agrawal, Sonia; Tettelin, Hervé

2014-01-01

Streptococcus pyogenes (group A streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed. PMID:25460818

Growth and etching characteristics of (001) β-Ga2O3 by plasma-assisted molecular beam epitaxy

Science.gov (United States)

Oshima, Yuichi; Ahmadi, Elaheh; Kaun, Stephen; Wu, Feng; Speck, James S.

2018-01-01

We investigated the homoepitaxial growth and etching characteristics of (001) β-Ga2O3 by plasma-assisted molecular beam epitaxy. The growth rate of β-Ga2O3 increased with increasing Ga-flux, reaching a clear plateau of 56 nm h-1, and then decreased at higher Ga-flux. The growth rate decreased from 56 to 42 nm h-1 when the substrate temperature was increased from 750 °C to 800 °C. The growth rate was negative (net etching) when only Ga-flux was supplied. The etching rate proportionally increased with increasing the Ga-flux, reaching 84 nm h-1. The etching was enhanced at higher temperatures. It was found that Ga-etching of (001) β-Ga2O3 substrates prior to the homoepitaxial growth markedly improved the surface roughness of the film.

A Global Multi-Objective Optimization Tool for Design of Mechatronic Components using Generalized Differential Evolution

DEFF Research Database (Denmark)

Bech, Michael Møller; Nørgård, Christian; Roemer, Daniel Beck

2016-01-01

This paper illustrates how the relatively simple constrained multi-objective optimization algorithm Generalized Differential Evolution 3 (GDE3), can assist with the practical sizing of mechatronic components used in e.g. digital displacement fluid power machinery. The studied bi- and tri-objectiv......This paper illustrates how the relatively simple constrained multi-objective optimization algorithm Generalized Differential Evolution 3 (GDE3), can assist with the practical sizing of mechatronic components used in e.g. digital displacement fluid power machinery. The studied bi- and tri...... different optimization control parameter settings and it is concluded that GDE3 is a reliable optimization tool that can assist mechatronic engineers in the design and decision making process....

Evolution of the metazoan mitochondrial replicase.

Science.gov (United States)

Oliveira, Marcos T; Haukka, Jani; Kaguni, Laurie S

2015-03-03

The large number of complete mitochondrial DNA (mtDNA) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. By investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtDNA polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by exploring the relationships between DNA replication and animal mitochondrial genome diversity. We identified three evolutionary patterns among metazoan pol γs. First, a trend toward stabilization of both sequence and structure occurred in vertebrates, with both subunits evolving distinctly from those of other animal groups, and acquiring at least four novel structural elements, the most important of which is the HLH-3β (helix-loop-helix, 3 β-sheets) domain that allows the accessory subunit to homodimerize. Second, both subunits of arthropods and tunicates have become shorter and evolved approximately twice as rapidly as their vertebrate homologs. And third, nematodes have lost the gene for the accessory subunit, which was accompanied by the loss of its interacting domain in the catalytic subunit of pol γ, and they show the highest rate of molecular evolution among all animal taxa. These findings correlate well with the mtDNA genomic features of each group described above, and with their modes of DNA replication, although a substantive amount of biochemical work is needed to draw conclusive links regarding the latter. Describing the parallels between evolution of pol γ and metazoan mtDNA architecture may also help in understanding the processes that lead to mitochondrial dysfunction and to human disease-related phenotypes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolution of Karyotypes in Chameleons

Czech Academy of Sciences Publication Activity Database

Rovatsos, M.; Altmanová, M.; Johnson Pokorná, Martina; Velenský, P.; Baca, A. S.; Kratochvíl, L.

2017-01-01

Roč. 8, č. 12 (2017), č. článku 382. ISSN 2073-4425 Institutional support: RVO:67985904 Keywords : karyotype evolution * ITS * rDNA Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 3.600, year: 2016

ON THE SIMULTANEOUS EVOLUTION OF MASSIVE PROTOSTARS AND THEIR HOST CORES

International Nuclear Information System (INIS)

Kuiper, R.; Yorke, H. W.

2013-01-01

Studies of the evolution of massive protostars and the evolution of their host molecular cloud cores are commonly treated as separate problems. However, interdependencies between the two can be significant. Here, we study the simultaneous evolution of massive protostars and their host molecular cores using a multi-dimensional radiation hydrodynamics code that incorporates the effects of the thermal pressure and radiative acceleration feedback of the centrally forming protostar. The evolution of the massive protostar is computed simultaneously using the stellar evolution code STELLAR, modified to include the effects of variable accretion. The interdependencies are studied in three different collapse scenarios. For comparison, stellar evolutionary tracks at constant accretion rates and the evolution of the host cores using pre-computed stellar evolutionary tracks are computed. The resulting interdependencies of the protostellar evolution and the evolution of the environment are extremely diverse and depend on the order of events, in particular the time of circumstellar accretion disk formation with respect to the onset of the bloating phase of the star. Feedback mechanisms affect the instantaneous accretion rate and the protostar's radius, temperature, and luminosity on timescales t ≤ 5 kyr, corresponding to the accretion timescale and Kelvin-Helmholtz contraction timescale, respectively. Nevertheless, it is possible to approximate the overall protostellar evolution in many cases by pre-computed stellar evolutionary tracks assuming appropriate constant average accretion rates

Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

Science.gov (United States)

Izunobi, Josephat U.; Higginbotham, Clement L.

2011-01-01

The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…

The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae.

Science.gov (United States)

de Santana Lopes, Amanda; Gomes Pacheco, Túlio; Nimz, Tabea; do Nascimento Vieira, Leila; Guerra, Miguel P; Nodari, Rubens O; de Souza, Emanuel Maltempi; de Oliveira Pedrosa, Fábio; Rogalski, Marcelo

2018-04-01

The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.

Molecular evolution of the odorant and gustatory receptor genes in lepidopteran insects: implications for their adaptation and speciation.

Science.gov (United States)

Engsontia, Patamarerk; Sangket, Unitsa; Chotigeat, Wilaiwan; Satasook, Chutamas

2014-08-01

Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecular evolution of the lepidopteran odorant (Or) and gustatory receptor (Gr) genes using recently identified genes from Bombyx mori, Danaus plexippus, Heliconius melpomene, Plutella xylostella, Heliothis virescens, Manduca sexta, Cydia pomonella, and Spodoptera littoralis. A limited number of cases of large lineage-specific gene expansion are observed (except in the P. xylostella lineage), possibly due to selection against tandem gene duplication. There has been strong purifying selection during the evolution of both lepidopteran odorant and gustatory genes, as shown by the low ω values estimated through CodeML analysis, ranging from 0.0093 to 0.3926. However, purifying selection has been relaxed on some amino acid sites in these receptors, leading to sequence divergence, which is a precursor of positive selection on these sequences. Signatures of positive selection were detected only in a few loci from the lineage-specific analysis. Estimation of gene gains and losses suggests that the common ancestor of the Lepidoptera had fewer Or genes compared to extant species and an even more reduced number of Gr genes, particularly within the bitter receptor clade. Multiple gene gains and a few gene losses occurred during the evolution of Lepidoptera. Gene family expansion may be associated with the adaptation of lepidopteran species to plant hosts, especially after angiosperm radiation. Phylogenetic analysis of the moth sex pheromone receptor genes suggested that chromosomal translocations have occurred several times. New sex pheromone receptors have arisen through tandem gene duplication. Positive selection was detected at some amino acid sites predicted to be

Mobile DNA and evolution in the 21st century

Directory of Open Access Journals (Sweden)

Shapiro James A

2010-01-01

Full Text Available Abstract Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs. The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification.

Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges

Science.gov (United States)

Schuster, Astrid; Erpenbeck, Dirk; Pisera, Andrzej; Hooper, John; Bryce, Monika; Fromont, Jane; Wörheide, Gert

2015-01-01

Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). ‘Lithistida’, a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of ‘lithistid’ demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous ‘order Lithistida’. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences), we show that 8 out of 13 ‘Lithistida’ families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae – we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different �

Crystal plasticity assisted prediction on the yield locus evolution and forming limit curves

Science.gov (United States)

Lian, Junhe; Liu, Wenqi; Shen, Fuhui; Münstermann, Sebastian

2017-10-01

The aim of this study is to predict the plastic anisotropy evolution and its associated forming limit curves of bcc steels purely based on their microstructural features by establishing an integrated multiscale modelling approach. Crystal plasticity models are employed to describe the micro deformation mechanism and correlate the microstructure with mechanical behaviour on micro and mesoscale. Virtual laboratory is performed considering the statistical information of the microstructure, which serves as the input for the phenomenological plasticity model on the macroscale. For both scales, the microstructure evolution induced evolving features, such as the anisotropic hardening, r-value and yield locus evolution are seamlessly integrated. The predicted plasticity behaviour by the numerical simulations are compared with experiments. These evolutionary features of the material deformation behaviour are eventually considered for the prediction of formability.

Morphological and Molecular Evolution of Flesh Flies of Sarcophaginae (Diptera: Sarcophagidae)

DEFF Research Database (Denmark)

Buenaventura Ruiz, Ingrid Eliana

))). Peckiamyia was sister to Retrocitomyia,and Titanogrypa was sister to Villegasia, which together with Engelimyia formed a lineageemerging in a basal divergence with regard to the clade with no median stylus. Alternativehomology interpretations of the median stylus were also studied and tested......, this will help to understand male genitalia evolution and the use of these8structures as a source of phylogenetic information, but it could also provide a contribution to ourgeneral understanding on insect morphological evolution....

On the Evolution of the Mammalian Brain.

Science.gov (United States)

Torday, John S; Miller, William B

2016-01-01

Hobson and Friston have hypothesized that the brain must actively dissipate heat in order to process information (Hobson et al., 2014). This physiologic trait is functionally homologous with the first instantation of life formed by lipids suspended in water forming micelles- allowing the reduction in entropy (heat dissipation). This circumvents the Second Law of Thermodynamics permitting the transfer of information between living entities, enabling them to perpetually glean information from the environment, that is felt by many to correspond to evolution per se. The next evolutionary milestone was the advent of cholesterol, embedded in the cell membranes of primordial eukaryotes, facilitating metabolism, oxygenation and locomotion, the triadic basis for vertebrate evolution. Lipids were key to homeostatic regulation of calcium, forming calcium channels. Cell membrane cholesterol also fostered metazoan evolution by forming lipid rafts for receptor-mediated cell-cell signaling, the origin of the endocrine system. The eukaryotic cell membrane exapted to all complex physiologic traits, including the lung and brain, which are molecularly homologous through the function of neuregulin, mediating both lung development and myelinization of neurons. That cooption later exapted as endothermy during the water-land transition (Torday, 2015a), perhaps being the functional homolog for brain heat dissipation and conscious/mindful information processing. The skin and brain similarly share molecular homologies through the "skin-brain" hypothesis, giving insight to the cellular-molecular "arc" of consciousness from its unicellular origins to integrated physiology. This perspective on the evolution of the central nervous system clarifies self-organization, reconciling thermodynamic and informational definitions of the underlying biophysical mechanisms, thereby elucidating relations between the predictive capabilities of the brain and self-organizational processes.

Molecular anthropology in the genomic era.

Science.gov (United States)

Destro-Bisol, Giovanni; Jobling, Mark A; Rocha, Jorge; Novembre, John; Richards, Martin B; Mulligan, Connie; Batini, Chiara; Manni, Franz

2010-01-01

Molecular Anthropology is a relatively young field of research. In fact, less than 50 years have passed since the symposium "Classification and Human Evolution" (1962, Burg Wartenstein, Austria), where the term was formally introduced by Emil Zuckerkandl. In this time, Molecular Anthropology has developed both methodologically and theoretically and extended its applications, so covering key aspects of human evolution such as the reconstruction of the history of human populations and peopling processes, the characterization of DNA in extinct humans and the role of adaptive processes in shaping the genetic diversity of our species. In the current scientific panorama, molecular anthropologists have to face a double challenge. As members of the anthropological community, we are strongly committed to the integration of biological findings and other lines of evidence (e.g. linguistic and archaeological), while keeping in line with methodological innovations which are moving the approach from the genetic to the genomic level. In this framework, the meeting "DNA Polymorphisms in Human Populations: Molecular Anthropology in the Genomic Era" (Rome, December 3-5, 2009) offered an opportunity for discussion among scholars from different disciplines, while paying attention to the impact of recent methodological innovations. Here we present an overview of the meeting and discuss perspectives and prospects of Molecular Anthropology in the genomic era.

Molecular markers for use in plant molecular breeding and germplasm evaluation

International Nuclear Information System (INIS)

Edwards, J.D.; McCouch, S.R.

2007-01-01

A number of molecular marker technologies exist, each with different advantages and disadvantages. When available, genome sequence allows for the development of greater numbers and higher quality molecular markers. When genome sequence is limited in the organism of interest, related species may serve as sources of molecular markers. Some molecular marker technologies combine the discovery and assay of DNA sequence variations, and therefore can be used in species without the need for prior sequence information and up-front investment in marker development. As a prerequisite for marker-assisted selection (MAS), there must be a known association between genetic markers and genes affecting the phenotype to be modified. Comparative databases can facilitate the transfer of knowledge of genetic marker-phenotype association across species so that discoveries in one species may be applied to many others. Further genomics research and reductions in the costs associated with molecular markers will continue to provide new opportunities to employ MAS. (author)

Phonon-assisted decoherence and tunneling in quantum dot molecules

DEFF Research Database (Denmark)

Grodecka-Grad, Anna; Foerstner, Jens

2011-01-01

processes with relevant acoustic phonons. We show that the relaxation is dominated by phonon-assisted electron tunneling between constituent quantum dots and occurs on a picosecond time scale. The dependence of the time evolution of the quantum dot occupation probabilities on the energy mismatch between...

Hosting Early Evolution in Heated Pores of Rock

Science.gov (United States)

Mast, C. B.; Möller, F.; Lanzmich, S.; Keil, L.; Braun, D.

2017-07-01

Recent experiments with non-equilibrium micro­systems suggest that porous rock conditions drive early molecular evolution in many ways, including accumulation, polymerization, replication, length selection and gelation.

High incidence of monozygotic twinning after assisted reproduction is related to genetic information, but not to assisted reproduction technology itself

Czech Academy of Sciences Publication Activity Database

Sobek Jr., A.; Zbořilová, B.; Procházka, M.; Šilhánová, E.; Koutná, O.; Klásková, E.; Tkadlec, Emil; Sobek, A.

2015-01-01

Roč. 103, č. 3 (2015), s. 756-760 ISSN 0015-0282 Institutional support: RVO:68081766 Keywords : monozygotic twins * genetics * assisted reproduction techniques * infertility Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.426, year: 2015

Molecular Evolution and Expression Divergence of HMT Gene Family in Plants

Directory of Open Access Journals (Sweden)

Man Zhao

2018-04-01

Full Text Available Homocysteine methyltransferase (HMT converts homocysteine to methionine using S-methylmethionine (SMM or S-adenosylmethionine (SAM as methyl donors in organisms, playing an important role in supplying methionine for the growth and the development of plants. To better understand the functions of the HMT genes in plants, we conducted a wide evolution and expression analysis of these genes. Reconstruction of the phylogenetic relationship showed that the HMT gene family was divided into Class 1 and Class 2. In Class 1, HMTs were only found in seed plants, while Class 2 presented in all land plants, which hinted that the HMT genes might have diverged in seed plants. The analysis of gene structures and selection pressures showed that they were relatively conserved during evolution. However, type I functional divergence had been detected in the HMTs. Furthermore, the expression profiles of HMTs showed their distinct expression patterns in different tissues, in which some HMTs were widely expressed in various organs, whereas the others were highly expressed in some specific organs, such as seeds or leaves. Therefore, according to our results in the evolution, functional divergence, and expression, the HMT genes might have diverged during evolution. Further analysis in the expression patterns of AthHMTs with their methyl donors suggested that the diverged HMTs might be related to supply methionine for the development of plant seeds.

Towards an alternative evolution model.

Science.gov (United States)

van Waesberghe, H

1982-01-01

Lamarck and Darwin agreed on the inconstancy of species and on the exclusive gradualism of evolution (nature does not jump). Darwinism, revived as neo-Darwinism, was almost generally accepted from about 1930 till 1960. In the sixties the evolutionary importance of selection has been called in question by the neutralists. The traditional conception of the gene is disarranged by recent molecular-biological findings. Owing to the increasing confusion about the concept of genotype, this concept is reconsidered. The idea of the genotype as a cluster of genes is replaced by a cybernetical interpretation of the genotype. As nature does jump, exclusive gradualism is dismissed. Saltatory evolution is a natural phenomenon, provided by a sudden collapse of the thresholds which resist against evolution. The fossil record and the taxonomic system call for a macromutational interpretation. As Lamarck and Darwin overlooked the resistance of evolutionary thresholds, an alternative evolution model is needed, the first to be constructed on a palaeontological and taxonomic basis.

Rapid molecular evolution across amniotes of the IIS/TOR network.

Science.gov (United States)

McGaugh, Suzanne E; Bronikowski, Anne M; Kuo, Chih-Horng; Reding, Dawn M; Addis, Elizabeth A; Flagel, Lex E; Janzen, Fredric J; Schwartz, Tonia S

2015-06-02

The insulin/insulin-like signaling and target of rapamycin (IIS/TOR) network regulates lifespan and reproduction, as well as metabolic diseases, cancer, and aging. Despite its vital role in health, comparative analyses of IIS/TOR have been limited to invertebrates and mammals. We conducted an extensive evolutionary analysis of the IIS/TOR network across 66 amniotes with 18 newly generated transcriptomes from nonavian reptiles and additional available genomes/transcriptomes. We uncovered rapid and extensive molecular evolution between reptiles (including birds) and mammals: (i) the IIS/TOR network, including the critical nodes insulin receptor substrate (IRS) and phosphatidylinositol 3-kinase (PI3K), exhibit divergent evolutionary rates between reptiles and mammals; (ii) compared with a proxy for the rest of the genome, genes of the IIS/TOR extracellular network exhibit exceptionally fast evolutionary rates; and (iii) signatures of positive selection and coevolution of the extracellular network suggest reptile- and mammal-specific interactions between members of the network. In reptiles, positively selected sites cluster on the binding surfaces of insulin-like growth factor 1 (IGF1), IGF1 receptor (IGF1R), and insulin receptor (INSR); whereas in mammals, positively selected sites clustered on the IGF2 binding surface, suggesting that these hormone-receptor binding affinities are targets of positive selection. Further, contrary to reports that IGF2R binds IGF2 only in marsupial and placental mammals, we found positively selected sites clustered on the hormone binding surface of reptile IGF2R that suggest that IGF2R binds to IGF hormones in diverse taxa and may have evolved in reptiles. These data suggest that key IIS/TOR paralogs have sub- or neofunctionalized between mammals and reptiles and that this network may underlie fundamental life history and physiological differences between these amniote sister clades.

Molecular evolution of the crustacean hyperglycemic hormone family in ecdysozoans

Directory of Open Access Journals (Sweden)

Soyez Daniel

2010-02-01

Full Text Available Abstract Background Crustacean Hyperglycemic Hormone (CHH family peptides are neurohormones known to regulate several important functions in decapod crustaceans such as ionic and energetic metabolism, molting and reproduction. The structural conservation of these peptides, together with the variety of functions they display, led us to investigate their evolutionary history. CHH family peptides exist in insects (Ion Transport Peptides and may be present in all ecdysozoans as well. In order to extend the evolutionary study to the entire family, CHH family peptides were thus searched in taxa outside decapods, where they have been, to date, poorly investigated. Results CHH family peptides were characterized by molecular cloning in a branchiopod crustacean, Daphnia magna, and in a collembolan, Folsomia candida. Genes encoding such peptides were also rebuilt in silico from genomic sequences of another branchiopod, a chelicerate and two nematodes. These sequences were included in updated datasets to build phylogenies of the CHH family in pancrustaceans. These phylogenies suggest that peptides found in Branchiopoda and Collembola are more closely related to insect ITPs than to crustacean CHHs. Datasets were also used to support a phylogenetic hypothesis about pancrustacean relationships, which, in addition to gene structures, allowed us to propose two evolutionary scenarios of this multigenic family in ecdysozoans. Conclusions Evolutionary scenarios suggest that CHH family genes of ecdysozoans originate from an ancestral two-exon gene, and genes of arthropods from a three-exon one. In malacostracans, the evolution of the CHH family has involved several duplication, insertion or deletion events, leading to neuropeptides with a wide variety of functions, as observed in decapods. This family could thus constitute a promising model to investigate the links between gene duplications and functional divergence.

VO2 Thermochromic Films on Quartz Glass Substrate Grown by RF-Plasma-Assisted Oxide Molecular Beam Epitaxy

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Dong Zhang

2017-03-01

Full Text Available Vanadium dioxide (VO2 thermochromic thin films with various thicknesses were grown on quartz glass substrates by radio frequency (RF-plasma assisted oxide molecular beam epitaxy (O-MBE. The crystal structure, morphology and chemical stoichiometry were investigated systemically by X-ray diffraction (XRD, atomic force microscopy (AFM, Raman spectroscopy and X-ray photoelectron spectroscopy (XPS analyses. An excellent reversible metal-to-insulator transition (MIT characteristics accompanied by an abrupt change in both electrical resistivity and optical infrared (IR transmittance was observed from the optimized sample. Remarkably, the transition temperature (TMIT deduced from the resistivity-temperature curve was reasonably consistent with that obtained from the temperature-dependent IR transmittance. Based on Raman measurement and XPS analyses, the observations were interpreted in terms of residual stresses and chemical stoichiometry. This achievement will be of great benefit for practical application of VO2-based smart windows.

Hydrogen evolution by a metal-free electrocatalyst

KAUST Repository

Zheng, Yao; Jiao, Yan; Zhu, Yihan; Li, Luhua; Han, Yu; Chen, Ying; Du, Aijun; Jaronieć, Mietek; Qiao, Shizhang

2014-01-01

Electrocatalytic reduction of water to molecular hydrogen via the hydrogen evolution reaction may provide a sustainable energy supply for the future, but its commercial application is hampered by the use of precious platinum catalysts. All

Ribosome evolution: Emergence of peptide synthesis machinery

Indian Academy of Sciences (India)

suggested the dynamic movement of ribosomal proteins. The L2 protein (a .... Such kinds of interactions are important in elucidating the evolution of RNA .... Tamura K 2009 Molecular handedness of life: significance of RNA aminoacylation.

Heme pathway evolution in kinetoplastid protists

Czech Academy of Sciences Publication Activity Database

Cenci, U.; Moog, D.; Curtis, B.A.; Tanifuji, G.; Eme, L.; Lukeš, Julius; Archibald, J.M.

2016-01-01

Roč. 16, MAY 18 (2016), č. článku 109. ISSN 1471-2148 Institutional support: RVO:60077344 Keywords : heme * kinetoplastea * Paramoeba pemaquidensis * Perkinsela * evolution * endosymbiosis * Prokinetoplastina * lateral gene transfer Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.221, year: 2016

Molecular Elucidation of Disease Biomarkers at the Interface of Chemistry and Biology.

Science.gov (United States)

Zhang, Liqin; Wan, Shuo; Jiang, Ying; Wang, Yanyue; Fu, Ting; Liu, Qiaoling; Cao, Zhijuan; Qiu, Liping; Tan, Weihong

2017-02-22

Disease-related biomarkers are objectively measurable molecular signatures of physiological status that can serve as disease indicators or drug targets in clinical diagnosis and therapy, thus acting as a tool in support of personalized medicine. For example, the prostate-specific antigen (PSA) biomarker is now widely used to screen patients for prostate cancer. However, few such biomarkers are currently available, and the process of biomarker identification and validation is prolonged and complicated by inefficient methods of discovery and few reliable analytical platforms. Therefore, in this Perspective, we look at the advanced chemistry of aptamer molecules and their significant role as molecular probes in biomarker studies. As a special class of functional nucleic acids evolved from an iterative technology termed Systematic Evolution of Ligands by Exponential Enrichment (SELEX), these single-stranded oligonucleotides can recognize their respective targets with selectivity and affinity comparable to those of protein antibodies. Because of their fast turnaround time and exceptional chemical properties, aptamer probes can serve as novel molecular tools for biomarker investigations, particularly in assisting identification of new disease-related biomarkers. More importantly, aptamers are able to recognize biomarkers from complex biological environments such as blood serum and cell surfaces, which can provide direct evidence for further clinical applications. This Perspective highlights several major advancements of aptamer-based biomarker discovery strategies and their potential contribution to the practice of precision medicine.

Molecular Theory of the Living Cell Concepts, Molecular Mechanisms, and Biomedical Applications

CERN Document Server

Ji, Sungchul

2012-01-01

This book presents a comprehensive molecular theory of the living cell based on over thirty concepts, principles and laws imported from thermodynamics, statistical mechanics, quantum mechanics, chemical kinetics, informatics, computer science, linguistics, semiotics, and philosophy. The author formulates physically, chemically and enzymologically realistic molecular mechanisms to account for the basic living processes such as ligand-receptor interactions, protein folding, single-molecule enzymic catalysis, force-generating mechanisms in molecular motors, signal transduction, regulation of the genome-wide RNA metabolism, morphogenesis, the micro-macro coupling in coordination dynamics, the origin of life, and the mechanisms of biological evolution itself. Possible solutions to basic and practical problems facing contemporary biology and biomedical sciences have been suggested, including pharmacotheragnostics and personalized medicine.

A novel C-type lysozyme from Mytilus galloprovincialis: insight into innate immunity and molecular evolution of invertebrate C-type lysozymes.

Directory of Open Access Journals (Sweden)

Qing Wang

Full Text Available A c-type lysozyme (named as MgCLYZ gene was cloned from the mussel Mytilus galloprovincialis. Blast analysis indicated that MgCLYZ was a salivary c-type lysozyme which was mainly found in insects. The nucleotide sequence of MgCLYZ was predicted to encode a polypeptide of 154 amino acid residues with the signal peptide comprising the first 24 residues. The deduced mature peptide of MgCLYZ was of a calculated molecular weight of 14.4 kD and a theoretical isoelectric point (pI of 8.08. Evolution analysis suggested that bivalve branch of the invertebrate c-type lysozymes phylogeny tree underwent positive selection during evolution. By quantitative real-time RT-PCR (qRT-PCR analysis, MgCLYZ transcript was widely detected in all examined tissues and responded sensitively to bacterial challenge in hemocytes and hepatopancreas. The optimal temperature and pH of recombinant MgCLYZ (rMgCLYZ were 20°C and 4, respectively. The rMgCLYZ displayed lytic activities against Gram-positive bacteria including Micrococcus luteus and Staphyloccocus aureus, and Gram-negative bacteria including Vibrio anguillarum, Enterobacter cloacae, Pseudomonas putida, Proteus mirabilis and Bacillus aquimaris. These results suggest that MgCLYZ perhaps play an important role in innate immunity of M. galloprovincialis, and invertebrate c-type lysozymes might be under positive selection in a species-specific manner during evolution for undergoing adaptation to different environment and diverse pathogens.

PROTOPLANETARY DISK STRUCTURE WITH GRAIN EVOLUTION: THE ANDES MODEL

International Nuclear Information System (INIS)

Akimkin, V.; Wiebe, D.; Pavlyuchenkov, Ya.; Zhukovska, S.; Semenov, D.; Henning, Th.; Vasyunin, A.; Birnstiel, T.

2013-01-01

We present a self-consistent model of a protoplanetary disk: 'ANDES' ('AccretioN disk with Dust Evolution and Sedimentation'). ANDES is based on a flexible and extendable modular structure that includes (1) a 1+1D frequency-dependent continuum radiative transfer module, (2) a module to calculate the chemical evolution using an extended gas-grain network with UV/X-ray-driven processes and surface reactions, (3) a module to calculate the gas thermal energy balance, and (4) a 1+1D module that simulates dust grain evolution. For the first time, grain evolution and time-dependent molecular chemistry are included in a protoplanetary disk model. We find that grain growth and sedimentation of large grains onto the disk midplane lead to a dust-depleted atmosphere. Consequently, dust and gas temperatures become higher in the inner disk (R ∼ 50 AU), in comparison with the disk model with pristine dust. The response of disk chemical structure to the dust growth and sedimentation is twofold. First, due to higher transparency a partly UV-shielded molecular layer is shifted closer to the dense midplane. Second, the presence of big grains in the disk midplane delays the freeze-out of volatile gas-phase species such as CO there, while in adjacent upper layers the depletion is still effective. Molecular concentrations and thus column densities of many species are enhanced in the disk model with dust evolution, e.g., CO 2 , NH 2 CN, HNO, H 2 O, HCOOH, HCN, and CO. We also show that time-dependent chemistry is important for a proper description of gas thermal balance.

Early evolution without a tree of life.

Science.gov (United States)

Martin, William F

2011-06-30

Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause.

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

OpenAIRE

He, Jiangfeng; Zhao, Xiaoqing; Laroche, André; Lu, Zhen-Xiang; Liu, HongKui; Li, Ziqin

2014-01-01

Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broad...

Molecular evolution of a-kinase anchoring protein (AKAP-7: implications in comparative PKA compartmentalization

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Johnson Keven R

2012-07-01

Full Text Available Abstract Background A-Kinase Anchoring Proteins (AKAPs are molecular scaffolding proteins mediating the assembly of multi-protein complexes containing cAMP-dependent protein kinase A (PKA, directing the kinase in discrete subcellular locations. Splice variants from the AKAP7 gene (AKAP15/18 are vital components of neuronal and cardiac phosphatase complexes, ion channels, cardiac Ca2+ handling and renal water transport. Results Shown in evolutionary analyses, the formation of the AKAP7-RI/RII binding domain (required for AKAP/PKA-R interaction corresponds to vertebrate-specific gene duplication events in the PKA-RI/RII subunits. Species analyses of AKAP7 splice variants shows the ancestral AKAP7 splice variant is AKAP7α, while the ancestral long form AKAP7 splice variant is AKAP7γ. Multi-species AKAP7 gene alignments, show the recent formation of AKAP7δ occurs with the loss of native AKAP7γ in rats and basal primates. AKAP7 gene alignments and two dimensional Western analyses indicate that AKAP7γ is produced from an internal translation-start site that is present in the AKAP7δ cDNA of mice and humans but absent in rats. Immunofluorescence analysis of AKAP7 protein localization in both rat and mouse heart suggests AKAP7γ replaces AKAP7δ at the cardiac sarcoplasmic reticulum in species other than rat. DNA sequencing identified Human AKAP7δ insertion-deletions (indels that promote the production of AKAP7γ instead of AKAP7δ. Conclusions This AKAP7 molecular evolution study shows that these vital scaffolding proteins developed in ancestral vertebrates and that independent mutations in the AKAP7 genes of rodents and early primates has resulted in the recent formation of AKAP7δ, a splice variant of likely lesser importance in humans than currently described.

Carbon Isotope Chemistry in Molecular Clouds

Science.gov (United States)

Robertson, Amy N.; Willacy, Karen

2012-01-01

Few details of carbon isotope chemistry are known, especially the chemical processes that occur in astronomical environments like molecular clouds. Observational evidence shows that the C-12/C-13 abundance ratios vary due to the location of the C-13 atom within the molecular structure. The different abundances are a result of the diverse formation pathways that can occur. Modeling can be used to explore the production pathways of carbon molecules in an effort to understand and explain the chemical evolution of molecular clouds.

DYNAMICALLY DRIVEN EVOLUTION OF THE INTERSTELLAR MEDIUM IN M51

International Nuclear Information System (INIS)

Koda, Jin; Scoville, Nick; Potts, Ashley E.; Carpenter, John M.; Corder, Stuartt A.; Patience, Jenny; Sargent, Anneila I.; Sawada, Tsuyoshi; La Vigne, Misty A.; Vogel, Stuart N.; White, Stephen M.; Zauderer, B. Ashley; Pound, Marc W.; Wright, Melvyn C. H.; Plambeck, Richard L.; Bock, Douglas C. J.; Hawkins, David; Hodges, Mark; Lamb, James W.; Kemball, Athol

2009-01-01

Massive star formation occurs in giant molecular clouds (GMCs); an understanding of the evolution of GMCs is a prerequisite to develop theories of star formation and galaxy evolution. We report the highest-fidelity observations of the grand-design spiral galaxy M51 in carbon monoxide (CO) emission, revealing the evolution of GMCs vis-a-vis the large-scale galactic structure and dynamics. The most massive GMCs (giant molecular associations (GMAs)) are first assembled and then broken up as the gas flow through the spiral arms. The GMAs and their H 2 molecules are not fully dissociated into atomic gas as predicted in stellar feedback scenarios, but are fragmented into smaller GMCs upon leaving the spiral arms. The remnants of GMAs are detected as the chains of GMCs that emerge from the spiral arms into interarm regions. The kinematic shear within the spiral arms is sufficient to unbind the GMAs against self-gravity. We conclude that the evolution of GMCs is driven by large-scale galactic dynamics-their coagulation into GMAs is due to spiral arm streaming motions upon entering the arms, followed by fragmentation due to shear as they leave the arms on the downstream side. In M51, the majority of the gas remains molecular from arm entry through the interarm region and into the next spiral arm passage.

Nuclear magnetic resonance in solids: evolution of spin temperature under multipulse irradiation and high symmetry molecular motions

International Nuclear Information System (INIS)

Quiroga, Luis

1982-01-01

In a first part, autocorrelation functions are calculated taking into account the symmetry of molecular motions by group theoretical techniques. This very general calculation method is then used to evaluate the NMR spin-lattice relaxation times T 1 and T 1 p as a function of the relative orientations of the magnetic field, the crystal and the rotation axis, in particular for cyclic, dihedral and cubic groups. Models of molecular reorientations such as jumps between a finite number of allowed orientations, rotational diffusion and superimposed reorientations are all investigated with the same formalism. In part two, the effect of the coherent excitation of spins, by multipulse sequences of the WHH-4 type, on the evolution of the heat capacity and spin temperature of the dipolar reservoir is analysed. It is shown both theoretically and experimentally that adiabatic (reversible) reduction of the dipolar Hamiltonian and its spin temperature is obtained when the amplitude of pulses (rotation angle) is slowly raised. The sudden switching on and off of the HW-8 sequence is then shown to lead to the same reversible reduction in a shorter time. It is also shown that, by this way, sensibility and selectivity of double resonance measurements of weak gyromagnetic ratio nuclei are strongly increased. This is experimentally illustrated in some cases. (author) [fr

Dynamical decoupling assisted acceleration of two-spin evolution in XY spin-chain environment

Energy Technology Data Exchange (ETDEWEB)

Wei, Yong-Bo; Zou, Jian [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Wang, Zhao-Ming [Department of Physics, Ocean University of China, Qingdao 266100 (China); Shao, Bin, E-mail: sbin610@bit.edu.cn [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Li, Hai [School of Information and Electronic Engineering, Shandong Institute of Business and Technology, Yantai 264000 (China)

2016-01-28

We study the speed-up role of dynamical decoupling in an open system, which is modeled as two central spins coupled to their own XY spin-chain environment. We show that the fast bang–bang pulses can suppress the system evolution, which manifests the quantum Zeno effect. In contrast, with the increasing of the pulse interval time, the bang–bang pulses can enhance the decay of the quantum speed limit time and induce the speed-up process, which displays the quantum anti-Zeno effect. In addition, we show that the random pulses can also induce the speed-up of quantum evolution. - Highlights: • We propose a scheme to accelerate the dynamical evolution of central spins in an open system. • The quantum speed limit of central spins can be modulated by changing pulse frequency. • The random pulses can play the same role as the regular pulses do for small perturbation.

Evolution of Life and SETI (Evo-SETI)

Science.gov (United States)

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

Kinetics and Thermodynamics of Ultrasound-Assisted Depolymerization of κ-Carrageenan

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Ratnawati Ratnawati

2016-03-01

Full Text Available The ultrasound-assisted depolymerization of κ-carrageenan has been studied at various temperatures and times. The κ-carrageenan with initial molecular weight of 545 kDa was dispersed in water to form a 5 g/L solution, which was then depolymerized in an ultrasound device at various temperatures and times. The viscosity of the solution was measured using Brookfield viscometer, which was then used to find the number-average molecular weight by Mark-Houwink equation. To obtain the kinetics of κ-carrageenan depolymerization, the number-average molecular weight data was treated using midpoint-chain scission kinetics model. The pre-exponential factor and activation energies for the reaction are 2.683×10-7 mol g-1 min-1 and 6.43 kJ mol-1, respectively. The limiting molecular weight varies from 160 kDa to 240 kDa, and it is linearly correlated to temperature. The results are compared to the result of thermal depolymerization by calculating the half life. It is revealed that ultrasound assisted depolymerization of κ-carrageenan is faster than thermal depolymerization at temperatures below 72.2°C. Compared to thermal depolymerization, the ultrasound-assisted process has lower values of Ea, ΔG‡, ΔH‡, and ΔS‡, which can be attributed to the ultrasonically induced breakage of non-covalent bonds in κ-carrageenan molecules. Copyright © 2016 BCREC GROUP. All rights reserved Received: 10th November 2015; Revised: 18th January 2016; Accepted: 19th January 2016 How to Cite: Ratnawati, R., Prasetyaningrum, A., Wardhani, D.H. (2016. Kinetics and Thermodynamics of Ultrasound-Assisted Depolymerization of κ-Carrageenan. Bulletin of Chemical Reaction Engineering & Catalysis, 11(1: 48-58. (doi:10.9767/bcrec.11.1.415.48-58 Permalink/DOI: http://dx.doi.org/10.9767/bcrec.11.1.415.48-58

LGI1, CASPR2 and related antibodies: a molecular evolution of the phenotypes.

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Binks, Sophie N M; Klein, Christopher J; Waters, Patrick; Pittock, Sean J; Irani, Sarosh R

2018-05-01

Recent biochemical observations have helped redefine antigenic components within the voltage-gated potassium channel (VGKC) complex. The related autoantibodies may be now divided into likely pathogenic entities, which target the extracellular domains of leucine-rich glioma-inactivated 1 (LGI1) and contactin-associated protein-like 2 (CASPR2), and species that target intracellular neuronal components and are likely non-pathogenic. This distinction has enhanced clinical practice as direct determination of LGI1 and CASPR2 antibodies offers optimal sensitivity and specificity. In this review, we describe and compare the clinical features associated with pathogenic LGI1 and CASPR2 antibodies, illustrate emerging laboratory techniques for antibody determination and describe the immunological mechanisms that may mediate antibody-induced pathology. We highlight marked clinical overlaps between patients with either LGI1 or CASPR2 antibodies that include frequent focal seizures, prominent amnesia, dysautonomia, neuromyotonia and neuropathic pain. Although occurring at differing rates, these commonalities are striking and only faciobrachial dystonic seizures reliably differentiate these two conditions. Furthermore, the coexistence of both LGI1 and CASPR2 antibodies in an individual occurs surprisingly frequently. Patients with either antibody respond well to immunotherapies, although systematic studies are required to determine the magnitude of the effect beyond placebo. Finally, data have suggested that CASPR2 and LGI1 modulation via genetic or autoimmune mechanisms may share common intermediate molecules. Taken together, the biochemical distinction of antigenic targets has led to important clinical advances for patient care. However, the striking syndrome similarities, coexistence of two otherwise rare antibodies and molecular insights suggest the VGKC complex may yet be a common functional effector of antibody action. Hence, we argue for a molecular evolution alongside a

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

Science.gov (United States)

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

2016-06-01

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

Chirality in molecular collision dynamics

Science.gov (United States)

Lombardi, Andrea; Palazzetti, Federico

2018-02-01

Chirality is a phenomenon that permeates the natural world, with implications for atomic and molecular physics, for fundamental forces and for the mechanisms at the origin of the early evolution of life and biomolecular homochirality. The manifestations of chirality in chemistry and biochemistry are numerous, the striking ones being chiral recognition and asymmetric synthesis with important applications in molecular sciences and in industrial and pharmaceutical chemistry. Chiral discrimination phenomena, due to the existence of two enantiomeric forms, very well known in the case of interaction with light, but still nearly disregarded in molecular collision studies. Here we review some ideas and recent advances about the role of chirality in molecular collisions, designing and illustrating molecular beam experiments for the demonstration of chiral effects and suggesting a scenario for a stereo-directional origin of chiral selection.

Molecular docking.

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Morris, Garrett M; Lim-Wilby, Marguerita

2008-01-01

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair.

Science.gov (United States)

Wu, Dong-Dong; Irwin, David M; Zhang, Ya-Ping

2008-08-23

Hair is unique to mammals. Keratin associated proteins (KRTAPs), which contain two major groups: high/ultrahigh cysteine and high glycine-tyrosine, are one of the major components of hair and play essential roles in the formation of rigid and resistant hair shafts. The KRTAP family was identified as being unique to mammals, and near-complete KRTAP gene repertoires for eight mammalian genomes were characterized in this study. An expanded KRTAP gene repertoire was found in rodents. Surprisingly, humans have a similar number of genes as other primates despite the relative hairlessness of humans. We identified several new subfamilies not previously reported in the high/ultrahigh cysteine KRTAP genes. Genes in many subfamilies of the high/ultrahigh cysteine KRTAP genes have evolved by concerted evolution with frequent gene conversion events, yielding a higher GC base content for these gene sequences. In contrast, the high glycine-tyrosine KRTAP genes have evolved more dynamically, with fewer gene conversion events and thus have a lower GC base content, possibly due to positive selection. Most of the subfamilies emerged early in the evolution of mammals, thus we propose that the mammalian ancestor should have a diverse KRTAP gene repertoire. We propose that hair content characteristics have evolved and diverged rapidly among mammals because of rapid divergent evolution of KRTAPs between species. In contrast, subfamilies of KRTAP genes have been homogenized within each species due to concerted evolution.

On the evolution of the mammalian brain

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John Steven Torday

2016-04-01

Full Text Available Hobson and Friston have hypothesized that the brain must actively dissipate heat in order to process information (Virtual reality and consciousness inference in dreaming. Front Psychol. 2014 Oct 9;5:1133.. This physiologic trait is functionally homologous with the first instantation of life formed by lipids suspended in water forming micelles- allowing the reduction in entropy (heat dissipation, circumventing the Second Law of Thermodynamics permitting the transfer of information between living entities, enabling them to perpetually glean information from the environment (= evolution. The next evolutionary milestone was the advent of cholesterol, embedded in the cell membranes of primordial eukaryotes, facilitating metabolism, oxygenation and locomotion, the triadic basis for vertebrate evolution. Lipids were key to homeostatic regulation of calcium, forming calcium channels. Cell membrane cholesterol also fostered metazoan evolution by forming lipid rafts for receptor-mediated cell-cell signaling, the origin of the endocrine system. The eukaryotic cell membrane exapted to all complex physiologic traits, including the lung and brain, which are molecularly homologous through the function of neuregulin, mediating both lung development and myelinization of neurons. That cooption later exapted as endothermy during the water-land transition (Torday JS. A Central Theory of Biology. Med Hypotheses. 2015 Jul;85(1:49-57, perhaps being the functional homolog for brain heat dissipation and consciousness/mind. The skin and brain similarly share molecular homologies through the ‘skin-brain’ hypothesis, giving insight to the cellular-molecular ‘arc’ of consciousness from its unicellular origins to integrated physiology. This perspective on the evolution of the central nervous system clarifies self-organization, reconciling thermodynamic and informational definitions of the underlying biophysical mechanisms, thereby elucidating relations between the

Spontaneous chiral symmetry breaking in early molecular networks

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Markovitch Omer

2010-05-01

Full Text Available Abstract Background An important facet of early biological evolution is the selection of chiral enantiomers for molecules such as amino acids and sugars. The origin of this symmetry breaking is a long-standing question in molecular evolution. Previous models addressing this question include particular kinetic properties such as autocatalysis or negative cross catalysis. Results We propose here a more general kinetic formalism for early enantioselection, based on our previously described Graded Autocatalysis Replication Domain (GARD model for prebiotic evolution in molecular assemblies. This model is adapted here to the case of chiral molecules by applying symmetry constraints to mutual molecular recognition within the assembly. The ensuing dynamics shows spontaneous chiral symmetry breaking, with transitions towards stationary compositional states (composomes enriched with one of the two enantiomers for some of the constituent molecule types. Furthermore, one or the other of the two antipodal compositional states of the assembly also shows time-dependent selection. Conclusion It follows that chiral selection may be an emergent consequence of early catalytic molecular networks rather than a prerequisite for the initiation of primeval life processes. Elaborations of this model could help explain the prevalent chiral homogeneity in present-day living cells. Reviewers This article was reviewed by Boris Rubinstein (nominated by Arcady Mushegian, Arcady Mushegian, Meir Lahav (nominated by Yitzhak Pilpel and Sergei Maslov.

Molecular outflows in the L1641 region of Orion

International Nuclear Information System (INIS)

Morgan, J.A.

1990-01-01

Little is known about the interaction between molecular outflows associated with young stellar objects and the parent molecular cloud that produced them. This is because molecular outflows are a recently discovered phenomenon and, so, have not had their global properties studied in great detail and molecular clouds were not mapped to sufficiently high spatial resolution to resolve the interaction. The interaction between molecular outflows and the L1641 molecular cloud is addressed by both identifying and mapping all the molecular outflows as well as the detailed structure of the cloud. Candidate molecular outflows were found from single point 12-CO observations of young stellar objects identified from the IRAS survey data. The candidate sources were then mapped to confirm their molecular outflow nature. From these maps, molecular outflow characteristics such as their morphology, orientation, and energetics were determined. In addition, the Orion molecular cloud was mapped to compare directly with the molecular outflows. The molecular outflows identified were found to have rising infrared spectra, radio continuum emission that suggests a stellar wind or optically thick H II region, and molecular line strengths that indicate that they are embedded within a very dense environment. The lack of an optical counterpart for many molecular outflows suggests that they occur at the earliest stages of stellar evolution. The lack of an optical counterpart for many molecular outflows suggest that they occur at the earliest stages of stellar evolution. The orientations of the molecular outflows appear to lie in no preferred direction and they have shapes that indicate that the molecular cloud is responsible for determining their direction and collimation

Improving Blast Resistance of a Thermo-Sensitive Genic Male Sterile Rice Line GD-8S by Molecular Marker-Assisted Selection

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Wu-ge LIU

2008-09-01

Full Text Available The broad-spectrum blast resistance gene Pi-1, from donor line BL122, was introduced into a thermo-sensitive genic male sterile rice line GD-8S, which possessed good grain quality but high susceptibility to rice blast, by using backcross breeding and molecular marker-assisted selection. Five elite improved male sterile lines, RGD8S-1, RGD8S-2, RGD8S-3, RGD8S-4 and RGD8S-5, were selected based on the results of molecular marker analysis, spikelet sterility, recovery rate of genetic background and agronomic traits. Thirty-three representative blast isolates collected from Guangdong Province, China were used to inoculate the improved lines and the original line GD-8S artificially. The resistance frequencies of the improved lines ranged from 76.47% to 100%, much higher than that of the original line GD-8S (9.09%. On the agronomic characters, there were no significant differences between the improved lines and GD-8S except for flag leaf length and panicle number per plant. The improved lines could be used for breeding hybrid rice with high blast resistance.

Role of Chromosome Changes in Evolution and Diversity

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Kornsorn Srikulnath

2015-12-01

Full Text Available The karyotypes of most species of crocodilians were studied using conventional and molecular cytogenetics. These provided an important contribution of chromosomal rearrangements for the evolutionary processes of Crocodylia and Sauropsida (birds and reptiles. The karyotypic features of crocodilians contain small diploid chromosome numbers (30~42, with little interspecific variation of the chromosome arm number (fundamental number among crocodiles (56~60. This suggested that centric fusion and/or fission events occurred in the lineage, leading to crocodilian evolution and diversity. The chromosome numbers of Alligator, Caiman, Melanosuchus, Paleosuchus, Gavialis, Tomistoma, Mecistops, and Osteolaemus were stable within each genus, whereas those of Crocodylus (crocodylians varied within the taxa. This agreed with molecular phylogeny that suggested a highly recent radiation of Crocodylus species. Karyotype analysis also suggests the direction of molecular phylogenetic placement among Crocodylus species and their migration from the Indo-Pacific to Africa and The New World. Crocodylus species originated from an ancestor in the Indo-Pacific around 9~16 million years ago (MYA in the mid-Miocene, with a rapid radiation and dispersion into Africa 8~12 MYA. This was followed by a trans-Atlantic dispersion to the New World between 4~8 MYA in the Pliocene. The chromosomes provided a better understanding of crocodilian evolution and diversity, which will be useful for further study of the genome evolution in Crocodylia.

Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches.

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Lukoschek, Vimoksalehi; Scott Keogh, J; Avise, John C

2012-01-01

Evolutionary and biogeographic studies increasingly rely on calibrated molecular clocks to date key events. Although there has been significant recent progress in development of the techniques used for molecular dating, many issues remain. In particular, controversies abound over the appropriate use and placement of fossils for calibrating molecular clocks. Several methods have been proposed for evaluating candidate fossils; however, few studies have compared the results obtained by different approaches. Moreover, no previous study has incorporated the effects of nucleotide saturation from different data types in the evaluation of candidate fossils. In order to address these issues, we compared three approaches for evaluating fossil calibrations: the single-fossil cross-validation method of Near, Meylan, and Shaffer (2005. Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am. Nat. 165:137-146), the empirical fossil coverage method of Marshall (2008. A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. Am. Nat. 171:726-742), and the Bayesian multicalibration method of Sanders and Lee (2007. Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds. Biol. Lett. 3:275-279) and explicitly incorporate the effects of data type (nuclear vs. mitochondrial DNA) for identifying the most reliable or congruent fossil calibrations. We used advanced (Caenophidian) snakes as a case study; however, our results are applicable to any taxonomic group with multiple candidate fossils, provided appropriate taxon sampling and sufficient molecular sequence data are available. We found that data type strongly influenced which fossil calibrations were identified as outliers, regardless of which method was used. Despite the use of complex partitioned models of sequence evolution and multiple calibrations throughout the tree, saturation

Evolution of parasitism in kinetoplastid flagellates

Czech Academy of Sciences Publication Activity Database

Lukeš, Julius; Skalický, Tomáš; Týč, Jiří; Votýpka, Jan; Yurchenko, Vyacheslav

2014-01-01

Roč. 195, č. 2 (2014), s. 115-122 ISSN 0166-6851 R&D Projects: GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : Evolution * Phylogeny * Vectors * Diversity * Parasitism * Trypanosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.787, year: 2014

Modular co-evolution of metabolic networks

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Yu Zhong-Hao

2007-08-01

Full Text Available Abstract Background The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular network affects the evolution of its member proteins remains unclear. Results In this work, the functional and evolutionary modularity of Homo sapiens (H. sapiens metabolic network were investigated from a topological point of view. Network decomposition shows that the metabolic network is organized in a highly modular core-periphery way, in which the core modules are tightly linked together and perform basic metabolism functions, whereas the periphery modules only interact with few modules and accomplish relatively independent and specialized functions. Moreover, over half of the modules exhibit co-evolutionary feature and belong to specific evolutionary ages. Peripheral modules tend to evolve more cohesively and faster than core modules do. Conclusion The correlation between functional, evolutionary and topological modularity suggests that the evolutionary history and functional requirements of metabolic systems have been imprinted in the architecture of metabolic networks. Such systems level analysis could demonstrate how the evolution of genes may be placed in a genome-scale network context, giving a novel perspective on molecular evolution.

Transparency of Reporting in Molecular Diagnostics

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Stephen Bustin

2013-07-01

Full Text Available The major advances made over the past few years in molecular and cell biology are providing a progressively more detailed understanding of the molecular pathways that control normal processes and become dysregulated in disease [1]. This has resulted in the documentation of numerous genetic, epigenetic, transcriptomic, proteomic and metabolomic biomarkers that promise earlier disease detection, more accurate patient stratification and better prognosis [2–5]. Furthermore, molecular fingerprinting of diseases can be predictive of drug response and so assist with specific targeting of drugs against disease-associated molecules and function [6]. [...

Practical aspects of protein co-evolution.

Science.gov (United States)

Ochoa, David; Pazos, Florencio

2014-01-01

Co-evolution is a fundamental aspect of Evolutionary Theory. At the molecular level, co-evolutionary linkages between protein families have been used as indicators of protein interactions and functional relationships from long ago. Due to the complexity of the problem and the amount of genomic data required for these approaches to achieve good performances, it took a relatively long time from the appearance of the first ideas and concepts to the quotidian application of these approaches and their incorporation to the standard toolboxes of bioinformaticians and molecular biologists. Today, these methodologies are mature (both in terms of performance and usability/implementation), and the genomic information that feeds them large enough to allow their general application. This review tries to summarize the current landscape of co-evolution-based methodologies, with a strong emphasis on describing interesting cases where their application to important biological systems, alone or in combination with other computational and experimental approaches, allowed getting new insight into these.

Influence of the molecular modifications on the properties of EPDM elastomers under irradiation

Energy Technology Data Exchange (ETDEWEB)

Davenas, J. E-mail: joel.davenas@univ-lyon1.fr; Stevenson, I.; Celette, N.; Vigier, G.; David, L

2003-08-01

The degradation of the mechanical behaviour of EPDM elastomers used as cable insulation materials has been investigated by mechanical spectroscopy and tensile tests for different formulations: unvulcanised EPDM, vulcanised and stabilised elastomer with an antioxidant. In all cases, {gamma}-irradiation of EPDM under oxygen leads to a reduction of the molecular mobility indicated by the shift of the glass transition relaxation temperature towards higher temperatures. Moreover, the molecular flow occurring above T{sub g} is suppressed after irradiation for the unvulcanised EPDM providing evidence of cross-linking. The competition between cross-linking and chain scissions is shown by the decrease of the storage modulus above the crystallites melting temperature ({approx}40 deg. C) at doses larger than 100 kGy. A strong increase of the Young modulus and reduction of the elongation at break of the non-vulcanised EPDM becoming more brittle are shown by stress/strain characterisations performed at 80 deg. C. At the opposite vulcanised EPDM exhibits higher elongation at break after crystallites melting. This evolution is interpreted by the competition between cross-linking and chain scissions, being hindered by the crystallites at room temperature. The intrinsic irradiation effects can be isolated after crystallite melting. The reduction of the molecular mobility can be explained by a chemi-crystallisation process assisted by chain scissions, leading to a more rigid phase upon irradiation.

Influence of the molecular modifications on the properties of EPDM elastomers under irradiation

International Nuclear Information System (INIS)

Davenas, J.; Stevenson, I.; Celette, N.; Vigier, G.; David, L.

2003-01-01

The degradation of the mechanical behaviour of EPDM elastomers used as cable insulation materials has been investigated by mechanical spectroscopy and tensile tests for different formulations: unvulcanised EPDM, vulcanised and stabilised elastomer with an antioxidant. In all cases, γ-irradiation of EPDM under oxygen leads to a reduction of the molecular mobility indicated by the shift of the glass transition relaxation temperature towards higher temperatures. Moreover, the molecular flow occurring above T g is suppressed after irradiation for the unvulcanised EPDM providing evidence of cross-linking. The competition between cross-linking and chain scissions is shown by the decrease of the storage modulus above the crystallites melting temperature (∼40 deg. C) at doses larger than 100 kGy. A strong increase of the Young modulus and reduction of the elongation at break of the non-vulcanised EPDM becoming more brittle are shown by stress/strain characterisations performed at 80 deg. C. At the opposite vulcanised EPDM exhibits higher elongation at break after crystallites melting. This evolution is interpreted by the competition between cross-linking and chain scissions, being hindered by the crystallites at room temperature. The intrinsic irradiation effects can be isolated after crystallite melting. The reduction of the molecular mobility can be explained by a chemi-crystallisation process assisted by chain scissions, leading to a more rigid phase upon irradiation

Macromolecular crowding-assisted fabrication of liquid-crystalline imprinted polymers.

Science.gov (United States)

Zhang, Chen; Zhang, Jing; Huang, Yan-Ping; Liu, Zhao-Sheng

2015-04-01

A macromolecular crowding-assisted liquid-crystalline molecularly imprinted monolith (LC-MIM) was prepared successfully for the first time. The imprinted stationary phase was synthesized with polymethyl methacrylate (PMMA) or polystyrene (PS) as the crowding agent, 4-cyanophenyl dicyclohexyl propylene (CPCE) as the liquid-crystal monomer, and hydroquinidine as the pseudo-template for the chiral separation of cinchona alkaloids in HPLC. A low level of cross-linker (26%) has been found to be sufficient to achieve molecular recognition on the crowding-assisted LC-MIM due to the physical cross-linking of mesogenic groups in place of chemical cross-linking, and baseline separation of quinidine and quinine could be achieved with good resolution (R(s) = 2.96), selectivity factor (α = 2.16), and column efficiency (N = 2650 plates/m). In contrast, the LC-MIM prepared without crowding agents displayed the smallest diastereoselectivity (α = 1.90), while the crowding-assisted MIM with high level of cross-linker (80%) obtained the greatest selectivity factor (α = 7.65), but the lowest column efficiency (N = 177 plates/m).

Evolution of the Normal State of a Strongly Interacting Fermi Gas from a Pseudogap Phase to a Molecular Bose Gas

International Nuclear Information System (INIS)

Perali, A.; Palestini, F.; Pieri, P.; Strinati, G. C.; Stewart, J. T.; Gaebler, J. P.; Drake, T. E.; Jin, D. S.

2011-01-01

Wave-vector resolved radio frequency spectroscopy data for an ultracold trapped Fermi gas are reported for several couplings at T c , and extensively analyzed in terms of a pairing-fluctuation theory. We map the evolution of a strongly interacting Fermi gas from the pseudogap phase into a fully gapped molecular Bose gas as a function of the interaction strength, which is marked by a rapid disappearance of a remnant Fermi surface in the single-particle dispersion. We also show that our theory of a pseudogap phase is consistent with a recent experimental observation as well as with quantum Monte Carlo data of thermodynamic quantities of a unitary Fermi gas above T c .

Plasma-assisted Molecular Beam Epitaxy of N-polar InAlN-barrier High-electron-mobility Transistors.

Science.gov (United States)

Hardy, Matthew T; Storm, David F; Katzer, D Scott; Downey, Brian P; Nepal, Neeraj; Meyer, David J

2016-11-24

Plasma-assisted molecular beam epitaxy is well suited for the epitaxial growth of III-nitride thin films and heterostructures with smooth, abrupt interfaces required for high-quality high-electron-mobility transistors (HEMTs). A procedure is presented for the growth of N-polar InAlN HEMTs, including wafer preparation and growth of buffer layers, the InAlN barrier layer, AlN and GaN interlayers and the GaN channel. Critical issues at each step of the process are identified, such as avoiding Ga accumulation in the GaN buffer, the role of temperature on InAlN compositional homogeneity, and the use of Ga flux during the AlN interlayer and the interrupt prior to GaN channel growth. Compositionally homogeneous N-polar InAlN thin films are demonstrated with surface root-mean-squared roughness as low as 0.19 nm and InAlN-based HEMT structures are reported having mobility as high as 1,750 cm 2 /V∙sec for devices with a sheet charge density of 1.7 x 10 13 cm -2 .

Model assisted multiobjective optimization with {lambda}-control; Multikriterielle Optimierung mit {lambda}-geregelten modellgestuetzten Evolutionsstrategien

Energy Technology Data Exchange (ETDEWEB)

Braun, Jan; Hoffmann, Frank; Krettek, Johannes; Bertram, Torsten [Technische Univ. Dortmund (Germany). Lehrstuhl RST

2009-07-01

Evolutionary algorithms require a large number of fitness evaluations in order to find an optimal solution. This property limits their application to hardware in the loop optimization or optimization of time-consuming simulations and calculations. This contribution proposes a preselection with data based models in order to reduce the number of true fitness evaluations. It extends previous approaches for model assisted scalar optimization to multiobjective problems by a proper redefinition of model quality and ?-control. The application to multiobjective benchmark optimization problems underlies the improved convergence of the model assisted evolution strategy compared to a multiobjective evolution strategy as well as the advantages of a {lambda}-controlled variant compared to a static preselection. (orig.)

Radiation and the evolution of life

International Nuclear Information System (INIS)

Gentner, N.E.; Myers, D.K.

1980-08-01

A general review is presented of the nature of various forms of radiation; radiant energy which reaches the earth from the sun; the role of this energy in prebiotic chemical evolution; current ideas on the origin of life; the dependence of living organisms upon radiant energy; the mechanisms responsible for the evolution of life, from the viewpoint of modern genetics and molecular biology; the biological consequences of alterations in the genetic material; and the role of ionizing radiation in production of genetic changes and in evolution. In the final analysis, the biosynthetic processes of life are driven by radiant energy from the sun. This overview is necessarily focussed on the infrared, visible and ultraviolet regions of the solar output spectrum since these particular radiations are responsible for most of the radiant energy that reaches the earth's surface. Ionizing radiation appears to have played at best a minor role in biological evolution. Small increments in the amounts of ionizing radiation are therefore unlikely to have a significant effect on life or its evolution. (auth)

Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenalf.

Science.gov (United States)

Sunagar, Kartik; Fry, Bryan Grieg; Jackson, Timothy N W; Casewell, Nicholas R; Undheim, Eivind A B; Vidal, Nicolas; Ali, Syed A; King, Glenn F; Vasudevan, Karthikeyan; Vasconcelos, Vitor; Antunes, Agostinho

2013-01-01

Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF), brain-derived neurotrophic factors (BDNF) and neurotrophin-3 (NT-3), which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae) have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74%) and on the molecular surface of the protein (92%), while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation.

Molecular marker systems for Oenothera genetics.

Science.gov (United States)

Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G; Greiner, Stephan

2008-11-01

The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome-genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9.8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed.

Bacterial flagella and Type III secretion: case studies in the evolution of complexity.

Science.gov (United States)

Pallen, M J; Gophna, U

2007-01-01

Bacterial flagella at first sight appear uniquely sophisticated in structure, so much so that they have even been considered 'irreducibly complex' by the intelligent design movement. However, a more detailed analysis reveals that these remarkable pieces of molecular machinery are the product of processes that are fully compatible with Darwinian evolution. In this chapter we present evidence for such processes, based on a review of experimental studies, molecular phylogeny and microbial genomics. Several processes have played important roles in flagellar evolution: self-assembly of simple repeating subunits, gene duplication with subsequent divergence, recruitment of elements from other systems ('molecular bricolage'), and recombination. We also discuss additional tentative new assignments of homology (FliG with MgtE, FliO with YscJ). In conclusion, rather than providing evidence of intelligent design, flagellar and non-flagellar Type III secretion systems instead provide excellent case studies in the evolution of complex systems from simpler components.

New genes as drivers of phenotypic evolution

Science.gov (United States)

Chen, Sidi; Krinsky, Benjamin H.; Long, Manyuan

2014-01-01

During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution. PMID:23949544

Genomic evolution of Saccharomyces cerevisiae under Chinese rice wine fermentation.

Science.gov (United States)

Li, Yudong; Zhang, Weiping; Zheng, Daoqiong; Zhou, Zhan; Yu, Wenwen; Zhang, Lei; Feng, Lifang; Liang, Xinle; Guan, Wenjun; Zhou, Jingwen; Chen, Jian; Lin, Zhenguo

2014-09-10

Rice wine fermentation represents a unique environment for the evolution of the budding yeast, Saccharomyces cerevisiae. To understand how the selection pressure shaped the yeast genome and gene regulation, we determined the genome sequence and transcriptome of a S. cerevisiae strain YHJ7 isolated from Chinese rice wine (Huangjiu), a popular traditional alcoholic beverage in China. By comparing the genome of YHJ7 to the lab strain S288c, a Japanese sake strain K7, and a Chinese industrial bioethanol strain YJSH1, we identified many genomic sequence and structural variations in YHJ7, which are mainly located in subtelomeric regions, suggesting that these regions play an important role in genomic evolution between strains. In addition, our comparative transcriptome analysis between YHJ7 and S288c revealed a set of differentially expressed genes, including those involved in glucose transport (e.g., HXT2, HXT7) and oxidoredutase activity (e.g., AAD10, ADH7). Interestingly, many of these genomic and transcriptional variations are directly or indirectly associated with the adaptation of YHJ7 strain to its specific niches. Our molecular evolution analysis suggested that Japanese sake strains (K7/UC5) were derived from Chinese rice wine strains (YHJ7) at least approximately 2,300 years ago, providing the first molecular evidence elucidating the origin of Japanese sake strains. Our results depict interesting insights regarding the evolution of yeast during rice wine fermentation, and provided a valuable resource for genetic engineering to improve industrial wine-making strains. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The role of fusion in ant chromosome evolution: insights from cytogenetic analysis using a molecular phylogenetic approach in the genus mycetophylax.

Science.gov (United States)

Cardoso, Danon Clemes; das Graças Pompolo, Silvia; Cristiano, Maykon Passos; Tavares, Mara Garcia

2014-01-01

Among insect taxa, ants exhibit one of the most variable chromosome numbers ranging from n = 1 to n = 60. This high karyotype diversity is suggested to be correlated to ants diversification. The karyotype evolution of ants is usually understood in terms of Robertsonian rearrangements towards an increase in chromosome numbers. The ant genus Mycetophylax is a small monogynous basal Attini ant (Formicidae: Myrmicinae), endemic to sand dunes along the Brazilian coastlines. A recent taxonomic revision validates three species, Mycetophylax morschi, M. conformis and M. simplex. In this paper, we cytogenetically characterized all species that belongs to the genus and analyzed the karyotypic evolution of Mycetophylax in the context of a molecular phylogeny and ancestral character state reconstruction. M. morschi showed a polymorphic number of chromosomes, with colonies showing 2n = 26 and 2n = 30 chromosomes. M. conformis presented a diploid chromosome number of 30 chromosomes, while M. simplex showed 36 chromosomes. The probabilistic models suggest that the ancestral haploid chromosome number of Mycetophylax was 17 (Likelihood framework) or 18 (Bayesian framework). The analysis also suggested that fusions were responsible for the evolutionary reduction in chromosome numbers of M. conformis and M. morschi karyotypes whereas fission may determines the M. simplex karyotype. These results obtained show the importance of fusions in chromosome changes towards a chromosome number reduction in Formicidae and how a phylogenetic background can be used to reconstruct hypotheses about chromosomes evolution.

Photoelectron photoion molecular beam spectroscopy

International Nuclear Information System (INIS)

Trevor, D.J.

1980-12-01

The use of supersonic molecular beams in photoionization mass spectroscopy and photoelectron spectroscopy to assist in the understanding of photoexcitation in the vacuum ultraviolet is described. Rotational relaxation and condensation due to supersonic expansion were shown to offer new possibilities for molecular photoionization studies. Molecular beam photoionization mass spectroscopy has been extended above 21 eV photon energy by the use of Stanford Synchrotron Radiation Laboratory (SSRL) facilities. Design considerations are discussed that have advanced the state-of-the-art in high resolution vuv photoelectron spectroscopy. To extend gas-phase studies to 160 eV photon energy, a windowless vuv-xuv beam line design is proposed

Atomic molecular and optical physics

International Nuclear Information System (INIS)

Anon.

1986-01-01

Laser-assisted manufacturing and fiber-optics communications are but two of the products of atomic, molecular, and optical physics, (AMO) research. AMO physics provides theoretical and experimental methods and essential data to neighboring areas of science such as chemistry, astrophysics, condensed-matter physics, plasma physics, surface science, biology, and medicine. This book addresses advances in atomic, molecular, and optical fields and provides recommendations for further research. It also looks at scientific applications in national security, manufacturing, medicine, and other fields

Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History

Directory of Open Access Journals (Sweden)

N.L.P Indi Dharmayanti

2011-03-01

Full Text Available Phylogenetic is described as taxonomy classification of an organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1 Maximum parsimony, (2 Distance, and (3 Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data.

Analysis of the complement and molecular evolution of tRNA genes in cow

Directory of Open Access Journals (Sweden)

Barris Wesley C

2009-04-01

set of cow tRNA genes that will facilitate further studies in understanding the molecular evolution of cow tRNA genes.

Universal pacemaker of genome evolution.

Science.gov (United States)

Snir, Sagi; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome. This correlation could be explained by a model that we denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, the correlation between the evolutionary rates of genes could be a simple consequence of molecular clock (MC). We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in the evolution of archaea and bacteria and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, although similarly to the MC, the UPM is strongly overdispersed. Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life.

Homochiral Evolution in Self-Assembled Chiral Polymers and Block Copolymers.

Science.gov (United States)

Wen, Tao; Wang, Hsiao-Fang; Li, Ming-Chia; Ho, Rong-Ming

2017-04-18

The significance of chirality transfer is not only involved in biological systems, such as the origin of homochiral structures in life but also in man-made chemicals and materials. How the chiral bias transfers from molecular level (molecular chirality) to helical chain (conformational chirality) and then to helical superstructure or phase (hierarchical chirality) from self-assembly is vital for the chemical and biological processes in nature, such as communication, replication, and enzyme catalysis. In this Account, we summarize the methodologies for the examination of homochiral evolution at different length scales based on our recent studies with respect to the self-assembly of chiral polymers and chiral block copolymers (BCPs*). A helical (H*) phase to distinguish its P622 symmetry from that of normal hexagonally packed cylinder phase was discovered in the self-assembly of BCPs* due to the chirality effect on BCP self-assembly. Enantiomeric polylactide-containing BCPs*, polystyrene-b-poly(l-lactide) (PS-PLLA) and polystyrene-b-poly(d-lactide) (PS-PDLA), were synthesized for the examination of homochiral evolution. The optical activity (molecular chirality) of constituted chiral repeating unit in the chiral polylactide is detected by electronic circular dichroism (ECD) whereas the conformational chirality of helical polylactide chain can be explicitly determined by vibrational circular dichroism (VCD). The H* phases of the self-assembled polylactide-containing BCPs* can be directly visualized by 3D transmission electron microscopy (3D TEM) technique at which the handedness (hierarchical chirality) of the helical nanostructure is thus determined. The results from the ECD, VCD, and 3D TEM for the investigated chirality at different length scales suggest the homochiral evolution in the self-assembly of the BCPs*. For chiral polylactides, twisted lamellae in crystalline banded spherulite can be formed by dense packing scheme and effective interactions upon helical

Diversification and the rate of molecular evolution: no evidence of a link in mammals

Directory of Open Access Journals (Sweden)

Bromham Lindell

2011-10-01

Full Text Available Abstract Background Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences. Results We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported. Conclusions Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.

Diversification and the rate of molecular evolution: no evidence of a link in mammals.

Science.gov (United States)

Goldie, Xavier; Lanfear, Robert; Bromham, Lindell

2011-10-04

Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences. We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported. Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.

alpha-Crystallin A sequences of Alligator mississippiensis and the lizard Tupinambis teguixin: molecular evolution and reptilian phylogeny.

Science.gov (United States)

de Jong, W W; Zweers, A; Versteeg, M; Dessauer, H C; Goodman, M

1985-11-01

The amino acid sequences of the eye lens protein alpha-crystallin A from many mammalian and avian species, two frog species, and a dogfish have provided detailed information about the molecular evolution of this protein and allowed some useful inferences about phylogenetic relationships among these species. We now have isolated and sequenced the alpha-crystallins of the American alligator and the common tegu lizard. The reptilian alpha A chains appear to have evolved as slowly as those of other vertebrates, i.e., at two to three amino acid replacements per 100 residues in 100 Myr. The lack of charged replacements and the general types and distribution of replacements also are similar to those in other vertebrate alpha A chains. Maximum-parsimony analyses of the total data set of 67 vertebrate alpha A sequences support the monophyletic origin of alligator, tegu, and birds and favor the grouping of crocodilians and birds as surviving sister groups in the subclass Archosauria.

Molecular spintronics using single-molecule magnets

Science.gov (United States)

Bogani, Lapo; Wernsdorfer, Wolfgang

2008-03-01

A revolution in electronics is in view, with the contemporary evolution of the two novel disciplines of spintronics and molecular electronics. A fundamental link between these two fields can be established using molecular magnetic materials and, in particular, single-molecule magnets. Here, we review the first progress in the resulting field, molecular spintronics, which will enable the manipulation of spin and charges in electronic devices containing one or more molecules. We discuss the advantages over more conventional materials, and the potential applications in information storage and processing. We also outline current challenges in the field, and propose convenient schemes to overcome them.

Arbitrarily amplified DNA: New molecular approaches to plant breeding, ecology and evolution

Energy Technology Data Exchange (ETDEWEB)

Caetano-Anolles, G [Department of Biology, University of Oslo, Oslo (Norway)

2001-11-01

Several DNA fingerprinting techniques that use arbitrary primers to characterize, scan and tag genomic DNA were optimized and used to study plants and microbial pathogens. The generated arbitrarily amplified DNA (AAD) profiles could be tailored in their complexity and polymorphic content, allowing analysis of closely related organisms, such as vegetatively-propagated horticultural crops or clonal fungal populations. AAD markers were used in cultivar and strain identification, map-based cloning, and marker-assisted breeding, sometimes as sequence-tagged sites. Phenetic analysis using parsimony, cluster, and numerical methods was applied successfully to the identification of genetic relationships in turfgrass species such as bermudagrass, woody plants such as dogwoods, and floricultural species such as petunia and chrysanthemum. AAD profiles were used to measure for the first time a genome-wide mutation rate, directly in a plant. Mutation rates in vegetatively propagated bermudagrass were comparable to those in human, mice, fruit flies, and worms. In combination with established tools used in molecular systematics (e.g. rDNA sequence analysis), AAD markers tracked the introduction of exotic dogwood anthracnose-causing fungi in North America. As part of a breeding effort to combat dogwood diseases, AAD was used in pseudo-testcross mapping of the tree at the intra-specific level. Markers were efficiently generated despite the close relatedness of parental dogwood material. Finally, DNA markers and tags were also generated in soybean, and were used to construct high density maps and walk towards defined genomic regions in the positional cloning of the supernodulation nts-1 symbiotic gene. (author)

Arbitrarily amplified DNA: New molecular approaches to plant breeding, ecology and evolution

International Nuclear Information System (INIS)

Caetano-Anolles, G.

2001-01-01

Several DNA fingerprinting techniques that use arbitrary primers to characterize, scan and tag genomic DNA were optimized and used to study plants and microbial pathogens. The generated arbitrarily amplified DNA (AAD) profiles could be tailored in their complexity and polymorphic content, allowing analysis of closely related organisms, such as vegetatively-propagated horticultural crops or clonal fungal populations. AAD markers were used in cultivar and strain identification, map-based cloning, and marker-assisted breeding, sometimes as sequence-tagged sites. Phenetic analysis using parsimony, cluster, and numerical methods was applied successfully to the identification of genetic relationships in turfgrass species such as bermudagrass, woody plants such as dogwoods, and floricultural species such as petunia and chrysanthemum. AAD profiles were used to measure for the first time a genome-wide mutation rate, directly in a plant. Mutation rates in vegetatively propagated bermudagrass were comparable to those in human, mice, fruit flies, and worms. In combination with established tools used in molecular systematics (e.g. rDNA sequence analysis), AAD markers tracked the introduction of exotic dogwood anthracnose-causing fungi in North America. As part of a breeding effort to combat dogwood diseases, AAD was used in pseudo-testcross mapping of the tree at the intra-specific level. Markers were efficiently generated despite the close relatedness of parental dogwood material. Finally, DNA markers and tags were also generated in soybean, and were used to construct high density maps and walk towards defined genomic regions in the positional cloning of the supernodulation nts-1 symbiotic gene. (author)

Marker-assisted selection in wheat: Evolution, not revolution

International Nuclear Information System (INIS)

Koebner, R.; Summers, R.

2007-01-01

This chapter reviews the uptake of marker-assisted selection (MAS) in wheat in a European context. Although less intense than the scale of its application in maize, reflecting the fact that maize varieties are predominantly F 1 hybrids, the use of MAS in wheat has grown over the last few years. This growth has been encouraged by an increase in the number of amenable target traits, but more significantly by a combination of technological improvements, particularly in the areas of DNA acquisition, laboratory management systems and integration into the breeding cycle, which together have served to reduce the per unit cost of each data point. Microsatellites (simple sequence repeats [SSRs]) are, and will likely remain for some time, the marker of choice because of their flexibility and the knowledge base associated with them. Some current examples are provided of the use of MAS in a major United Kingdom commercial breeding programme. (author)

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

Science.gov (United States)

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

2015-09-01

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

Evolution of spirals during molecular beam epitaxy of GaN on 6H-SiC(0001)

International Nuclear Information System (INIS)

Cui, Y.; Li, L.

2002-01-01

Evolution of spirals during molecular beam epitaxy growth of GaN films on 6H-SiC(0001) was studied by in situ scanning tunneling microscopy. It was found that dislocations emerge at the film surface, creating straight steps with orientation along directions with a density of 10 10 cm -2 for 40-nm-thick films. During subsequent growth, these straight steps wind around dislocations and develop into spirals with a density of 10 9 cm -2 for 100-nm-thick films. The spirals can be classified into three types: single arm, interlocking double arm, and closed loop. The first two types originate from steps with one end pinned, and the third type results from steps with both ends pinned. At film thickness larger than 200 nm, these spirals further evolve into spiral mounds with a density of 10 7 cm -2 . Based on the Burton, Cabrera, and Frank theory, a model is proposed to explain the formation of different types of spirals and the reduction of their densities

Improvement of molecular techniques: A multidisciplinar vision

Directory of Open Access Journals (Sweden)

Bruno do Amaral Crispim

2016-08-01

Full Text Available The advances in molecular technologies since the discovery of the PCR (Polymerase Chain Reaction and their association with the use of molecular markers, allowed a rapid progress in the development of technologies and equipment able to generate and analyze data on a large scale, revolutionizing research that until recently was only based on single marker, like the analysis of Single Nucleotide Polymorphism (SNP, and nowadays with the genomic era is already possible in a few hours genotyping millions or even thousands of SNPs. This evolution has allowed improvements in research to the knowledge of genomes creating expectations and real possibilities of application of these techniques in various fields, from medicine to animal production. These new technologies of molecular analysis of DNA variability determining points of interest in chromosomes, which are technically called as molecular markers. These markers can be used in various applications, including paternity test, construction of genetic maps, mapping of quantitative inheritance of characteristics, isolation of genes, marker-assisted selection and characterization of the genetic diversity of different species. The improvement of sequencing and bioinformatics technologies were crucial to studies with characteristics of interest using high-density genetic information. The SNP genotyping panels stimulated researches in the human area, especially in studies of cancer and exoma, and also in agribusiness, aiming the search for superior genotypes for domestic plants and animals. The differential use of the panels is the possibility to seek complex characteristics, once the wide distribution of markers favors through the linkage disequilibrium, the identification of genomic regions associated with expression phenotypes in study. Therefore, this advance has become essential for greater accuracy and speed in molecular diagnostics, increasing the accuracy in the selection of individuals with

Life-history evolution and mitogenomic phylogeny of caecilian amphibians.

Science.gov (United States)

San Mauro, Diego; Gower, David J; Müller, Hendrik; Loader, Simon P; Zardoya, Rafael; Nussbaum, Ronald A; Wilkinson, Mark

2014-04-01

We analyze mitochondrial genomes to reconstruct a robust phylogenetic framework for caecilian amphibians and use this to investigate life-history evolution within the group. Our study comprises 45 caecilian mitochondrial genomes (19 of them newly reported), representing all families and 27 of 32 currently recognized genera, including some for which molecular data had never been reported. Support for all relationships in the inferred phylogenetic tree is high to maximal, and topology tests reject all investigated alternatives, indicating an exceptionally robust molecular phylogenetic framework of caecilian evolution consistent with current morphology-based supraspecific classification. We used the mitogenomic phylogenetic framework to infer ancestral character states and to assess correlation among three life-history traits (free-living larvae, viviparity, specialized pre-adult or vernal teeth), each of which occurs only in some caecilian species. Our results provide evidence that an ancestor of the Seychelles caecilians abandoned direct development and re-evolved a free-living larval stage. This study yields insights into the concurrent evolution of direct development and of vernal teeth in an ancestor of Teresomata that likely gave rise to skin-feeding (maternal dermatophagy) behavior and subsequently enabled evolution of viviparity, with skin feeding possibly a homologous precursor of oviduct feeding in viviparous caecilians. Copyright © 2014 Elsevier Inc. All rights reserved.

Structure and evolution of the Y-chromosomal and mitochondrial DNA of cattle

NARCIS (Netherlands)

Verkaar, Edward Louis Christian

2003-01-01

The research described in this thesis is focused on the structure and evolution of the bovine Y-chromosome and the use of paternal markers in molecular diagnostics. The Y-chromosome has emerged together with the X-chromosome early during the evolution of the mammals by differentiation of a pair of

Exploring the correlations between sequence evolution rate and ...

Indian Academy of Sciences (India)

2012-10-15

Oct 15, 2012 ... The vast functional divergence within mammalian lineages that ... Keywords. Phylogenetics; molecular clock; sequence evolutionary rate; phenotypic evolution; morphology; genomics .... entire lineages during periods with ecosystem-level commu- ... increases from fish to amphibians to birds to mammals.

New Gene Evolution: Little Did We Know

Science.gov (United States)

Long, Manyuan; VanKuren, Nicholas W.; Chen, Sidi; Vibranovski, Maria D.

2014-01-01

Genes are perpetually added to and deleted from genomes during evolution. Thus, it is important to understand how new genes are formed and evolve as critical components of the genetic systems determining the biological diversity of life. Two decades of effort have shed light on the process of new gene origination, and have contributed to an emerging comprehensive picture of how new genes are added to genomes, ranging from the mechanisms that generate new gene structures to the presence of new genes in different organisms to the rates and patterns of new gene origination and the roles of new genes in phenotypic evolution. We review each of these aspects of new gene evolution, summarizing the main evidence for the origination and importance of new genes in evolution. We highlight findings showing that new genes rapidly change existing genetic systems that govern various molecular, cellular and phenotypic functions. PMID:24050177

Physicochemical evolution and positive selection of the ...

Indian Academy of Sciences (India)

2010-04-08

Apr 8, 2010 ... It is not clear whether matK evolves under Darwinian selection. In this study, the gymnosperm Taxaceae, Cephalotaxaceae and Pinaceae were used to illustrate the physicochemical evolution, molecular adaptation and evolutionary dynamics of gene divergence in matKs. matK sequences were amplified ...

Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenalf.

Directory of Open Access Journals (Sweden)

Kartik Sunagar

Full Text Available Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF, brain-derived neurotrophic factors (BDNF and neurotrophin-3 (NT-3, which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74% and on the molecular surface of the protein (92%, while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation.

Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf

Science.gov (United States)

Sunagar, Kartik; Fry, Bryan Grieg; Jackson, Timothy N. W.; Casewell, Nicholas R.; Undheim, Eivind A. B.; Vidal, Nicolas; Ali, Syed A.; King, Glenn F.; Vasudevan, Karthikeyan; Vasconcelos, Vitor; Antunes, Agostinho

2013-01-01

Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF), brain-derived neurotrophic factors (BDNF) and neurotrophin-3 (NT-3), which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae) have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74%) and on the molecular surface of the protein (92%), while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation. PMID:24312363

Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.

Science.gov (United States)

Hao, Da-Cheng; Xiao, Pei-Gen

2015-01-01

Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

Properties of InSbN grown on GaAs by radio frequency nitrogen plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Lim, K P; Yoon, S F; Pham, H T

2009-01-01

We report the growth of InSbN on a lattice-mismatched GaAs substrate using radio frequency nitrogen plasma-assisted molecular beam epitaxy. The effects of a two-step thin InSb buffer layer grown at 330 and 380 deg. C and substrate temperature (270-380 deg. C) on the properties of the InSbN are studied. The crystalline quality of the InSbN is significantly improved by the two-step buffer layer due to defect suppression. The shifting in the absorption edge of the InSbN from ∼5 to 8 μm following an increase in the substrate temperature is correlated with the reduction in free carrier concentration from ∼10 18 to 10 16 cm -3 and increase in concentration of N substituting Sb from ∼0.2 to 1%. These results will be beneficial to those working on the pseudo-monolithic integration of InSbN detectors on a GaAs platform.

Plant breeding with marker-assisted selection in Brazil

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Ney Sussumu Sakiyama

2014-03-01

Full Text Available Over the past three decades, molecular marker studies reached extraordinary advances, especially for sequencing and bioinformatics techniques. Marker-assisted selection became part of the breeding program routines of important seed companies, in order to accelerate and optimize the cultivar developing processes. Private seed companies increasingly use marker-assisted selection, especially for the species of great importance to the seed market, e.g. corn, soybean, cotton, and sunflower. In the Brazilian public institutions few breeding programs use it efficiently. The possible reasons are: lack of know-how, lack of appropriate laboratories, few validated markers, high cost, and lack of urgency in obtaining cultivars. In this article we analyze the use and the constraints of marker-assisted selection in plant breeding programs of Brazilian public institutes

Temperature-dependent structure evolution in liquid gallium

International Nuclear Information System (INIS)

Xiong, L.H.; Wang, X.D.; Yu, Q.; Zhang, H.; Zhang, F.; Sun, Y.; Cao, Q.P.; Xie, H.L.; Xiao, T.Q.; Zhang, D.X.; Wang, C.Z.; Ho, K.M.

2017-01-01

Temperature-dependent atomistic structure evolution of liquid gallium (Ga) has been investigated by using in situ high energy X-ray diffraction experiment and ab initio molecular dynamics simulation. Both experimental and theoretical results reveal the existence of a liquid structural change around 1000 K in liquid Ga. Below and above this temperature the liquid exhibits differences in activation energy for self-diffusion, temperature-dependent heat capacity, coordination numbers, density, viscosity, electric resistivity and thermoelectric power, which are reflected from structural changes of the bond-orientational order parameter Q_6, fraction of covalent dimers, averaged string length and local atomic packing. This finding will trigger more studies on the liquid-to-liquid crossover in metallic melts. - Graphical abstract: Atomistic structure evolution of liquid gallium has been investigated by using in situ high energy X-ray diffraction and ab initio molecular dynamics simulations, which both demonstrate the existence of a liquid structural change together with reported density, viscosity, electric resistivity and absolute thermoelectric power data.

Adaptive Evolution of Gene Expression in Drosophila.

Science.gov (United States)

Nourmohammad, Armita; Rambeau, Joachim; Held, Torsten; Kovacova, Viera; Berg, Johannes; Lässig, Michael

2017-08-08

Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. Here, we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. Our results are derived from time-resolved data of gene expression divergence across a family of related species, using a probabilistic inference method for gene-specific selection. Adaptive gene expression is stronger in specific functional classes, including regulation, sensory perception, sexual behavior, and morphology. Moreover, we identify a large group of genes with sex-specific adaptation of expression, which predominantly occurs in males. Our analysis opens an avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Adaptive Evolution of Gene Expression in Drosophila

Directory of Open Access Journals (Sweden)

Armita Nourmohammad

2017-08-01

Full Text Available Gene expression levels are important quantitative traits that link genotypes to molecular functions and fitness. In Drosophila, population-genetic studies have revealed substantial adaptive evolution at the genomic level, but the evolutionary modes of gene expression remain controversial. Here, we present evidence that adaptation dominates the evolution of gene expression levels in flies. We show that 64% of the observed expression divergence across seven Drosophila species are adaptive changes driven by directional selection. Our results are derived from time-resolved data of gene expression divergence across a family of related species, using a probabilistic inference method for gene-specific selection. Adaptive gene expression is stronger in specific functional classes, including regulation, sensory perception, sexual behavior, and morphology. Moreover, we identify a large group of genes with sex-specific adaptation of expression, which predominantly occurs in males. Our analysis opens an avenue to map system-wide selection on molecular quantitative traits independently of their genetic basis.

The Art of Building Small : From Molecular Switches to Motors (Nobel Lecture)

NARCIS (Netherlands)

Feringa, Ben L.

2017-01-01

A journey into the nano-world: The ability to design, use and control motor-like functions at the molecular level sets the stage for numerous dynamic molecular systems. In his Nobel Lecture, B. L. Feringa describes the evolution of the field of molecular motors and explains how to program and

Emerging and Future Applications of Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry in the Clinical Microbiology Laboratory: A Report of the Association for Molecular Pathology.

Science.gov (United States)

Doern, Christopher D; Butler-Wu, Susan M

2016-11-01

The performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MS) for routine bacterial and yeast identification as well as direct-from-blood culture bottle identification has been thoroughly evaluated in the peer-reviewed literature. Microbiologists are now moving beyond these methods to apply MS to other areas of the diagnostic process. This review discusses the emergence of advanced matrix-assisted laser desorption ionization time-of-flight MS applications, including the identification of filamentous fungi and mycobacteria and the current and future state of antimicrobial resistance testing. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Molecular mechanisms involved in convergent crop domestication.

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Lenser, Teresa; Theißen, Günter

2013-12-01

Domestication has helped to understand evolution. We argue that, vice versa, novel insights into evolutionary principles could provide deeper insights into domestication. Molecular analyses have demonstrated that convergent phenotypic evolution is often based on molecular changes in orthologous genes or pathways. Recent studies have revealed that during plant domestication the causal mutations for convergent changes in key traits are likely to be located in particular genes. These insights may contribute to defining candidate genes for genetic improvement during the domestication of new plant species. Such efforts may help to increase the range of arable crops available, thus increasing crop biodiversity and food security to help meet the predicted demands of the continually growing global population under rapidly changing environmental conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Adaptation and evolution of drug-resistant Mycobacterium tuberculosis

NARCIS (Netherlands)

Bergval, I.L.

2013-01-01

Many studies have been conducted on drug resistance and the evolution of Mycobacterium tuberculosis. Notwithstanding, many molecular mechanisms facilitating the emergence, adaptation and spread of drug-resistant tuberculosis have yet to be discovered. This thesis reports studies of the adaptive

Step-flow anisotropy of the m-plane GaN (1100) grown under nitrogen-rich conditions by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Sawicka, Marta; Siekacz, Marcin; Skierbiszewski, Czeslaw; Turski, Henryk; Krysko, Marcin; DziePcielewski, Igor; Grzegory, Izabella; Smalc-Koziorowska, Julita

2011-01-01

The homoepitaxial growth of m-plane (1100) GaN was investigated by plasma-assisted molecular beam epitaxy under nitrogen-rich conditions. The surface morphologies as a function of sample miscut were studied, providing evidence for a strong growth anisotropy that is a consequence of the anisotropy of Ga adatom diffusion barriers on the m-plane surface recently calculated ab initio[Lymperakis and Neugebauer, Phys. Rev. B 79, 241308(R) (2009)]. We found that substrate miscut toward [0001] implies a step flow toward while substrate miscut toward [0001] causes formation of atomic steps either perpendicular or parallel to the [0001] direction, under N-rich conditions at 730 deg C. We describe the growth conditions for achieving atomically flat m-plane GaN layers with parallel atomic steps.

Photoionization-regulated star formation and the structure of molecular clouds

Science.gov (United States)

Mckee, Christopher F.

1989-01-01

A model for the rate of low-mass star formation in Galactic molecular clouds and for the influence of this star formation on the structure and evolution of the clouds is presented. The rate of energy injection by newly formed stars is estimated, and the effect of this energy injection on the size of the cloud is determined. It is shown that the observed rate of star formation appears adequate to support the observed clouds against gravitational collapse. The rate of photoionization-regulated star formation is estimated and it is shown to be in agreement with estimates of the observed rate of star formation if the observed molecular cloud parameters are used. The mean cloud extinction and the Galactic star formation rate per unit mass of molecular gas are predicted theoretically from the condition that photionization-regulated star formation be in equilibrium. A simple model for the evolution of isolated molecular clouds is developed.

Microwave-assisted RAFT polymerization of well-constructed magnetic surface molecularly imprinted polymers for specific recognition of benzimidazole residues

Science.gov (United States)

Chen, Fangfang; Wang, Jiayu; Chen, Huiru; Lu, Ruicong; Xie, Xiaoyu

2018-03-01

Magnetic nanoparticles have been widely used as support core for fast separation, which could be directly separated from complicated matrices using an external magnet in few minutes. Surface imprinting based on magnetic core has shown favorable adsorption and separation performance, including good adsorption capacity, fast adsorption kinetics and special selectivity adsorption. Reversible addition-fragmentation chain transfer (RAFT) is an ideal choice for producing well-defined complex architecture with mild reaction conditions. We herein describe the preparation of well-constructed magnetic molecularly imprinted polymers (MMIPs) for the recognition of benzimidazole (BMZ) residues via the microwave-assisted RAFT polymerization. The merits of RAFT polymerization assisting with microwave heating allowed successful and more efficient preparation of well-constructed imprinted coats. Moreover, the polymerization time dramatically shortened and was just 1/24th of the time taken by conventional heating. The results indicated that a uniform nanoscale imprinted layer was formed on the Fe3O4 core successfully, and enough saturation magnetization of MMIPs (16.53 emu g-1) was got for magnetic separation. The desirable adsorption capacity (30.18 μmol g-1) and high selectivity toward template molecule with a selectivity coefficient (k) of 13.85 of MMIPs were exhibited by the adsorption isothermal assay and competitive binding assay, respectively. A solid phase extraction enrichment approach was successfully established for the determination of four BMZ residues from apple samples using MMIPs coupled to HPLC. Overall, this study provides a versatile approach for highly efficient fabrication of well-constructed MMIPs for enrichment and determination of target molecules from complicated samples.

Evolution and mass extinctions as lognormal stochastic processes

Science.gov (United States)

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.

The Organization as Client: Broadening the Concept of Employee Assistance Programs.

Science.gov (United States)

Googins, Bradley; Davidson, Bruce N.

1993-01-01

Notes that many employee assistance programs (EAPs) are broadening their function to address rapidly changing human and social issues of environments in which they operate, refocusing practice to include organization as the client. Discusses traditional EAP practice, evolution of EAPs, changes confronting corporations, and alternative model in…

Evolution of size distribution, optical properties, and structure of Si nanoparticles obtained by laser-assisted fragmentation

Science.gov (United States)

Plautz, G. L.; Graff, I. L.; Schreiner, W. H.; Bezerra, A. G.

2017-05-01

We investigate the physical properties of Si-based nanoparticles produced by an environment-friendly three-step method relying on: (1) laser ablation of a solid target immersed in water, (2) centrifugation and separation, and (3) laser-assisted fragmentation. The evolution of size distribution is followed after each step by means of dynamic light scattering (DLS) measurements and crosschecked by transmission electron microscopy (TEM). The as-ablated colloidal suspension of Si nanoparticles presents a large size distribution, ranging from a few to hundreds of nanometers. Centrifugation drives the very large particles to the bottom eliminating them from the remaining suspension. Subsequent irradiation of height-separated suspensions with a second high-fluence (40 mJ/pulse) Nd:YAG laser operating at the fourth harmonic (λ =266 nm) leads to size reduction and ultra-small nanoparticles are obtainable depending on the starting size. Si nanoparticles as small as 1.5 nm with low dispersion (± 0.7 nm) are observed for the uppermost part after irradiation. These nanoparticles present a strong blue photoluminescence that remains stable for at least 8 weeks. Optical absorption (UV-Vis) measurements demonstrate an optical gap widening as a consequence of size decrease. Raman spectra present features related to pure silicon and silicon oxides for the irradiated sample. Interestingly, a defect band associated with silicon oxide is also identified, indicating the possible formation of defect states, which, in turn, supports the idea that the blue photoluminescence has its origin in defects.

Pulse-reverse electrodeposition for mesoporous metal films: combination of hydrogen evolution assisted deposition and electrochemical dealloying.

Science.gov (United States)

Cherevko, Serhiy; Kulyk, Nadiia; Chung, Chan-Hwa

2012-01-21

Hydrogen evolution assisted electrodeposition is a new bottom-up technique allowing the fast and simple synthesis of nanometals. Electrochemical dealloying is a top-down approach with the same purpose. In this work, we show that a combination of these two methods in sequence by pulse-reverse electrodeposition can be used to prepare high-surface-area nanostructured metals. Highly porous adherent platinum is obtained by the deposition of CuPt alloy during the cathodic cycles and the selective dissolution of copper during the anodic cycles. The convection created by the movement of the hydrogen bubbles increases the deposition rate and removes the dissolved copper ions from the diffusion layer, which ensures the deposition of a film with the same stoichiometry throughout the whole process. Due to the relatively high ratio of copper atoms on the surface in the as-deposited layer, it is proposed that the dealloying kinetics is significantly higher than that usually observed during the dealloying process in a model system. The proposed approach has several advantages over other methods, such as a very high growth rate and needlessness of any post-treatment processes. A detailed analysis of the effect of pulse-reverse waveform parameters on the properties of the films is presented. Mesoporous platinum with pores and ligaments having characteristic sizes of less than 10 nm, an equivalent surface area of up to ca. 220 m(2) cm(-3), and a roughness factor of more than 1000 is fabricated.

Evolution viewed from physics, physiology and medicine.

Science.gov (United States)

Noble, Denis

2017-10-06

Stochasticity is harnessed by organisms to generate functionality. Randomness does not, therefore, necessarily imply lack of function or 'blind chance' at higher levels. In this respect, biology must resemble physics in generating order from disorder. This fact is contrary to Schrödinger's idea of biology generating phenotypic order from molecular- level order, which inspired the central dogma of molecular biology. The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of transcription factors and various epigenetic and reorganization mechanisms. These processes can occur in response to environmental stress, so that the genome becomes 'a highly sensitive organ of the cell' (McClintock). Organisms have evolved to be able to cope with many variations at the molecular level. Organisms also make use of physical processes in evolution and development when it is possible to arrive at functional development without the necessity to store all information in DNA sequences. This view of development and evolution differs radically from that of neo-Darwinism with its emphasis on blind chance as the origin of variation. Blind chance is necessary, but the origin of functional variation is not at the molecular level. These observations derive from and reinforce the principle of biological relativity, which holds that there is no privileged level of causation. They also have important implications for medical science.

Molecular phylogenetic evaluation of classification and scenarios of character evolution in calcareous sponges (Porifera, Class Calcarea.

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Oliver Voigt

Full Text Available Calcareous sponges (Phylum Porifera, Class Calcarea are known to be taxonomically difficult. Previous molecular studies have revealed many discrepancies between classically recognized taxa and the observed relationships at the order, family and genus levels; these inconsistencies question underlying hypotheses regarding the evolution of certain morphological characters. Therefore, we extended the available taxa and character set by sequencing the complete small subunit (SSU rDNA and the almost complete large subunit (LSU rDNA of additional key species and complemented this dataset by substantially increasing the length of available LSU sequences. Phylogenetic analyses provided new hypotheses about the relationships of Calcarea and about the evolution of certain morphological characters. We tested our phylogeny against competing phylogenetic hypotheses presented by previous classification systems. Our data reject the current order-level classification by again finding non-monophyletic Leucosolenida, Clathrinida and Murrayonida. In the subclass Calcinea, we recovered a clade that includes all species with a cortex, which is largely consistent with the previously proposed order Leucettida. Other orders that had been rejected in the current system were not found, but could not be rejected in our tests either. We found several additional families and genera polyphyletic: the families Leucascidae and Leucaltidae and the genus Leucetta in Calcinea, and in Calcaronea the family Amphoriscidae and the genus Ute. Our phylogeny also provided support for the vaguely suspected close relationship of several members of Grantiidae with giantortical diactines to members of Heteropiidae. Similarly, our analyses revealed several unexpected affinities, such as a sister group relationship between Leucettusa (Leucaltidae and Leucettidae and between Leucascandra (Jenkinidae and Sycon carteri (Sycettidae. According to our results, the taxonomy of Calcarea is in

The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex.

Science.gov (United States)

Merker, Matthias; Kohl, Thomas A; Niemann, Stefan; Supply, Philip

2017-01-01

Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.

Molecular biology: Self-sustaining chemistry

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Wrede Paul

2007-10-01

Full Text Available Abstract Molecular biology is an established interdisciplinary field within biology that deals fundamentally with the function of any nucleic acid in the cellular context. The molecular biology section in Chemistry Central Journal focusses on the genetically determined chemistry and biochemistry occuring in the cell. How can thousands of chemical reactions interact smoothly to maintain the life of cells, even in a variable environment? How is this self-sustaining system achieved? These are questions that should be answered in the light of molecular biology and evolution, but with the application of biophysical, physico-chemical, analytical and preparative technologies. As the Section Editor for the molecular biology section in Chemistry Central Journal, I hope to receive manuscripts that present new approaches aimed at better answering and shedding light upon these fascinating questions related to the chemistry of livings cells.

A Molecular Framework for Understanding DCIS

Science.gov (United States)

2015-10-01

hour per response , including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and...LCM, RNAseq, DNAseq, evolution 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF RESPONSIBLE PERSON...Nearest person month worked: 6 CM Funding support: philanthropic support Name : Jian Xian Project Role: senior research assistant - contributed to

Sex-determination systems and their evolution: Mammals

International Nuclear Information System (INIS)

Colorado Garzon, Fredy A; Matta Camacho, Nubia E; Sanchez, Antonio

2012-01-01

Sex-determination methods are very diverse as they have become an enduring research field, understanding the causes of gonadal development and elucidating the main factors involved in sex-determination of offspring required relating information from far-ranging areas such as cytology, embryology, morphology, molecular biology and even ecology and evolution. This article presents an overview of sex-determination in placental mammals, encompassing several levels of biological organization. The importance of the underlying molecular tools in the context of sex-determination assays and their implications in conservation genetics is also discussed.

Store-Assistance Management for a Supply Chain with Consumer Return under Consignment Contract

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Zhihui Wu

2017-01-01

Full Text Available In this paper, the strategy problems of pricing and store-assistance service investment are investigated for a supply chain with consumer return, where the considered supply chain under consignment contract consists of a single manufacturer and a single retailer. Firstly, we use differential equation to model the evolution of store-assistance service level and depict the effect of store-assistance service level on the return rate. By applying two-stage game, both optimal pricing and store-assistance service strategies are obtained based on the presented optimal control model. Subsequently, the committed dynamic consignment price contract is designed to coordinate and improve the performance of supply chain. Finally, a numerical example is provided to illustrate the impacts of the effectiveness of store-assistance service level and decay rate on the feasible region of corresponding contract.

Exploiting social evolution in biofilms

DEFF Research Database (Denmark)

Boyle, Kerry E; Heilmann, Silja; van Ditmarsch, Dave

2013-01-01

Bacteria are highly social organisms that communicate via signaling molecules, move collectively over surfaces and make biofilm communities. Nonetheless, our main line of defense against pathogenic bacteria consists of antibiotics-drugs that target individual-level traits of bacterial cells...... and thus, regrettably, select for resistance against their own action. A possible solution lies in targeting the mechanisms by which bacteria interact with each other within biofilms. The emerging field of microbial social evolution combines molecular microbiology with evolutionary theory to dissect...... the molecular mechanisms and the evolutionary pressures underpinning bacterial sociality. This exciting new research can ultimately lead to new therapies against biofilm infections that exploit evolutionary cheating or the trade-off between biofilm formation and dispersal....

Genomic organization and molecular phylogenies of the beta (β keratin multigene family in the chicken (Gallus gallus and zebra finch (Taeniopygia guttata: implications for feather evolution

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Sawyer Roger H

2010-05-01

Full Text Available Abstract Background The epidermal appendages of reptiles and birds are constructed of beta (β keratins. The molecular phylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian β-keratin genes are closely related to those of birds, the published genomes of the chicken and zebra finch provide an opportunity not only to compare the genomic organization of their β-keratins, but to study their molecular evolution in archosaurians. Results The subfamilies (claw, feather, feather-like, and scale of β-keratin genes are clustered in the same 5' to 3' order on microchromosome 25 in chicken and zebra finch, although the number of claw and feather genes differs between the species. Molecular phylogenies show that the monophyletic scale genes are the basal group within birds and that the monophyletic avian claw genes form the basal group to all feather and feather-like genes. Both species have a number of feather clades on microchromosome 27 that form monophyletic groups. An additional monophyletic cluster of feather genes exist on macrochromosome 2 for each species. Expression sequence tag analysis for the chicken demonstrates that all feather β-keratin clades are expressed. Conclusions Similarity in the overall genomic organization of β-keratins in Galliformes and Passeriformes suggests similar organization in all Neognathae birds, and perhaps in the ancestral lineages leading to modern birds, such as the paravian Anchiornis huxleyi. Phylogenetic analyses demonstrate that evolution of archosaurian epidermal appendages in the lineage leading to birds was accompanied by duplication and divergence of an ancestral β-keratin gene cluster. As morphological diversification of epidermal appendages occurred and the β-keratin multigene family expanded, novel β-keratin genes were selected for novel functions within appendages such as feathers.

Molecular basis of the evolution of sex

International Nuclear Information System (INIS)

Bernstein, H.; Hopf, F.A.; Michod, R.E.

1987-01-01

In this review, the authors present evidence for a hypothesis that the primary benefit of sexual reproduction is repair of DNA and masking of mutations, as opposed to the traditional view that sexual reproduction is an adaptation for producing genetic variation through allelic recombination. The two fundamental aspects of sex, recombination and outcrossing, are adaptive responses to the two major sources of noise in transmitting genetic information, DNA damage and replication errors. The authors refer to this view as the repair hypothesis, and review types of DNA damage that occur in various organisms. In dealing with damage, recombination produces a form of informational noise, allelic recombination, as a by-product. Recombinational repair is the only repair process known which can overcome double-strand damages in DNA. The authors provide a rationale for their theory of the origin and evolution of sex explained as a continuum by the repair hypothesis. Alternate theories are also described

Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes.

Science.gov (United States)

Christie, Joshua R; Beekman, Madeleine

2017-03-01

Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Early evolution without a tree of life

Directory of Open Access Journals (Sweden)

Martin William F

2011-06-01

Full Text Available Abstract Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause. This article was reviewed by Dan Graur, W. Ford Doolittle, Eugene V. Koonin and Christophe Malaterre.

Molecular evolution of candidate genes for crop-related traits in sunflower (Helianthus annuus L.).

Science.gov (United States)

Mandel, Jennifer R; McAssey, Edward V; Nambeesan, Savithri; Garcia-Navarro, Elena; Burke, John M

2014-01-01

Evolutionary analyses aimed at detecting the molecular signature of selection during crop domestication and/or improvement can be used to identify genes or genomic regions of likely agronomic importance. Here, we describe the DNA sequence-based characterization of a pool of candidate genes for crop-related traits in sunflower. These genes, which were identified based on homology to genes of known effect in other study systems, were initially sequenced from a panel of improved lines. All genes that exhibited a paucity of sequence diversity, consistent with the possible effects of selection during the evolution of cultivated sunflower, were then sequenced from a panel of wild sunflower accessions an outgroup. These data enabled formal tests for the effects of selection in shaping sequence diversity at these loci. When selection was detected, we further sequenced these genes from a panel of primitive landraces, thereby allowing us to investigate the likely timing of selection (i.e., domestication vs. improvement). We ultimately identified seven genes that exhibited the signature of positive selection during either domestication or improvement. Genetic mapping of a subset of these genes revealed co-localization between candidates for genes involved in the determination of flowering time, seed germination, plant growth/development, and branching and QTL that were previously identified for these traits in cultivated × wild sunflower mapping populations.

The evolution of mollusc shells.

Science.gov (United States)

McDougall, Carmel; Degnan, Bernard M

2018-05-01

Molluscan shells are externally fabricated by specialized epithelial cells on the dorsal mantle. Although a conserved set of regulatory genes appears to underlie specification of mantle progenitor cells, the genes that contribute to the formation of the mature shell are incredibly diverse. Recent comparative analyses of mantle transcriptomes and shell proteomes of gastropods and bivalves are consistent with shell diversity being underpinned by a rapidly evolving mantle secretome (suite of genes expressed in the mantle that encode secreted proteins) that is the product of (a) high rates of gene co-option into and loss from the mantle gene regulatory network, and (b) the rapid evolution of coding sequences, particular those encoding repetitive low complexity domains. Outside a few conserved genes, such as carbonic anhydrase, a so-called "biomineralization toolkit" has yet to be discovered. Despite this, a common suite of protein domains, which are often associated with the extracellular matrix and immunity, appear to have been independently and often uniquely co-opted into the mantle secretomes of different species. The evolvability of the mantle secretome provides a molecular explanation for the evolution and diversity of molluscan shells. These genomic processes are likely to underlie the evolution of other animal biominerals, including coral and echinoderm skeletons. This article is categorized under: Comparative Development and Evolution > Regulation of Organ Diversity Comparative Development and Evolution > Evolutionary Novelties. © 2018 Wiley Periodicals, Inc.

Nearly Neutral Evolution Across the Drosophila melanogaster Genome

DEFF Research Database (Denmark)

Esteve, David Castellano; James, Jennifer; Eyre-Walker, Adam

2017-01-01

Under the nearly neutral theory of molecular evolution the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from 128 North...

From evolutionary computation to the evolution of things

NARCIS (Netherlands)

Eiben, A.E.; Smith, J.E.

2015-01-01

Evolution has provided a source of inspiration for algorithm designers since the birth of computers. The resulting field, evolutionary computation, has been successful in solving engineering tasks ranging in outlook from the molecular to the astronomical. Today, the field is entering a new phase as

Chemical Evolution and the Evolutionary Definition of Life.

Science.gov (United States)

Higgs, Paul G

2017-06-01

Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding. Chemical evolution applies to short oligonucleotides that can be generated by random polymerization, as well as by template-directed replication, and which may be too short to encode a specific function. Chemical evolution is an important stage on the pathway to life, between the stage of "just chemistry" and the stage of full biological evolution. A mathematical model is presented here that illustrates the differences between these three stages. Chemical evolution leads to much larger differences in molecular concentrations than can be achieved by selection without replication. However, chemical evolution is not open-ended, unlike biological evolution. The ability to undergo Darwinian evolution is often considered to be a defining feature of life. Here, I argue that chemical evolution, although Darwinian, does not quite constitute life, and that a good place to put the conceptual boundary between non-life and life is between chemical and biological evolution.

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

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

Nastasja C. Hauck

2018-03-01

Full Text Available 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.

Monod and the spirit of molecular biology.

Science.gov (United States)

Morange, Michel

2015-06-01

The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly, Monod anticipated some recent evolutions of this discipline. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Structural properties and growth evolution of diamond-like carbon films with different incident energies: A molecular dynamics study

International Nuclear Information System (INIS)

Li, Xiaowei; Ke, Peiling; Zheng, He; Wang, Aiying

2013-01-01

Structural properties and growth evolution of diamond-like carbon (DLC) films with different incident energies were investigated systematically by the molecular dynamics simulation using a Tersoff interatomic potential for carbon-carbon interaction. The results revealed that the density, sp 3 fraction and residual compressive stress as a function of incident energy increased firstly and then decreased; when the incident energy was 70 eV/atom, the density could reach to 3.0 g/cm 3 with the maximal compressive stress of 15.5 GPa. Structure analysis indicated that the deviation of both bond angles and lengths from the equilibrium position led to the generation of a large residual stress, while the high compressive stress mainly attributed to the decrease of both bond angles and lengths among carbon atoms. The growth of DLC films underwent a formation process of “Line-Net” structure accompanied with the interaction of many atomic motion mechanisms, and the “Point” stage was only found for DLC films with low incident energy.

From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses.

Directory of Open Access Journals (Sweden)

Rafael Sanjuán

Full Text Available Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown. Viruses are an ideal system for addressing this question because their evolution is fast enough to be observed in real time, and experimentally-determined mutation rates are abundant. This article provides statistically supported evidence that the mutation rate determines molecular evolution across all types of viruses. Properties of the viral genome such as its size and chemical composition are identified as major determinants of these rates. Furthermore, a quantitative analysis reveals that, as expected, evolution rates increase linearly with mutation rates for slowly mutating viruses. However, this relationship plateaus for fast mutating viruses. A model is proposed in which deleterious mutations impose an evolutionary speed limit and set an extinction threshold in nature. The model is consistent with data from replication kinetics, selection strength and chemical mutagenesis studies.

Changes in Diversification Patterns and Signatures of Selection during the Evolution of Murinae-Associated Hantaviruses

Directory of Open Access Journals (Sweden)

Guillaume Castel

2014-03-01

Full Text Available In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses’ molecular evolution at different geographical scales (global and local. We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space.

Nanoscale Morphology Evolution Under Ion Irradiation

Energy Technology Data Exchange (ETDEWEB)

Aziz, Michael J. [President & Fellows of Harvard College, Cambridge, MA (United States)

2014-11-10

We showed that the half-century-old paradigm of morphological instability under irradiation due to the curvature-dependence of the sputter yield, can account neither for the phase diagram nor the amplification or decay rates that we measure in the simplest possible experimental system -- an elemental semiconductor with an amorphous surface under noble-gas ion irradiation; We showed that a model of pattern formation based on the impact-induced redistribution of atoms that do not get sputtered away explains our experimental observations; We developed a first-principles, parameter-free approach for predicting morphology evolution, starting with molecular dynamics simulations of single ion impacts, lasting picoseconds, and upscaling through a rigorous crater-function formalism to develop a partial differential equation that predicts morphology evolution on time scales more than twelve orders of magnitude longer than can be covered by the molecular dynamics; We performed the first quantitative comparison of the contributions to morphological instability from sputter removal and from impact-induced redistribution of atoms that are removed, and showed that the former is negligible compared to the latter; We established a new paradigm for impact-induced morphology evolution based on crater functions that incorporate both redistribution and sputter effects; and We developed a model of nanopore closure by irradiation-induced stress and irradiationenhanced fluidity, for the near-surface irradiation regime in which nuclear stopping predominates, and showed that it explains many aspects of pore closure kinetics that we measure experimentally.

Temporal evolution of event-related desynchronization in acute stroke: A pilot study

NARCIS (Netherlands)

Tangwiriyasakul, Chayanin; Verhagen, Rens; Rutten, Wim; van Putten, Michel Johannes Antonius Maria

2014-01-01

Objective Assessment of event-related desynchronization (ERD) may assist in predicting recovery from stroke and rehabilitation, for instance in BCI applications. Here, we explore the temporal evolution of ERD during stroke recovery. Methods Ten stroke patients and eleven healthy controls were

Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria.

Science.gov (United States)

Ku, Chuan; Lo, Wen-Sui; Kuo, Chih-Horng

2014-04-18

The mreB gene family encodes actin-like proteins that determine cell shape by directing cell wall synthesis and often exists in one to three copies in the genomes of non-spherical bacteria. Intriguingly, while most wall-less bacteria do not have this gene, five to seven mreB homologs are found in Spiroplasma and Haloplasma, which are both characterized by cell contractility. To investigate the molecular evolution of this gene family in wall-less bacteria, we sampled the available genome sequences from these two genera and other related lineages for comparative analysis. The gene phylogenies indicated that the mreB homologs in Haloplasma are more closely related to those in Firmicutes, whereas those in Spiroplasma form a separate clade. This finding suggests that the gene family expansions in these two lineages are the results of independent ancient duplications. Moreover, the Spiroplasma mreB homologs can be classified into five clades, of which the genomic positions are largely conserved. The inference of gene gains and losses suggests that there has been an overall trend to retain only one homolog from each of the five mreB clades in the evolutionary history of Spiroplasma. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

Czech Academy of Sciences Publication Activity Database

Allen, A. E.; Dupont, Ch. L.; Oborník, Miroslav; Horák, Aleš; Nunes-Nesi, A.; McCrow, J. P.; Zheng, H.; Johnson, D. A.; Hu, H.; Fernie, A. R.; Bowler, Ch.

2011-01-01

Roč. 473, č. 7346 (2011), s. 203-209 ISSN 0028-0836 R&D Projects: GA ČR GA206/08/1423 Institutional research plan: CEZ:AV0Z60220518 Keywords : CARBAMOYL-PHOSPHATE SYNTHETASE * PHAEODACTYLUM-TRICORNUTUM * MAXIMUM-LIKELIHOOD * PHYLOGENETIC RECONSTRUCTION * MOLECULAR EVOLUTION * SEQUENCE ALIGNMENT * DIVERGENCE TIMES * MARINE DIATOMS * MIXED MODELS * TREE Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 36.280, year: 2011

Plant cell walls throughout evolution: towards a molecular understanding of their design principles

OpenAIRE

Sarkar, Purbasha

2009-01-01

Throughout their life, plants typically remain in one location utilizing sunlight for the synthesis of carbohydrates, which serve as their sole source of energy as well as building blocks of a protective extracellular matrix, called the cell wall. During the course of evolution, plants have repeatedly adapted to their respective niche,which is reflected in the changes of their body plan and the specific design of cell walls. Cell walls not only changed throughout evolution but also are consta...

Vapor-solid-solid grown Ge nanowires at integrated circuit compatible temperature by molecular beam epitaxy

Science.gov (United States)

Zhu, Zhongyunshen; Song, Yuxin; Zhang, Zhenpu; Sun, Hao; Han, Yi; Li, Yaoyao; Zhang, Liyao; Xue, Zhongying; Di, Zengfeng; Wang, Shumin

2017-09-01

We demonstrate Au-assisted vapor-solid-solid (VSS) growth of Ge nanowires (NWs) by molecular beam epitaxy at the substrate temperature of ˜180 °C, which is compatible with the temperature window for Si-based integrated circuit. Low temperature grown Ge NWs hold a smaller size, similar uniformity, and better fit with Au tips in diameter, in contrast to Ge NWs grown at around or above the eutectic temperature of Au-Ge alloy in the vapor-liquid-solid (VLS) growth. Six ⟨110⟩ growth orientations were observed on Ge (110) by the VSS growth at ˜180 °C, differing from only one vertical growth direction of Ge NWs by the VLS growth at a high temperature. The evolution of NWs dimension and morphology from the VLS growth to the VSS growth is qualitatively explained by analyzing the mechanism of the two growth modes.

Directed evolution: selecting today's biocatalysts : selecting today's biocatalysts

NARCIS (Netherlands)

Otten, Linda; Quax, Wim

2005-01-01

Directed evolution has become a full-grown tool in molecular biology nowadays. The methods that are involved in creating a mutant library are extensive and can be divided into several categories according to their basic ideas. Furthermore, both screening and selection can be used to target the

Investigation of the growth of In2O3 on Y-stabilized ZrO2(100) by oxygen plasma assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Bourlange, A.; Payne, D.J.; Palgrave, R.G.; Foord, J.S.; Egdell, R.G.; Jacobs, R.M.J.; Schertel, A.; Hutchison, J.L.; Dobson, P.J.

2009-01-01

Thin films of In 2 O 3 have been grown on Y-stabilised ZrO 2 (100) substrates by oxygen plasma assisted molecular beam epitaxy over a range of substrate temperatures between 650 o C and 900 o C. Growth at 650 o C leads to continuous but granular films and complete extinction of substrate core level structure in X-ray photoelectron spectroscopy. However with increasing substrate temperature the films break up into a series of discrete micrometer sized islands. Both the continuous and the island films have excellent epitaxial relationship with the substrate as gauged by X-ray diffraction and selected area electron diffraction and lattice imaging in high resolution transmission electron microscopy.

High Al-content AlxGa1-xN epilayers grown on Si substrate by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Hussein, A.SH.; Thahab, S.M.; Hassan, Z.; Chin, C.W.; Abu Hassan, H.; Ng, S.S.

2009-01-01

The microstructure and optical properties of Al x Ga 1-x N/GaN/AlN films on Si (1 1 1) substrate grown by plasma-assisted molecular beam epitaxy (MBE) have been studied and investigated. Reflection high energy electron diffraction (RHEED), scanning electron microscopy (SEM), high-resolution X-ray diffraction (HR-XRD), energy dispersive X-ray spectroscopy (EDS) line analysis and photoluminescence (PL) were used to investigate a reconstruction pattern, cross-section, mole fraction and crystalline quality of the heterostructure. By applying the Vegard's law, a high Al-mole fraction of Al x Ga 1-x N sample with value of 0.43 has been obtained and compared with EDS line analysis measurement value. PL spectrum has exhibited a sharp and intense band edge emission of GaN with the absence of yellow emission band, indicating good crystal quality of the Al x Ga 1-x N has been successfully grown on Si substrate.

Interaction-based evolution: how natural selection and nonrandom mutation work together

Science.gov (United States)

2013-01-01

Background The modern evolutionary synthesis leaves unresolved some of the most fundamental, long-standing questions in evolutionary biology: What is the role of sex in evolution? How does complex adaptation evolve? How can selection operate effectively on genetic interactions? More recently, the molecular biology and genomics revolutions have raised a host of critical new questions, through empirical findings that the modern synthesis fails to explain: for example, the discovery of de novo genes; the immense constructive role of transposable elements in evolution; genetic variance and biochemical activity that go far beyond what traditional natural selection can maintain; perplexing cases of molecular parallelism; and more. Presentation of the hypothesis Here I address these questions from a unified perspective, by means of a new mechanistic view of evolution that offers a novel connection between selection on the phenotype and genetic evolutionary change (while relying, like the traditional theory, on natural selection as the only source of feedback on the fit between an organism and its environment). I hypothesize that the mutation that is of relevance for the evolution of complex adaptation—while not Lamarckian, or “directed” to increase fitness—is not random, but is instead the outcome of a complex and continually evolving biological process that combines information from multiple loci into one. This allows selection on a fleeting combination of interacting alleles at different loci to have a hereditary effect according to the combination’s fitness. Testing and implications of the hypothesis This proposed mechanism addresses the problem of how beneficial genetic interactions can evolve under selection, and also offers an intuitive explanation for the role of sex in evolution, which focuses on sex as the generator of genetic combinations. Importantly, it also implies that genetic variation that has appeared neutral through the lens of traditional

Evolution of heavy ions (He{sup 2+}, H{sup +}) radiolytic yield of molecular hydrogen vs. ''Track-Segment'' LET values

Energy Technology Data Exchange (ETDEWEB)

Crumiere, Francis; Vandenborre, Johan; Blain, Guillaume; Fattahi, Massoud [Nantes Univ., CNRS/IN2P3 (France). SUBATECH Unite Mixte de Recherche 6457; Haddad, Ferid [Nantes Univ., CNRS/IN2P3 (France). SUBATECH Unite Mixte de Recherche 6457; Cyclotron Arronax, Saint Herblain (France)

2017-08-01

Ionizing radiation's effects onto water molecules lead to the ionization and/or the excitation of them. Then, these phenomena are followed by the formation of radicals and molecular products. The linear energy transfer (LET), which defines the energy deposition density along the radiation length, is different according to the nature of ionizing particles. Thus, the values of radiolytic yields, defined as the number of radical and molecular products formed or consumed by unit of deposited energy, evolve according to this parameter. This work consists in following the evolution of radiolytic yield of molecular hydrogen and ferric ions according to the ''Track-Segment'' LET of ionizing particles (protons, helions). Concerning G(Fe{sup 3+}) values, it seems that the energy deposited into the Bragg peak does not play the main role for the Fe{sup 3+} radiolytic formation, whereas for the G(H{sub 2}) it is the case with a component around 40% of the Bragg peak in the dihydrogen production. Therefore, as main results of this work, for high energetic Helion and Proton beams, the G(Fe{sup 3+}) values, which can be used for further dosimetry studies for example during the α radiolysis experiments, and the primary g(H{sub 2}) values for the Track-Segment LET, which can be used to determine the dihydrogen production by α-emitters, are published.

A reagent-assisted method in SERS detection of methyl salicylate

Science.gov (United States)

Li, Yali; Li, Qianwen; Wang, Yanan; Oh, Joohee; Jin, Sila; Park, Yeonju; Zhou, Tieli; Zhao, Bing; Ruan, Weidong; Jung, Young Mee

2018-04-01

With the explosive application of methyl salicylate (MS) molecules in food and cosmetics, the further detection of MS molecules becomes particularly important. Here we investigated the detection of MS molecules based on surface-enhanced Raman scattering (SERS) in a novel molecule/assistant/metal system constructed with MS, 4,4‧-(hexafluoroisopropylidene) bis (benzoic acid) and Ag nanoparticles (AgNPs). The minimum detection concentration is 10-4 M. To explore the function of assisted reagent, we also referred another system without assistant molecules. The result demonstrates that SERS signals were not acquired, which proves that the assistant molecules are critical for the capture of MS molecules. Two possible mechanisms of MS/assistant/AgNPs system were speculated through two patterns of hydrogen bonds. The linker molecules acted as the role of the bridge between metallic substrates and target molecules through the molecular recognition. This strategy is very beneficial to the expanding of MS detection techniques and other hydrogen bond based coupling detections with SERS.

Hydrogen evolution by a metal-free electrocatalyst

KAUST Repository

Zheng, Yao

2014-04-28

Electrocatalytic reduction of water to molecular hydrogen via the hydrogen evolution reaction may provide a sustainable energy supply for the future, but its commercial application is hampered by the use of precious platinum catalysts. All alternatives to platinum thus far are based on nonprecious metals, and, to our knowledge, there is no report about a catalyst for electrocatalytic hydrogen evolution beyond metals. Here we couple graphitic-carbon nitride with nitrogen-doped graphene to produce a metal-free hybrid catalyst, which shows an unexpected hydrogen evolution reaction activity with comparable overpotential and Tafel slope to some of well-developed metallic catalysts. Experimental observations in combination with density functional theory calculations reveal that its unusual electrocatalytic properties originate from an intrinsic chemical and electronic coupling that synergistically promotes the proton adsorption and reduction kinetics. © 2014 Macmillan Publishers Limited. All rights reserved.

Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

Science.gov (United States)

Viscogliosi, E.; Edgcomb, V. P.; Gerbod, D.; Noel, C.; Delgado-Viscogliosi, P.; Sogin, M. L. (Principal Investigator)

1999-01-01

The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.

Molecular evolution of the two-component system BvgAS involved in virulence regulation in Bordetella.

Directory of Open Access Journals (Sweden)

Julien Herrou

Full Text Available The whooping cough agent Bordetella pertussis is closely related to Bordetella bronchiseptica, which is responsible for chronic respiratory infections in various mammals and is occasionally found in humans, and to Bordetella parapertussis, one lineage of which causes mild whooping cough in humans and the other ovine respiratory infections. All three species produce similar sets of virulence factors that are co-regulated by the two-component system BvgAS. We characterized the molecular diversity of BvgAS in Bordetella by sequencing the two genes from a large number of diverse isolates. The response regulator BvgA is virtually invariant, indicating strong functional constraints. In contrast, the multi-domain sensor kinase BvgS has evolved into two different types. The pertussis type is found in B. pertussis and in a lineage of essentially human-associated B. bronchiseptica, while the bronchiseptica type is associated with the majority of B. bronchiseptica and both ovine and human B. parapertussis. BvgS is monomorphic in B. pertussis, suggesting optimal adaptation or a recent population bottleneck. The degree of diversity of the bronchiseptica type BvgS is markedly different between domains, indicating distinct evolutionary pressures. Thus, absolute conservation of the putative solute-binding cavities of the two periplasmic Venus Fly Trap (VFT domains suggests that common signals are perceived in all three species, while the external surfaces of these domains vary more extensively. Co-evolution of the surfaces of the two VFT domains in each type and domain swapping experiments indicate that signal transduction in the periplasmic region may be type-specific. The two distinct evolutionary solutions for BvgS confirm that B. pertussis has emerged from a specific B. bronchiseptica lineage. The invariant regions of BvgS point to essential parts for its molecular mechanism, while the variable regions may indicate adaptations to different lifestyles. The

Effect of growth temperature on defects in epitaxial GaN film grown by plasma assisted molecular beam epitaxy

Directory of Open Access Journals (Sweden)

S. S. Kushvaha

2014-02-01

Full Text Available We report the effect of growth temperature on defect states of GaN epitaxial layers grown on 3.5 μm thick GaN epi-layer on sapphire (0001 substrates using plasma assisted molecular beam epitaxy. The GaN samples grown at three different substrate temperatures at 730, 740 and 750 °C were characterized using atomic force microscopy and photoluminescence spectroscopy. The atomic force microscopy images of these samples show the presence of small surface and large hexagonal pits on the GaN film surfaces. The surface defect density of high temperature grown sample is smaller (4.0 × 108 cm−2 at 750 °C than that of the low temperature grown sample (1.1 × 109 cm−2 at 730 °C. A correlation between growth temperature and concentration of deep centre defect states from photoluminescence spectra is also presented. The GaN film grown at 750 °C exhibits the lowest defect concentration which confirms that the growth temperature strongly influences the surface morphology and affects the optical properties of the GaN epitaxial films.

The Environmental and Molecular Sciences Laboratory project -- Continuous evolution in leadership

International Nuclear Information System (INIS)

Knutson, D.E.; McClusky, J.K.

1994-10-01

The Environmental and Molecular Sciences Laboratory (EMSL) construction project at Pacific Northwest Laboratory (PNL) in Richland, Washington, is a $230M Major Systems Acquisition for the US Department of Energy (DOE). The completed laboratory will be a national user facility that provides unparalleled capabilities for scientists involved in environmental molecular science research. This project, approved for construction by the Secretary of Energy in October 1993, is underway. The United States is embarking on an environmental cleanup effort that dwarfs previous scientific enterprise. Using current best available technology, the projected costs of cleaning up the tens of thousands of toxic waste sites, including DOE sites, is estimated to exceed one trillion dollars. The present state of scientific knowledge regarding the effects of exogenous chemicals on human biology is very limited. Long term environmental research at the molecular level is needed to resolve the concerns, and form the building blocks for a structure of cost effective process improvement and regulatory reform

The Environmental and Molecular Sciences Laboratory project -- Continuous evolution in leadership

Energy Technology Data Exchange (ETDEWEB)

Knutson, D.E.; McClusky, J.K.

1994-10-01

The Environmental and Molecular Sciences Laboratory (EMSL) construction project at Pacific Northwest Laboratory (PNL) in Richland, Washington, is a $230M Major Systems Acquisition for the US Department of Energy (DOE). The completed laboratory will be a national user facility that provides unparalleled capabilities for scientists involved in environmental molecular science research. This project, approved for construction by the Secretary of Energy in October 1993, is underway. The United States is embarking on an environmental cleanup effort that dwarfs previous scientific enterprise. Using current best available technology, the projected costs of cleaning up the tens of thousands of toxic waste sites, including DOE sites, is estimated to exceed one trillion dollars. The present state of scientific knowledge regarding the effects of exogenous chemicals on human biology is very limited. Long term environmental research at the molecular level is needed to resolve the concerns, and form the building blocks for a structure of cost effective process improvement and regulatory reform.

Trends in plant research using molecular markers.

Science.gov (United States)

Garrido-Cardenas, Jose Antonio; Mesa-Valle, Concepción; Manzano-Agugliaro, Francisco

2018-03-01

A deep bibliometric analysis has been carried out, obtaining valuable parameters that facilitate the understanding around the research in plant using molecular markers. The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.

Molecular stopwatches, cogwheels and ``spinflakes'': studying the dynamics of molecular superrotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2015-05-01

Using the technique of an optical centrifuge, we excite diatomic molecules to ultrafast synchronous rotation. Femtosecond velocity-map imaging allows us to visualize and study the coherent dynamics of molecular superrotors under field free conditions and in external magnetic field. We demonstrate that when the created rotational wave packet is narrow, its free evolution is nondispersing and follows the motion of a classically rotating dumbbell or a hand of the smallest natural stopwatch. For wider rotational distributions, we observe the breakdown of classical rotation, when a dumbbell shape changes to that of a ``quantum cogwheel'' - a molecular state simultaneously aligned along multiple direction. Our measurements in external magnetic field reveal other peculiar aspects of the rich dynamics of molecular superrotors. The rotation of a non-magnetic molecule interacts with the applied field only weakly, giving rise to slow precession of the molecular angular momentum around the field direction. In contrast, the electronic spin of a paramagnetic superrotor mediates this interaction, causing the initial disk-like angular distribution to split into several spatial components, each precessing with its own frequency determined by the spin projection.

Are there laws of genome evolution?

Directory of Open Access Journals (Sweden)

Eugene V Koonin

2011-08-01

Full Text Available Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.

Directory of Open Access Journals (Sweden)

Claudia Alvarez-Carreño

Full Text Available The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes.Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role.Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later evolution of the

Strong band edge luminescence from InN films grown on Si substrates by electron cyclotron resonance-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Yodo, Tokuo; Yona, Hiroaki; Ando, Hironori; Nosei, Daiki; Harada, Yoshiyuki

2002-01-01

We observed strong band edge luminescence at 8.5-200 K from 200-880 nm thick InN films grown on 10 nm thick InN buffer layers on Si(001) and Si(111) substrates by electron cyclotron resonance-assisted molecular beam epitaxy. The InN film on the Si(001) substrate exhibited strong band edge photoluminescence (PL) emission at 1.814 eV at 8.5 K, tentatively assigned as donor to acceptor pair [DAP (α-InN)] emission from wurtzite-InN (α-InN) crystal grains, while those on Si(111) showed other stronger band edge PL emissions at 1.880, 2.081 and 2.156 eV, tentatively assigned as donor bound exciton [D 0 X(α-InN)] from α-InN grains, DAP (β-InN) and D 0 X (β-InN) emissions from zinc blende-InN (β-InN) grains, respectively

Raman scattering and Rutherford backscattering studies on InN films grown by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Chung, Yee Ling; Peng Xingyu; Liao, Ying Chieh; Yao Shude; Chen, Li Chyong; Chen, Kuei Hsien; Feng, Zhe Chuan

2011-01-01

A series of InN thin films was grown on sapphire substrates via plasma-assisted molecular beam epitaxy (PA-MBE) with different nitrogen plasma power. Various characterization techniques, including Hall, photoluminescence, Raman scattering and Rutherford backscattering, have been employed to study these InN films. Good crystalline wurtzite structures have been identified for all PA-MBE grown InN films on sapphire substrate, which have narrower XRD wurtzite (0002) peaks, showed c-axis Raman scattering allowed longitudinal optical (LO) modes of A 1 and E 1 plus E 2 symmetry, and very weak backscattering forbidden transverse optical (TO) modes. The lower plasma power can lead to the lower carrier concentration, to have the InN film close to intrinsic material with the PL emission below 0.70 eV. With increasing the plasma power, high carrier concentration beyond 1 x 10 20 cm -3 can be obtained, keeping good crystalline perfection. Rutherford backscattering confirmed most of InN films keeping stoichiometrical In/N ratios and only with higher plasma power of 400 W leaded to obvious surface effect and interdiffusion between the substrate and InN film.

The Fact of Evolution: Implications for Science Education

Science.gov (United States)

Hofmann, James R.; Weber, Bruce H.

Creationists who object to evolution in the science curriculum of public schools often cite Jonathan Well's book Icons of Evolution in their support (Wells2000). In the third chapter of his book Wells claims that neither paleontological nor molecular evidence supports the thesis that the history of life is an evolutionary process of descent from preexisting ancestors. We argue that Wells inappropriately relies upon ambiguities inherent in the term `Darwinian' and the phrase `Darwin'stheory'. Furthermore, he does not accurately distinguish between the overwhelming evidence that supports the thesis of common descent and controversies that pertain to causal mechanisms such as natural selection. We also argue that Wells' attempts to undermine the evidence in support of common descent are flawed and his characterization of the relevant data is misleading. In particular, his assessment of the `Cambrian explosion' does not do justice to the fossil record. Nor do his selective references to debate about molecular and paleontological phylogenies constitute a case against common descent. We conclude that the fossil and molecular evidence is more than sufficient to warrant science educators to present common descent as a well-established scientific fact. We also argue that diagrams depicting the `tree of life' can be pedagogically useful as simplified representations of the history of life.

Parallel evolution of mound-building and grass-feeding in Australian nasute termites.

Science.gov (United States)

Arab, Daej A; Namyatova, Anna; Evans, Theodore A; Cameron, Stephen L; Yeates, David K; Ho, Simon Y W; Lo, Nathan

2017-02-01

Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6-8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets. Here, we investigate the evolution of termitid mound building and diet, through a comprehensive molecular phylogenetic analysis of Australian Nasutitermitinae. Molecular dating analysis indicates that the subfamily has colonized Australia on three occasions over the past approximately 20 Myr. Ancestral-state reconstruction showed that mound building arose on multiple occasions and from diverse ancestral nesting habits, including arboreal and wood or soil nesting. Grass feeding appears to have evolved from wood feeding via ancestors that fed on both wood and leaf litter. Our results underscore the adaptability of termites to ancient environmental change, and provide novel examples of parallel evolution of extended phenotypes. © 2017 The Author(s).

Glutamine synthetase gene evolution: A good molecular clock

International Nuclear Information System (INIS)

Pesole, G.; Lanvave, C.; Saccone, C.; Bozzetti, M.P.; Preparata, G.

1991-01-01

Glutamine synthetase gene evolution in various animals, plants, and bacteria was evaluated by a general stationary Markov model. The evolutionary process proved to be unexpectedly regular even for a time span as long as that between the divergence of prokaryotes from eukaryotes. This enabled us to draw phylogenetic trees for species whose phylogeny cannot be easily reconstructed from the fossil record. The calculation of the times of divergence of the various organelle-specific enzymes led us to hypothesize that the pea and bean chloroplast genes for these enzymes originated from the duplication of nuclear genes as a result of the different metabolic needs of the various species. The data indicate that the duplication of plastid glutamine synthetase genes occurred long after the endosymbiotic events that produced the organelles themselves

Nuclear medicine imaging instrumentations for molecular imaging

International Nuclear Information System (INIS)

Chung, Yong Hyun; Song, Tae Yong; Choi, Yong

2004-01-01

Small animal models are extensively utilized in the study of biomedical sciences. Current animal experiments and analysis are largely restricted to in vitro measurements and need to sacrifice animals to perform tissue or molecular analysis. This prevents researchers from observing in vivo the natural evolution of the process under study. Imaging techniques can provide repeatedly in vivo anatomic and molecular information noninvasively. Small animal imaging systems have been developed to assess biological process in experimental animals and increasingly employed in the field of molecular imaging studies. This review outlines the current developments in nuclear medicine imaging instrumentations including fused multi-modality imaging systems for small animal imaging

Pax genes in eye development and evolution

Czech Academy of Sciences Publication Activity Database

Kozmik, Zbyněk

2005-01-01

Roč. 15, č. 4 (2005), s. 430-438 ISSN 0959-437X R&D Projects: GA MŠk(CZ) 1M0520; GA ČR(CZ) GA204/04/1358 Institutional research plan: CEZ:AV0Z5052915 Keywords : paxpax * eye development * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.361, year: 2005

Optical polarimetry and molecular line studies of L1157 dark molecular cloud

Science.gov (United States)

Sharma, Ekta; Soam, Archana; Gopinathan, Maheswar

2018-04-01

Filaments are omnipresent in molecular clouds which are believed to fragment into cores. The detailed process of the evolution from filaments to cores depends critically on the physical conditions in the star forming region. This study aims at characterising gas motions using velocity structure and finding the dynamical importance of magnetic fields in the filament morphology. The plane-of-the-sky component of the magnetic field has been measured using optical polarization of the background stars. The orientation is found to be almost perpendicular to the filament implying its dynamical importance in the evolution of the cloud. Optical polarimetric results match very well with the sub millimetre polarization angles obtained in the inner core regions. The magnetic fields are found to have an orientation of 130° east with respect to north. The angular offset between the outflow axis and the magnetic field direction is found to be 25°. Values for parameters like the excitation temperature, optical depth and column densities have been derived using molecular lines. Optically thick lines show non-gaussian features. The non-thermal widths tell about the presence of turbulent motions whereas the C180 lines follow Gaussian features almost at all the locations observed in the filament.

Monte Carlo molecular simulations: improving the statistical efficiency of samples with the help of artificial evolution algorithms; Simulations moleculaires de Monte Carlo: amelioration de l'efficacite statistique de l'echantillonnage grace aux algorithmes d'evolution artificielle

Energy Technology Data Exchange (ETDEWEB)

Leblanc, B.

2002-03-01

Molecular simulation aims at simulating particles in interaction, describing a physico-chemical system. When considering Markov Chain Monte Carlo sampling in this context, we often meet the same problem of statistical efficiency as with Molecular Dynamics for the simulation of complex molecules (polymers for example). The search for a correct sampling of the space of possible configurations with respect to the Boltzmann-Gibbs distribution is directly related to the statistical efficiency of such algorithms (i.e. the ability of rapidly providing uncorrelated states covering all the configuration space). We investigated how to improve this efficiency with the help of Artificial Evolution (AE). AE algorithms form a class of stochastic optimization algorithms inspired by Darwinian evolution. Efficiency measures that can be turned into efficiency criteria have been first searched before identifying parameters that could be optimized. Relative frequencies for each type of Monte Carlo moves, usually empirically chosen in reasonable ranges, were first considered. We combined parallel simulations with a 'genetic server' in order to dynamically improve the quality of the sampling during the simulations progress. Our results shows that in comparison with some reference settings, it is possible to improve the quality of samples with respect to the chosen criterion. The same algorithm has been applied to improve the Parallel Tempering technique, in order to optimize in the same time the relative frequencies of Monte Carlo moves and the relative frequencies of swapping between sub-systems simulated at different temperatures. Finally, hints for further research in order to optimize the choice of additional temperatures are given. (author)

Molecular evolution of the Bovini tribe (Bovidae, Bovinae: Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

Directory of Open Access Journals (Sweden)

McCulloch Alan

2009-04-01

Full Text Available Abstract Background If mutation within the coding region of the genome is largely not adaptive, the ratio of nonsynonymous (dN to synonymous substitutions (dS per site (dN/dS should be approximately equal among closely related species. Furthermore, dN/dS in divergence between species should be equivalent to dN/dS in polymorphisms. This hypothesis is of particular interest in closely related members of the Bovini tribe, because domestication has promoted rapid phenotypic divergence through strong artificial selection of some species while others remain undomesticated. We examined a number of genes that may be involved in milk production in Domestic cattle and a number of their wild relatives for evidence that domestication had affected molecular evolution. Elevated rates of dN/dS were further queried to determine if they were the result of positive selection, low effective population size (Ne or reduced selective constraint. Results We have found that the domestication process has contributed to higher dN/dS ratios in cattle, especially in the lineages leading to the Domestic cow (Bos taurus and Mithan (Bos frontalis and within some breeds of Domestic cow. However, the high rates of dN/dS polymorphism within B. taurus when compared to species divergence suggest that positive selection has not elevated evolutionary rates in these genes. Likewise, the low rate of dN/dS in Bison, which has undergone a recent population bottleneck, indicates a reduction in population size alone is not responsible for these observations. Conclusion The effect of selection depends on effective population size and the selection coefficient (Nes. Typically under domestication both selection pressure for traits important in fitness in the wild and Ne are reduced. Therefore, reduced selective constraint could be responsible for the observed elevated evolutionary ratios in domesticated species, especially in B. taurus and B. frontalis, which have the highest dN/dS in the

Room temperature photoluminescence from In{sub x}Al{sub (1−x)}N films deposited by plasma-assisted molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Kong, W., E-mail: wei.kong@duke.edu; Jiao, W. Y.; Kim, T. H.; Brown, A. S. [Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina 27708 (United States); Mohanta, A. [Oak Ridge Institute for Science and Education, Research Participation Program, U.S. Army Aviation and Missile Research, Development and Engineering Center (AMRDEC), Redstone Arsenal, Alabama 35898 (United States); Roberts, A. T. [Charles Bowden Research Lab, Army Aviation and Missile RD and E Center, Redstone Arsenal, Alabama 35898 (United States); Fournelle, J. [Department of Geoscience, University of Wisconsin, Madison, Wisconsin 53706 (United States); Losurdo, M. [Plasma Chemistry Research Center-CNR, via Orabona, 4-70126 Bari (Italy); Everitt, H. O. [Charles Bowden Research Lab, Army Aviation and Missile RD and E Center, Redstone Arsenal, Alabama 35898 (United States); Department of Physics, Duke University, Durham, North Carolina 27708 (United States)

2014-09-29

InAlN films deposited by plasma-assisted molecular beam epitaxy exhibited a lateral composition modulation characterized by 10–12 nm diameter, honeycomb-shaped, columnar domains with Al-rich cores and In-rich boundaries. To ascertain the effect of this microstructure on its optical properties, room temperature absorption and photoluminescence characteristics of In{sub x}Al{sub (1−x)}N were comparatively investigated for indium compositions ranging from x = 0.092 to 0.235, including x = 0.166 lattice matched to GaN. The Stokes shift of the emission was significantly greater than reported for films grown by metalorganic chemical vapor deposition, possibly due to the phase separation in these nanocolumnar domains. The room temperature photoluminescence also provided evidence of carrier transfer from the InAlN film to the GaN template.

Parallel Evolution of Sperm Hyper-Activation Ca2+ Channels.

Science.gov (United States)

Cooper, Jacob C; Phadnis, Nitin

2017-07-01

Sperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+ into the sperm flagellum via CatSper ion channels. Surprisingly, all nine CatSper genes have been independently lost in several animal lineages. In Drosophila, sperm hyper-activation is performed through the cooption of the polycystic kidney disease 2 (pkd2) Ca2+ channel. The parallels between CatSpers in primates and pkd2 in Drosophila provide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by > 500 million years of divergence. Here, we use a comprehensive phylogenomic approach to investigate the selective pressures on these sperm hyper-activation channels. First, we find that the entire CatSper complex evolves rapidly under recurrent positive selection in primates. Second, we find that pkd2 has parallel patterns of adaptive evolution in Drosophila. Third, we show that this adaptive evolution of pkd2 is driven by its role in sperm hyper-activation. These patterns of selection suggest that the evolution of the sperm hyper-activation machinery is driven by sexual conflict with antagonistic ligands that modulate channel activity. Together, our results add sperm hyper-activation channels to the class of fast evolving reproductive proteins and provide insights into the mechanisms used by the sexes to manipulate sperm behavior. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Insights into the molecular evolution of the PDZ/LIM family and identification of a novel conserved protein motif.

Directory of Open Access Journals (Sweden)

Aartjan J W Te Velthuis

Full Text Available The PDZ and LIM domain-containing protein family is encoded by a diverse group of genes whose phylogeny has currently not been analyzed. In mammals, ten genes are found that encode both a PDZ- and one or several LIM-domains. These genes are: ALP, RIL, Elfin (CLP36, Mystique, Enigma (LMP-1, Enigma homologue (ENH, ZASP (Cypher, Oracle, LMO7 and the two LIM domain kinases (LIMK1 and LIMK2. As conventional alignment and phylogenetic procedures of full-length sequences fell short of elucidating the evolutionary history of these genes, we started to analyze the PDZ and LIM domain sequences themselves. Using information from most sequenced eukaryotic lineages, our phylogenetic analysis is based on full-length cDNA-, EST-derived- and genomic- PDZ and LIM domain sequences of over 25 species, ranging from yeast to humans. Plant and protozoan homologs were not found. Our phylogenetic analysis identifies a number of domain duplication and rearrangement events, and shows a single convergent event during evolution of the PDZ/LIM family. Further, we describe the separation of the ALP and Enigma subfamilies in lower vertebrates and identify a novel consensus motif, which we call 'ALP-like motif' (AM. This motif is highly-conserved between ALP subfamily proteins of diverse organisms. We used here a combinatorial approach to define the relation of the PDZ and LIM domain encoding genes and to reconstruct their phylogeny. This analysis allowed us to classify the PDZ/LIM family and to suggest a meaningful model for the molecular evolution of the diverse gene architectures found in this multi-domain family.

A Perspective on Robotic Assistance for Knee Arthroplasty

Directory of Open Access Journals (Sweden)

Nathan A. Netravali

2013-01-01

Full Text Available Knee arthroplasty is used to treat patients with degenerative joint disease of the knee to reduce pain and restore the function of the joint. Although patient outcomes are generally quite good, there are still a number of patients that are dissatisfied with their procedures. Aside from implant design which has largely become standard, surgical technique is one of the main factors that determine clinical results. Therefore, a lot of effort has gone into improving surgical technique including the use of computer-aided surgery. The latest generation of orthopedic surgical tools involves the use of robotics to enhance the surgeons’ abilities to install implants more precisely and consistently. This review presents an evolution of robot-assisted surgical systems for knee replacement with an emphasis on the clinical results available in the literature. Ever since various robotic-assistance systems were developed and used clinically worldwide, studies have demonstrated that these systems are as safe as and more accurate than conventional methods of manual implantation. Robotic surgical assistance will likely result in improved surgical technique and improved clinical results.

From Leonardo to da Vinci: the history of robot-assisted surgery in urology.

Science.gov (United States)

Yates, David R; Vaessen, Christophe; Roupret, Morgan

2011-12-01

What's known on the subject? and What does the study add? Numerous urological procedures can now be performed with robotic assistance. Though not definitely proven to be superior to conventional laparoscopy or traditional open surgery in the setting of a randomised trial, in experienced centres robot-assisted surgery allows for excellent surgical outcomes and is a valuable tool to augment modern surgical practice. Our review highlights the depth of history that underpins the robotic surgical platform we utilise today, whilst also detailing the current place of robot-assisted surgery in urology in 2011. The evolution of robots in general and as platforms to augment surgical practice is an intriguing story that spans cultures, continents and centuries. A timeline from Yan Shi (1023-957 bc), Archytas of Tarentum (400 bc), Aristotle (322 bc), Heron of Alexandria (10-70 ad), Leonardo da Vinci (1495), the Industrial Revolution (1790), 'telepresence' (1950) and to the da Vinci(®) Surgical System (1999), shows the incredible depth of history and development that underpins the modern surgical robot we use to treat our patients. Robot-assisted surgery is now well-established in Urology and although not currently regarded as a 'gold standard' approach for any urological procedure, it is being increasingly used for index operations of the prostate, kidney and bladder. We perceive that robotic evolution will continue infinitely, securing the place of robots in the history of Urological surgery. Herein, we detail the history of robots in general, in surgery and in Urology, highlighting the current place of robot-assisted surgery in radical prostatectomy, partial nephrectomy, pyeloplasty and radical cystectomy. © 2011 THE AUTHORS. BJU INTERNATIONAL © 2011 BJU INTERNATIONAL.

International bulletin on atomic and molecular data for fusion

International Nuclear Information System (INIS)

Stephens, J.A.; Bannister, M.E.; Fuhr, J.

1999-12-01

The International Bulletin on Atomic and Molecular Data for Fusion is prepared by the Atomic and Molecular Data Unit of the International Atomic Energy Agency. It is distributed free of charge by the IAEA to assist in the development of fusion research and technology. In part 1, the Atomic and Molecular Data Information System (AMDIS) is presented. In Part 2, the indexed papers are listed separately for structure and spectra, atomic and molecular collisions and surface interactions. Part 3 contains all the bibliographic data for both the indexed and non-indexed references. Finally, the Author Index (part 4) refers to the bibliographic references contained in part 3

Spinning gland transcriptomics from two main clades of spiders (order: Araneae--insights on their molecular, anatomical and behavioral evolution.

Directory of Open Access Journals (Sweden)

Francisco Prosdocimi

Full Text Available Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade. Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i anatomical differentiation of spinning glands and (ii behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution.

Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

Science.gov (United States)

Prosdocimi, Francisco; Bittencourt, Daniela; da Silva, Felipe Rodrigues; Kirst, Matias; Motta, Paulo C.; Rech, Elibio L.

2011-01-01

Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. PMID:21738742

Results of Evolution Supervised by Genetic Algorithms

Directory of Open Access Journals (Sweden)

Lorentz JÄNTSCHI

2010-09-01

Full Text Available The efficiency of a genetic algorithm is frequently assessed using a series of operators of evolution like crossover operators, mutation operators or other dynamic parameters. The present paper aimed to review the main results of evolution supervised by genetic algorithms used to identify solutions to agricultural and horticultural hard problems and to discuss the results of using a genetic algorithms on structure-activity relationships in terms of behavior of evolution supervised by genetic algorithms. A genetic algorithm had been developed and implemented in order to identify the optimal solution in term of estimation power of a multiple linear regression approach for structure-activity relationships. Three survival and three selection strategies (proportional, deterministic and tournament were investigated in order to identify the best survival-selection strategy able to lead to the model with higher estimation power. The Molecular Descriptors Family for structure characterization of a sample of 206 polychlorinated biphenyls with measured octanol-water partition coefficients was used as case study. Evolution using different selection and survival strategies proved to create populations of genotypes living in the evolution space with different diversity and variability. Under a series of criteria of comparisons these populations proved to be grouped and the groups were showed to be statistically different one to each other. The conclusions about genetic algorithm evolution according to a number of criteria were also highlighted.

Orion infrared nebula/molecular cloud

International Nuclear Information System (INIS)

Zuckerman, B.; Palmer, P.

1975-01-01

Observational and theoretical studies of the Orion Nebula and the associated molecular clouds have greatly increased our understanding of this and other regions in which star formation is taking place. Fundamental questions remain unanswered; and in this Letter we address three of them: (1) the chemical composition of the molecular cloud, (2) its internal motions, and (3) the role of magnetic fields in its evolution. We show that the gas phase chemistry and internal motions in one part of the cloud are distinctly different from those in the rest of the cloud, and two recent estimates of the magnetic field strengths are very uncertain. (auth)

Reflexions sur L'Evolution de L'Enseignement de la Biologie en Afrique.

Science.gov (United States)

Sasson, A.

1980-01-01

Reviews the main stages of the evolution of biology teaching in Africa. Discusses the UNESCO pilot project, the teaching aids produced for English- and French-speaking countries of Africa, and the "Teacher's Guide on the Biology of Human Populations" and projects needs for further assistance. (CS)

The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

Science.gov (United States)

Moser, Arvin; Pautler, Brent G

2016-05-15

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

EDTA-assisted synthesis of rose-like ZnO architectures

Energy Technology Data Exchange (ETDEWEB)

Li, Zhen [Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 201800 (China); Shanghai Applied Radiation Institute, Shanghai University, Shanghai 201800 (China); Fang, Yaoguo [Institute of Nanochemistry and Nanobiology, Shanghai University, Shanghai 201800 (China); Peng, Liwei; Wu, Minghong [Shanghai Applied Radiation Institute, Shanghai University, Shanghai 201800 (China); Pan, Dengyu

2010-10-15

Rose-like ZnO nanostructures were prepared by a low-temperature solution route with assistance of ethylenediaminetetraacetic acid disodium (EDTA-2Na). The morphology of ZnO nanostructures was found to change from nanowire arrays to rose- and tower-like architectures with increasing the molar ratio of EDTA-2Na/Zn{sup 2+}. Also, the shape evolution of ZnO nanostructures with time was observed from flat nanosheets to wrinkled nanosheets and to rose-like nanostructures. EDTA-2Na as a strong complexing agent was found to play a key role in the shape evolution. Photoluminescence spectra show that the rose-like ZnO architectures have more defects than the nanowire arrays. (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Structural, optical, and hydrogenation properties of ZnO nanowall networks grown on a Si (1 1 1) substrate by plasma-assisted molecular beam epitaxy

International Nuclear Information System (INIS)

Su, S.C.; Lu, Y.M.; Zhang, Z.Z.; Li, B.H.; Shen, D.Z.; Yao, B.; Zhang, J.Y.; Zhao, D.X.; Fan, X.W.

2008-01-01

ZnO nanowall networks were grown on a Si (1 1 1) substrate by plasma-assisted molecular beam epitaxy (P-MBE) without using catalysts. Scanning electronic microscopy (FE-SEM) confirmed the formation of nanowalls with a thickness of about 10-20 nm. X-ray diffraction (XRD) showed that the ZnO nanowall networks were crystallized in a wurtzite structure with their height parallel to the direction. Photoluminescence (PL) of the ZnO nanowall networks exhibited free excitons (FEs), donor-bound exciton (D 0 X), donor-acceptor pair (DAP), and free exciton to acceptor (FA) emissions. The growth mechanism of the ZnO nanowall networks was discussed, and their hydrogenation was also studied

The role of Pax genes in eye evolution

Czech Academy of Sciences Publication Activity Database

Kozmik, Zbyněk

2008-01-01

Roč. 75, 2-4 (2008), s. 335-339 ISSN 0361-9230 R&D Projects: GA AV ČR IAA500520604; GA MŠk(CZ) 1M0520 Institutional research plan: CEZ:AV0Z50520514 Keywords : eye * Pax * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.281, year: 2008

Communication: Molecular gears

Energy Technology Data Exchange (ETDEWEB)

Burnell, E. Elliott, E-mail: elliott.burnell@ubc.ca [Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1 (Canada); Lange, Cornelis A. de, E-mail: c.a.de.lange@vu.nl [Atomic, Molecular and Laser Physics, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam (Netherlands); Meerts, W. Leo, E-mail: leo.meerts@science.ru.nl [Atomic, Molecular and Laser Physics, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam (Netherlands); Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ Nijmegen (Netherlands)

2016-09-07

The {sup 1}H nuclear magnetic resonance spectrum of hexamethylbenzene orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy. The spectrum contains over 350 000 lines with many overlapping transitions, from which four independent direct dipolar couplings are obtained. The rotations of the six methyl groups appear to be correlated due to mutual steric hindrance. Adjacent methyl groups show counter-rotating or geared motion. Hexamethylbenzene thus behaves as a molecular hexagonal gear.

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

Directory of Open Access Journals (Sweden)

Reusch Thorsten BH

2011-01-01

Full Text Available Abstract Background 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. Results 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. Conclusions 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.

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

Science.gov (United States)

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.

Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

Science.gov (United States)

Halliday, C L; Kidd, S E; Sorrell, T C; Chen, S C-A

2015-04-01

Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa?

Czech Academy of Sciences Publication Activity Database

Flegontov, Pavel; Gray, M.W.; Burger, G.; Lukeš, Julius

2011-01-01

Roč. 57, č. 4 (2011), 225-232 ISSN 0172-8083 Institutional research plan: CEZ:AV0Z60220518 Keywords : Euglena * Diplonema * Mitochondrial genome * RNA editing * Constructive neutral evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.556, year: 2011

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

Science.gov (United States)

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.

Karyotype evolution in harvestmen of the suborder Cyphophthalmi (Opiliones)

Czech Academy of Sciences Publication Activity Database

Svojanovská, H.; Nguyen, Petr; Hiřman, M.; Tuf, I. H.; Wahab, R. A.; Haddad, C. R.; Šťáhlavský, F.

2016-01-01

Roč. 148, 2-3 (2016), s. 227-236 ISSN 1424-8581 R&D Projects: GA ČR(CZ) GP14-35819P Institutional support: RVO:60077344 Keywords : 18S rDNA * FISH * karyotype evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.354, year: 2016

16O+16O molecular nature of the superdeformed band of 32S and the evolution of the molecular structure

International Nuclear Information System (INIS)

Kimura, Masaaki; Horiuchi, Hisashi

2004-01-01

The relation between the superdeformed band of 32 S and 16 O+ 16 O molecular bands is studied by the deformed-basis antisymmetrized molecular dynamics with the Gogny D1S force. It is found that the obtained superdeformed band members of S have a considerable amount of the 16 O+ 16 O component. Above the superdeformed band, we have obtained two excited rotational bands which have more prominent character of the 16 O+ 16 O molecular band. These three rotational bands are regarded as a series of 16 O+ 16 O molecular bands which were predicted by using the unique 16 O- 16 O optical potential. As the excitation energy and principal quantum number of the relative motion increase, the 16 O+ 16 O cluster structure becomes more prominent but at the same time, the band members are fragmented into several states

Function and evolution of microRNAs in eusocial Hymenoptera

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Eirik eSovik

2015-05-01

Full Text Available The emergence of eusociality (true sociality in several insect lineages represents one of the most successful evolutionary adaptations in the animal kingdom in terms of species richness and global biomass. In contrast to solitary insects, eusocial insects evolved a set of unique behavioral and physiological traits such as reproductive division of labor and cooperative brood care, which likely played a major role in their ecological success. The molecular mechanisms that support the social regulation of behavior in eusocial insects, and their evolution, are mostly unknown. The recent whole-genome sequencing of several eusocial insect species set the stage for deciphering the molecular and genetic bases of eusociality, and the possible evolutionary modifications that led to it. Studies of mRNA expression patterns in the brains of diverse eusocial insect species have indicated that specific social behavioral states of individual workers and queens are often associated with particular tissue-specific transcriptional profiles. Here we discuss recent findings that highlight the role of non-coding microRNAs (miRNAs in modulating traits associated with reproductive and behavioral divisions of labor in eusocial insects. We provide bioinformatic and phylogenetic data, which suggest that some Hymenoptera-specific miRNA may have contributed to the evolution of traits important for the evolution of eusociality in this group.

Marker-assisted-selection (MAS): A fast track to increase genetic ...

African Journals Online (AJOL)

Mapping and tagging of agriculturally important genes have been greatly facilitated by an array of molecular markers in crop plants. Marker-assisted selection (MAS) is gaining considerable importance as it would improve the efficiency of plant breeding through precise transfer of genomic regions of interest (foreground ...

Molecular Evolution and Emergence of H5N6 Avian Influenza Virus in Central China.

Science.gov (United States)

Du, Yingying; Chen, Mingyue; Yang, Jiayun; Jia, Yane; Han, Shufang; Holmes, Edward C; Cui, Jie

2017-06-15

H5N6 avian influenza virus (AIV) has posed a potential threat to public health since its emergence in China in 2013. To understand the evolution and emergence of H5N6 AIV in the avian population, we performed molecular surveillance of live poultry markets (LPMs) in Wugang Prefecture, Hunan Province, in central China, during 2014 and 2015. Wugang Prefecture is located on the Eastern Asian-Australian migratory bird flyway, and a human death due to an H5N6 virus was reported in the prefecture on 21 November 2016. In total, we sampled and sequenced the complete genomes of 175 H5N6 AIVs. Notably, our analysis revealed that H5N6 AIVs contain at least six genotypes arising from segment reassortment, including a rare variant that possesses an HA gene derived from H5N1 clade 2.3.2 and a novel NP gene that has its origins with H7N3 viruses. In addition, phylogenetic analysis revealed that genetically similar H5N6 AIVs tend to cluster according to their geographic regions of origin. These results help to reveal the evolutionary behavior of influenza viruses prior to their emergence in humans. IMPORTANCE The newly emerged H5N6 influenza A virus has caused more than 10 human deaths in China since 2013. In November 2016, a human death due to an H5N6 virus, in Wugang Prefecture, Hunan Province, was confirmed by the WHO. To better understand the evolution and emergence of H5N6 viruses, we surveyed live poultry markets (LPMs) in Wugang Prefecture before the reported human death, with a focus on revealing the diversity and genomic origins of H5N6 in birds during 2014 and 2015. In general, H5N6 viruses in this region were most closely related to H5N1 clade 2.3.4.4, with the exception of one virus with an HA gene derived from clade 2.3.2 such that it represents a novel reassortant. Clearly, the ongoing surveillance of LPMs is central to monitoring the emergence of pathogenic influenza viruses. Copyright © 2017 American Society for Microbiology.

Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom.

Science.gov (United States)

Tzou, Wen-Shyong; Chu, Ying; Lin, Tzung-Yi; Hu, Chin-Hwa; Pai, Tun-Wen; Liu, Hsin-Fu; Lin, Han-Jia; Cases, Ildeofonso; Rojas, Ana; Sanchez, Mayka; You, Zong-Ye; Hsu, Ming-Wei

2014-01-01

Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5' untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.

Thermal and Chemical Evolution of Collapsing Filaments

Energy Technology Data Exchange (ETDEWEB)

Gray, William J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Scannapieco, Evan [Arizona State Univ., Mesa, AZ (United States). School of Earth and Space Exploration

2013-01-15

Intergalactic filaments form the foundation of the cosmic web that connect galaxies together, and provide an important reservoir of gas for galaxy growth and accretion. Here we present very high resolution two-dimensional simulations of the thermal and chemical evolution of such filaments, making use of a 32 species chemistry network that tracks the evolution of key molecules formed from hydrogen, oxygen, and carbon. We study the evolution of filaments over a wide range of parameters including the initial density, initial temperature, strength of the dissociating UV background, and metallicity. In low-redshift, Z ≈ 0.1Z_⊙ filaments, the evolution is determined completely by the initial cooling time. If this is sufficiently short, the center of the filament always collapses to form dense, cold core containing a substantial fraction of molecules. In high-redshift, Z = 10^-3Z_⊙ filaments, the collapse proceeds much more slowly. This is due mostly to the lower initial temperatures, which leads to a much more modest increase in density before the atomic cooling limit is reached, making subsequent molecular cooling much less efficient. Finally, we study how the gravitational potential from a nearby dwarf galaxy affects the collapse of the filament and compare this to NGC 5253, a nearby starbusting dwarf galaxy thought to be fueled by the accretion of filament gas. In contrast to our fiducial case, a substantial density peak forms at the center of the potential. This peak evolves faster than the rest of the filament due to the increased rate at which chemical species form and cooling occur. We find that we achieve similar accretion rates as NGC 5253, but our two-dimensional simulations do not recover the formation of the giant molecular clouds that are seen in radio observations.

Electron screening in molecular fusion reactions

International Nuclear Information System (INIS)

Shoppa, T.D.

1996-01-01

Recent laboratory experiments have measured fusion cross sections at center-of-mass energies low enough for the effects of atomic and molecular electrons to be important. To extract the cross section for bare nuclei from these data (as required for astrophysical applications), it is necessary to understand these screening effects. We study electron screening effects in the low-energy collisions of Z=1 nuclei with hydrogen molecules. Our model is based on a dynamical evolution of the electron wave functions within the TDHF scheme, while the motion of the nuclei is treated classically. We find that at the currently accessible energies the screening effects depend strongly on the molecular orientation. The screening is found to be larger for molecular targets than for atomic targets, due to the reflection symmetry in the latter. The results agree fairly well with data measured for deuteron collisions on molecular deuterium and tritium targets. (orig.)

ROLE OF MOLECULAR MARKERS IN THYROID NODULE MANAGEMENT: THEN AND NOW.

Science.gov (United States)

Nikiforov, Yuri E

2017-08-01

To describe the evolution and clinical utility of molecular testing for thyroid nodules and cancer achieved over the last 2 decades. Scientific reports on thyroid cancer genetics and molecular diagnostics in thyroid nodules. Over the last 2 decades, our understanding of the genetic mechanisms of thyroid cancer has dramatically expanded, such that most thyroid cancers now have known gene driver events. This knowledge provides the basis for establishing and further improving molecular tests for thyroid nodules and cancer and for the introduction of new entities such as noninvasive follicular thyroid neoplasm with papillary-like nuclear features. The progress with molecular tests for thyroid nodules started in the 1990s from demonstrating feasibility of detecting various molecular alterations in fine-needle aspiration (FNA) material collected from thyroid nodules. It was followed by the introduction of the first single-gene mutational markers, such as BRAF, and a small mutational panel into clinical practice in the mid 2000s. Currently, several more advanced molecular tests are available for clinical use. They are based on multiple molecular markers and have increasing impact on the clinical management of patients with thyroid nodules. The evolution of molecular tests for thyroid nodules followed the discovery of various diagnostic and prognostic molecular markers of thyroid cancer that can be applied to thyroid FNA samples to inform more individualized management of these patients. FNA = fine-needle aspiration miRNA = micro RNA NGS = next-generation sequencing NIFTP = noninvasive follicular thyroid neoplasm with papillary-like nuclear features NPV = negative predictive value PPV = positive predictive value PTC = papillary thyroid carcinoma RAI = radioactive iodine.

Prospects for the study of evolution in the deep biosphere.

Science.gov (United States)

Biddle, Jennifer F; Sylvan, Jason B; Brazelton, William J; Tully, Benjamin J; Edwards, Katrina J; Moyer, Craig L; Heidelberg, John F; Nelson, William C

2011-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).

An organismic critique of molecular darwinism.

Science.gov (United States)

Wicken, J S

1985-12-21

The molecular darwinian approach to the emergence of life treats the competition between RNA sequences for nucleotide resources as the primordial selective process in prebiotic evolution, which prescribes possible pathways for the subsequent elaboration of organizational relationships. Since success in this competition is determined by the "phenotypic" properties of RNA strands in the absence of organizational context, the genesis of biotic organization is dependent upon the establishment of co-operative, hypercyclic interactions between competing RNA sequences. The thesis of this paper is that hypercycle theory is based on unwarranted assumptions about the conditions of prebiotic evolution, and that the implications of these assumptions run counter to both empirical evidence and to the rational by which natural selection operates in evolution generally. An organismic alternative to hypercycle theory is suggested, based on the catalytic microsphere and the thermodynamics of selection.

Evolution of the osteoblast: skeletogenesis in gar and zebrafish

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Eames B Frank

2012-03-01

Full Text Available Abstract Background Although the vertebrate skeleton arose in the sea 500 million years ago, our understanding of the molecular fingerprints of chondrocytes and osteoblasts may be biased because it is informed mainly by research on land animals. In fact, the molecular fingerprint of teleost osteoblasts differs in key ways from that of tetrapods, but we do not know the origin of these novel gene functions. They either arose as neofunctionalization events after the teleost genome duplication (TGD, or they represent preserved ancestral functions that pre-date the TGD. Here, we provide evolutionary perspective to the molecular fingerprints of skeletal cells and assess the role of genome duplication in generating novel gene functions. We compared the molecular fingerprints of skeletogenic cells in two ray-finned fish: zebrafish (Danio rerio--a teleost--and the spotted gar (Lepisosteus oculatus--a "living fossil" representative of a lineage that diverged from the teleost lineage prior to the TGD (i.e., the teleost sister group. We analyzed developing embryos for expression of the structural collagen genes col1a2, col2a1, col10a1, and col11a2 in well-formed cartilage and bone, and studied expression of skeletal regulators, including the transcription factor genes sox9 and runx2, during mesenchymal condensation. Results Results provided no evidence for the evolution of novel functions among gene duplicates in zebrafish compared to the gar outgroup, but our findings shed light on the evolution of the osteoblast. Zebrafish and gar chondrocytes both expressed col10a1 as they matured, but both species' osteoblasts also expressed col10a1, which tetrapod osteoblasts do not express. This novel finding, along with sox9 and col2a1 expression in developing osteoblasts of both zebrafish and gar, demonstrates that osteoblasts of both a teleost and a basally diverging ray-fin fish express components of the supposed chondrocyte molecular fingerprint. Conclusions Our

The Evolution of Computer Based Learning Software Design: Computer Assisted Teaching Unit Experience.

Science.gov (United States)

Blandford, A. E.; Smith, P. R.

1986-01-01

Describes the style of design of computer simulations developed by Computer Assisted Teaching Unit at Queen Mary College with reference to user interface, input and initialization, input data vetting, effective display screen use, graphical results presentation, and need for hard copy. Procedures and problems relating to academic involvement are…

Adaptive laboratory evolution – principles and applications for biotechnology

Science.gov (United States)

2013-01-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering. PMID:23815749

Evolutionary anthropology and genes: investigating the genetics of human evolution from excavated skeletal remains.

Science.gov (United States)

Anastasiou, Evilena; Mitchell, Piers D

2013-10-01

The development of molecular tools for the extraction, analysis and interpretation of DNA from the remains of ancient organisms (paleogenetics) has revolutionised a range of disciplines as diverse as the fields of human evolution, bioarchaeology, epidemiology, microbiology, taxonomy and population genetics. The paper draws attention to some of the challenges associated with the extraction and interpretation of ancient DNA from archaeological material, and then reviews the influence of paleogenetics on the field of human evolution. It discusses the main contributions of molecular studies to reconstructing the evolutionary and phylogenetic relationships between extinct hominins (human ancestors) and anatomically modern humans. It also explores the evidence for evolutionary changes in the genetic structure of anatomically modern humans in recent millennia. This breadth of research has led to discoveries that would never have been possible using traditional approaches to human evolution. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular species identification and population genetics of ...

African Journals Online (AJOL)

Molecular genetic techniques, such as DNA barcoding and genotyping, are increasingly being used to assist with the conservation and management of chondrichthyans worldwide. Southern Africa is a shark biodiversity hotspot, with a large number of endemic species. According to the IUCN Red List, a quarter of South ...

Evolution and genome architecture in fungal plant pathogens.

Science.gov (United States)

Möller, Mareike; Stukenbrock, Eva H

2017-12-01

The fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.

The molecular evolution of the p120-catenin subfamily and its functional associations.

Directory of Open Access Journals (Sweden)

Robert H Carnahan

2010-12-01

Full Text Available p120-catenin (p120 is the prototypical member of a subclass of armadillo-related proteins that includes δ-catenin/NPRAP, ARVCF, p0071, and the more distantly related plakophilins 1-3. In vertebrates, p120 is essential in regulating surface expression and stability of all classical cadherins, and directly interacts with Kaiso, a BTB/ZF family transcription factor.To clarify functional relationships between these proteins and how they relate to the classical cadherins, we have examined the proteomes of 14 diverse vertebrate and metazoan species. The data reveal a single ancient δ-catenin-like p120 family member present in the earliest metazoans and conserved throughout metazoan evolution. This single p120 family protein is present in all protostomes, and in certain early-branching chordate lineages. Phylogenetic analyses suggest that gene duplication and functional diversification into "p120-like" and "δ-catenin-like" proteins occurred in the urochordate-vertebrate ancestor. Additional gene duplications during early vertebrate evolution gave rise to the seven vertebrate p120 family members. Kaiso family members (i.e., Kaiso, ZBTB38 and ZBTB4 are found only in vertebrates, their origin following that of the p120-like gene lineage and coinciding with the evolution of vertebrate-specific mechanisms of epigenetic gene regulation by CpG island methylation.The p120 protein family evolved from a common δ-catenin-like ancestor present in all metazoans. Through several rounds of gene duplication and diversification, however, p120 evolved in vertebrates into an essential, ubiquitously expressed protein, whereas loss of the more selectively expressed δ-catenin, p0071 and ARVCF are tolerated in most species. Together with phylogenetic studies of the vertebrate cadherins, our data suggest that the p120-like and δ-catenin-like genes co-evolved separately with non-neural (E- and P-cadherin and neural (N- and R-cadherin cadherin lineages, respectively. The

A Splash to Nano-Sized Inorganic Energy-Materials by the Low-Temperature Molecular Precursor Approach.

Science.gov (United States)

Driess, Matthias; Panda, Chakadola; Menezes, Prashanth Wilfried

2018-05-07

The low-temperature synthesis of inorganic materials and their interfaces at the atomic and molecular level provides numerous opportunities for the design and improvement of inorganic materials in heterogeneous catalysis for sustainable chemical energy conversion or other energy-saving areas. Using suitable molecular precursors for functional inorganic nanomaterial synthesis allows for facile control over uniform particle size distribution, stoichiometry, and leads to desired chemical and physical properties. This minireview outlines some advantages of the molecular precursor approach in light of selected recent developments of molecule-to-nanomaterials synthesis for renewable energy applications, relevant for the oxygen evolution reaction (OER), hydrogen evolution reaction (HER) and overall water-splitting. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Blue-violet InGaN laser diodes grown on bulk GaN substrates by plasma-assisted molecular-beam epitaxy

International Nuclear Information System (INIS)

Skierbiszewski, C.; Wasilewski, Z.R.; Siekacz, M.; Feduniewicz, A.; Perlin, P.; Wisniewski, P.; Borysiuk, J.; Grzegory, I.; Leszczynski, M.; Suski, T.; Porowski, S.

2005-01-01

We report on the InGaN multiquantum laser diodes (LDs) made by rf plasma-assisted molecular beam epitaxy (PAMBE). The laser operation at 408 nm is demonstrated at room temperature with pulsed current injections using 50 ns pulses at 0.25% duty cycle. The threshold current density and voltage for the LDs with cleaved uncoated mirrors are 12 kA/cm 2 (900 mA) and 9 V, respectively. High output power of 0.83 W is obtained during pulse operation at 3.6 A and 9.6 V bias with the slope efficiency of 0.35 W/A. The laser structures are deposited on the high-pressure-grown low dislocation bulk GaN substrates taking full advantage of the adlayer enhanced lateral diffusion channel for adatoms below the dynamic metallic cover. Our devices compare very favorably to the early laser diodes fabricated using the metalorganic vapor phase epitaxy technique, providing evidence that the relatively low growth temperatures used in this process pose no intrinsic limitations on the quality of the blue optoelectronic components that can be fabricated using PAMBE

Current Trends in Implantable Left Ventricular Assist Devices

Directory of Open Access Journals (Sweden)

Jens Garbade

2011-01-01

Full Text Available The shortage of appropriate donor organs and the expanding pool of patients waiting for heart transplantation have led to growing interest in alternative strategies, particularly in mechanical circulatory support. Improved results and the increased applicability and durability with left ventricular assist devices (LVADs have enhanced this treatment option available for end-stage heart failure patients. Moreover, outcome with newer pumps have evolved to destination therapy for such patients. Currently, results using nonpulsatile continuous flow pumps document the evolution in outcomes following destination therapy achieved subsequent to the landmark Randomized Evaluation of Mechanical Assistance for the Treatment of Congestive Heart Failure Trial (REMATCH, as well as the outcome of pulsatile designed second-generation LVADs. This review describes the currently available types of LVADs, their clinical use and outcomes, and focuses on the patient selection process.

Convergent Evolution of Hemoglobin Function in High-Altitude Andean Waterfowl Involves Limited Parallelism at the Molecular Sequence Level.

Directory of Open Access Journals (Sweden)

Chandrasekhar Natarajan

2015-12-01

Full Text Available A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we report a comparative analysis of hemoglobin (Hb function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages, and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization. In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.

Molecular phylogeny of the bivalve superfamily Galeommatoidea (Heterodonta, Veneroida) reveals dynamic evolution of symbiotic lifestyle and interphylum host switching

Science.gov (United States)

2012-01-01

Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA) and a nuclear (histone H3) and mitochondrial (cytochrome oxidase subunit I) protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in which they maintain filter

Molecular phylogeny of the bivalve superfamily Galeommatoidea (Heterodonta, Veneroida reveals dynamic evolution of symbiotic lifestyle and interphylum host switching

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Goto Ryutaro

2012-09-01

Full Text Available Abstract Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA and a nuclear (histone H3 and mitochondrial (cytochrome oxidase subunit I protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in

Proceedings of the Astrobiology Science Conference 2010. Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond

Science.gov (United States)

2010-01-01

The Program of the 2010 Astrobiology Science Conference: Evolution and Life: Surviving Catastrophes and Extremes on Earth and Beyond, included sessions on: 50 Years of Exobiology and Astrobiology: Greatest Hits; Extraterrestrial Molecular Evolution and Pre-Biological Chemistry: From the Interstellar Medium to the Solar System I; Human Exploration, Astronaut Health; Diversity in Astrobiology Research and Education; Titan: Past, Present, and Future; Energy Flow in Microbial Ecosystems; Extraterrestrial Molecular Evolution and Prebiological Chemistry: From the Interstellar Medium to the Solar System II; Astrobiology in Orbit; Astrobiology and Interdisciplinary Communication; Science from Rio Tinto: An Acidic Environment; Can We Rule Out Spontaneous Generation of RNA as the Key Step in the Origin of Life?; How Hellish Was the Hadean Earth?; Results from ASTEP and Other Astrobiology Field Campaigns I; Prebiotic Evolution: From Chemistry to Life I; Adaptation of Life in Hostile Space Environments; Extrasolar Terrestrial Planets I: Formation and Composition; Collaborative Tools and Technology for Astrobiology; Results from ASTEP and Other Astrobiology Field Campaigns II; Prebiotic Evolution: From Chemistry to Life II; Survival, Growth, and Evolution of Microrganisms in Model Extraterrestrial Environments; Extrasolar Terrestrial Planets II: Habitability and Life; Planetary Science Decadal Survey Update; Astrobiology Research Funding; Bioessential Elements Through Space and Time I; State of the Art in Life Detection; Terrestrial Evolution: Implications for the Past, Present, and Future of Life on Earth; Psychrophiles and Polar Environments; Life in Volcanic Environments: On Earth and Beyond; Geochronology and Astrobiology On and Off the Earth; Bioessential Elements Through Space and Time II; Origins and Evolution of Genetic Systems; Evolution of Advanced Life; Water-rich Asteroids and Moons: Composition and Astrobiological Potential; Impact Events and Evolution; A Warm, Wet

Effects of vibration frequency on vibration-assisted nano-scratch process of mono-crystalline copper via molecular dynamics simulation

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Bo Zhu

2016-03-01

Full Text Available It has always been a critical issue to understand the material removal behavior of Vibration-Assisted Machining (VAM, especially on atomic level. To find out the effects of vibration frequency on material removal response, a three-dimensional molecular dynamics (MD model has been established in this research to investigate the effects of scratched groove, crystal defects on the surface quality, comparing with the Von Mises shear strain and tangential force in simulations during nano-scratching process. Comparisons are made among the results of simulations from different vibration frequency with the same scratching feed, depth, amplitude and crystal orientation. Copper potential in this simulation is Embedded-Atom Method (EAM potential. Interaction between copper and carbon atoms is Morse potential. Simulational results show that higher frequency can make groove smoother. Simulation with high frequency creates more dislocations to improve the machinability of copper specimen. The changing frequency does not have evident effects on Von Mises shear strain. Higher frequency can decrease the tangential force to reduce the consumption of cutting energy and tool wear. In conclusion, higher vibration frequency in VAM on mono-crystalline copper has positive effects on surface finish, machinablility and tool wear reduction.

Effects of vibration frequency on vibration-assisted nano-scratch process of mono-crystalline copper via molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Zhu, Bo; Zhao, Hongwei, E-mail: hwzhao@jlu.edu.cn, E-mail: khl69@163.com; Zhao, Dan; Zhang, Peng; Yang, Yihan; Han, Lei [School of Mechanical Science and Engineering, Jilin University, 5988 Renmin Street, Changchun, Jilin 130025 (China); Kui, Hailin, E-mail: hwzhao@jlu.edu.cn, E-mail: khl69@163.com [School of Transportation, Jilin University, 5988 Renmin Street, Changchun, Jilin 130025 (China)

2016-03-15

It has always been a critical issue to understand the material removal behavior of Vibration-Assisted Machining (VAM), especially on atomic level. To find out the effects of vibration frequency on material removal response, a three-dimensional molecular dynamics (MD) model has been established in this research to investigate the effects of scratched groove, crystal defects on the surface quality, comparing with the Von Mises shear strain and tangential force in simulations during nano-scratching process. Comparisons are made among the results of simulations from different vibration frequency with the same scratching feed, depth, amplitude and crystal orientation. Copper potential in this simulation is Embedded-Atom Method (EAM) potential. Interaction between copper and carbon atoms is Morse potential. Simulational results show that higher frequency can make groove smoother. Simulation with high frequency creates more dislocations to improve the machinability of copper specimen. The changing frequency does not have evident effects on Von Mises shear strain. Higher frequency can decrease the tangential force to reduce the consumption of cutting energy and tool wear. In conclusion, higher vibration frequency in VAM on mono-crystalline copper has positive effects on surface finish, machinablility and tool wear reduction.

Direct growth of hexagonal boron nitride/graphene heterostructures on cobalt foil substrates by plasma-assisted molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Xu, Zhongguang; Khanaki, Alireza; Tian, Hao; Zheng, Renjing; Suja, Mohammad; Liu, Jianlin, E-mail: jianlin@ece.ucr.edu [Quantum Structures Laboratory, Department of Electrical and Computer Engineering, University of California, Riverside, California 92521 (United States); Zheng, Jian-Guo [Irvine Materials Research Institute, University of California, Irvine, California 92697-2800 (United States)

2016-07-25

Graphene/hexagonal boron nitride (G/h-BN) heterostructures have attracted a great deal of attention because of their exceptional properties and wide variety of potential applications in nanoelectronics. However, direct growth of large-area, high-quality, and stacked structures in a controllable and scalable way remains challenging. In this work, we demonstrate the synthesis of h-BN/graphene (h-BN/G) heterostructures on cobalt (Co) foil by sequential deposition of graphene and h-BN layers using plasma-assisted molecular beam epitaxy. It is found that the coverage of h-BN layers can be readily controlled on the epitaxial graphene by growth time. Large-area, uniform-quality, and multi-layer h-BN films on thin graphite layers were achieved. Based on an h-BN (5–6 nm)/G (26–27 nm) heterostructure, capacitor devices with Co(foil)/G/h-BN/Co(contact) configuration were fabricated to evaluate the dielectric properties of h-BN. The measured breakdown electric field showed a high value of ∼2.5–3.2 MV/cm. Both I-V and C-V characteristics indicate that the epitaxial h-BN film has good insulating characteristics.

Characterization of small HSPs from Anemonia viridis reveals insights into molecular evolution of alpha crystallin genes among cnidarians.

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Aldo Nicosia

Full Text Available Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive study of the molecular evolution of α-crystallin gene family among cnidarians. Most of the H. magnipapillata sHSP genes share the same gene organization described for AvHSP28.6 and AvHSP27, differing from the sHSP genes of N. vectensis which mainly show an intronless architecture. The different genomic organization of sHSPs, the phylogenetic analyses based on protein sequences, and the relationships among Cnidarians, suggest that the A.viridis sHSPs represent the common ancestor from which H. magnipapillata genes directly evolved through segmental genome duplication. Additionally retroposition events may be considered responsible for the divergence of sHSP genes of N. vectensis from A. viridis. Analyses of transcriptional expression profile showed that AvHSP28.6 was constitutively expressed among different tissues from both ectodermal and endodermal layers of the adult sea anemones, under normal physiological conditions and also under different stress condition. Specifically, we profiled the transcriptional activation of AvHSP28.6 after challenges with different abiotic/biotic stresses showing induction by extreme temperatures, heavy metals exposure and immune stimulation. Conversely, no AvHSP27 transcript was detected in such dissected tissues, in adult whole body cDNA library or under stress conditions. Hence, the involvement of AvHSP28.6 gene in the sea anemone defensome is strongly suggested.

Characterization of small HSPs from Anemonia viridis reveals insights into molecular evolution of alpha crystallin genes among cnidarians.

Science.gov (United States)

Nicosia, Aldo; Maggio, Teresa; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela; Costa, Salvatore

2014-01-01

Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain) are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive study of the molecular evolution of α-crystallin gene family among cnidarians. Most of the H. magnipapillata sHSP genes share the same gene organization described for AvHSP28.6 and AvHSP27, differing from the sHSP genes of N. vectensis which mainly show an intronless architecture. The different genomic organization of sHSPs, the phylogenetic analyses based on protein sequences, and the relationships among Cnidarians, suggest that the A.viridis sHSPs represent the common ancestor from which H. magnipapillata genes directly evolved through segmental genome duplication. Additionally retroposition events may be considered responsible for the divergence of sHSP genes of N. vectensis from A. viridis. Analyses of transcriptional expression profile showed that AvHSP28.6 was constitutively expressed among different tissues from both ectodermal and endodermal layers of the adult sea anemones, under normal physiological conditions and also under different stress condition. Specifically, we profiled the transcriptional activation of AvHSP28.6 after challenges with different abiotic/biotic stresses showing induction by extreme temperatures, heavy metals exposure and immune stimulation. Conversely, no AvHSP27 transcript was detected in such dissected tissues, in adult whole body cDNA library or under stress conditions. Hence, the involvement of AvHSP28.6 gene in the sea anemone defensome is strongly suggested.

Molecular Evolution and Genetic Variation of G2-Like Transcription Factor Genes in Maize.