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  1. Rapidly evolving homing CRISPR barcodes.

    PubMed

    Kalhor, Reza; Mali, Prashant; Church, George M

    2017-02-01

    We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing. This integrated approach will have wide-ranging applications, such as in deep lineage tracing, cellular barcoding, molecular recording, dissecting cancer biology, and connectome mapping.

  2. Hybridization Reveals the Evolving Genomic Architecture of Speciation

    PubMed Central

    Kronforst, Marcus R.; Hansen, Matthew E.B.; Crawford, Nicholas G.; Gallant, Jason R.; Zhang, Wei; Kulathinal, Rob J.; Kapan, Durrell D.; Mullen, Sean P.

    2014-01-01

    SUMMARY The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites. PMID:24183670

  3. Rapidly evolving microorganisms with high biofuel tolerance

    NASA Astrophysics Data System (ADS)

    Vyawahare, Saurabh; Zhang, Qiucen; Lang, Wendy; Austin, Robert

    2012-02-01

    Replacing non-renewable energy sources is one of the biggest and most exciting challenges of our generation. Algae and bacteria are poised to become major renewable biofuels if strains can be developed that provide a high,consistent and robust yield of oil. One major stumbling block towards this goal is the lack of tolerance to high concentrations of biofuels like isobutanol. Using traditional bioengineering techniques to remedy this face the hurdle of identifying the correct pathway or gene to modify. But the multiplicity of interactions inside a cell makes it very hard to determine what to modify a priori. Instead, we propose a technology that does not require prior knowledge of the genes or pathways to modify. In our approach that marries microfabrication and ecology, spatial heterogeneity is used as a knob to speed up evolution in the desired direction. Recently, we have successfully used this approach to demonstrate the rapid emergence of bacterial antibiotic resistance in as little as ten hours. Here, we describe our experimental results in developing new strains of micro-organisms with high oil tolerance. Besides biofuel production, our work is also relevant to oil spill clean-ups.

  4. Developing Collective Learning Extension for Rapidly Evolving Information System Courses

    ERIC Educational Resources Information Center

    Agarwal, Nitin; Ahmed, Faysal

    2017-01-01

    Due to rapidly evolving Information System (IS) technologies, instructors find themselves stuck in the constant game of catching up. On the same hand students find their skills obsolete almost as soon as they graduate. As part of IS curriculum and education, we need to emphasize more on teaching the students "how to learn" while keeping…

  5. Developing Collective Learning Extension for Rapidly Evolving Information System Courses

    ERIC Educational Resources Information Center

    Agarwal, Nitin; Ahmed, Faysal

    2017-01-01

    Due to rapidly evolving Information System (IS) technologies, instructors find themselves stuck in the constant game of catching up. On the same hand students find their skills obsolete almost as soon as they graduate. As part of IS curriculum and education, we need to emphasize more on teaching the students "how to learn" while keeping…

  6. Intrinsic immunogenicity of rapidly-degradable polymers evolves during degradation.

    PubMed

    Andorko, James I; Hess, Krystina L; Pineault, Kevin G; Jewell, Christopher M

    2016-03-01

    Recent studies reveal many biomaterial vaccine carriers are able to activate immunostimulatory pathways, even in the absence of other immune signals. How the changing properties of polymers during biodegradation impact this intrinsic immunogenicity is not well studied, yet this information could contribute to rational design of degradable vaccine carriers that help direct immune response. We use degradable poly(beta-amino esters) (PBAEs) to explore intrinsic immunogenicity as a function of the degree of polymer degradation and polymer form (e.g., soluble, particles). PBAE particles condensed by electrostatic interaction to mimic a common vaccine approach strongly activate dendritic cells, drive antigen presentation, and enhance T cell proliferation in the presence of antigen. Polymer molecular weight strongly influences these effects, with maximum stimulation at short degradation times--corresponding to high molecular weight--and waning levels as degradation continues. In contrast, free polymer is immunologically inert. In mice, PBAE particles increase the numbers and activation state of cells in lymph nodes. Mechanistic studies reveal that this evolving immunogenicity occurs as the physicochemical properties and concentration of particles change during polymer degradation. This work confirms the immunological profile of degradable, synthetic polymers can evolve over time and creates an opportunity to leverage this feature in new vaccines. Degradable polymers are increasingly important in vaccination, but how the inherent immunogenicity of polymers changes during degradation is poorly understood. Using common rapidly-degradable vaccine carriers, we show that the activation of immune cells--even in the absence of other adjuvants--depends on polymer form (e.g., free, particulate) and the extent of degradation. These changing characteristics alter the physicochemical properties (e.g., charge, size, molecular weight) of polymer particles, driving changes in

  7. ON THE NATURE OF RAPIDLY ROTATING SINGLE EVOLVED STARS

    SciTech Connect

    Da Silva, R. Rodrigues; Canto Martins, B. L.; De Medeiros, J. R.

    2015-03-01

    We present an analysis of the nature of the rapidly rotating, apparently single giant based on rotational and radial velocity measurements carried out by the CORAVEL spectrometers. From the analyzed sample, composed of 2010 spectroscopic, apparently single, evolved stars of luminosity classes IV, III, II, and Ib with spectral types G and K, we classified 30 stars that presented unusual, moderate to rapid rotation. This work reports, for the first time, the presence of these abnormal rotators among subgiant, bright giant, and Ib supergiant stars. To date, this class of stars was reported only among giant stars of luminosity class III. Most of these abnormal rotators present an IRAS infrared excess, which, in principle, can be related to dust around these stars.

  8. The rapidly evolving planetary nebula Hen 3-1357

    NASA Astrophysics Data System (ADS)

    Gry, C.

    Hen 3-1357 (known as the 'Stingray Nebula') is the youngest Planetary Nebula known in the sky. It has become ionized within the past few decades and its central star seems to be still rapidly evolving in the H-R diagram towards hotter effective temperatures. With this proposal we want to determine the current effective temperature of the central star and the characteristics of the stellar wind thirteen years after its discovery with IUE. This will enable us to determine whether the rapid spectral changes observed in the last few years are the consequence of an episodic post-AGB mass loss event or the result of a continuous evolution in the H-R digram. In any of these cases, the observations will help us to understand this short and, thus, still poorly known transition phase which leads to the formation of a new PN.

  9. Microsatellites evolve more rapidly in humans than in chimpanzees

    SciTech Connect

    Rubinsztein, D.C.; Leggo, J.; Amos, W.

    1995-12-10

    Microsatellites are highly polymorphic markers consisting of varying numbers of tandem repeats. At different loci, these repeats can consist of one to five nucleotides. Microsatellites have been used in many fields of genetics, including genetic mapping, linkage disequilibrium analyses, forensic studies, and population genetics. It is important that we understand their mutational processes better so that they can be exploited optimally for studies of human diversity and evolutionary genetics. We have analyzed 24 microsatellite loci in chimpanzees, East Anglians, and Sub-Saharan Africans. The stepwise-weighted genetic distances between the humans and the chimpanzees and between the two human populations were calculated according to the method described by Deka et al. The ratio of the genetic distances between the chimpanzees and the humans relative to that between the Africans and the East Anglians was more than 10 times smaller than expected. This suggests that microsatellites have evolved more rapidly in humans than in chimpanzees. 12 refs., 1 tab.

  10. How rapidly does the human mitochondrial genome evolve?

    SciTech Connect

    Howell, N.; Kubacka, I.; Mackey, D.A. |

    1996-09-01

    The results of an empirical nucleotide-sequencing approach indicate that the evolution of the human mitochondrial noncoding D-loop is both more rapid and more complex than is revealed by standard phylogenetic approaches. The nucleotide sequence of the D-loop region of the mitochondrial genome was determined for 45 members of a large matrilineal Leber hereditary optic neuropathy pedigree. Two germ-line mutations have arisen in members of one branch of the family, thereby leading to triplasmic descendants with three mitochondrial genotypes. Segregation toward the homoplasmic state can occur within a single generation in some of these descendants, a result that suggests rapid fixation of mitochondrial mutations as a result of developmental bottlenecking. However, slow segregation was observed in other offspring, and therefore no single or simple pattern of segregation can be generalized from the available data. Evidence for rare mtDNA recombination within the D-loop was obtained for one family member. In addition to these germ-line mutations, a somatic mutation was found in the D-loop of one family member. When this genealogical approach was applied to the nucleotide sequences of mitochondrial coding regions, the results again indicated a very rapid rate of evolution. 44 refs., 2 figs., 2 tabs.

  11. Cardiovascular disease prevention in women: a rapidly evolving scenario.

    PubMed

    Stranges, S; Guallar, E

    2012-12-01

    The past decade has witnessed a long overdue recognition of the importance of CVD in women, accompanied by an increasing awareness of gender differences in risk factors, natural history, preventive strategies, treatment, and prognosis of CVD. Reflecting the disease burden and the specific aspects of CVD in women, the American Heart Association has developed women-specific evidence-based guidelines and consensus documents for CVD prevention. The most recent update of these guidelines, published in 2011, is a milestone in the field and shows the rapidly evolving scenario of CVD prevention in women. We discuss some novel aspects of the 2011 update. The new guidelines change the focus from evidence-based to effectiveness-based, with consideration of both benefits and harms/costs of preventive interventions. The guidelines also introduce "ideal cardiovascular health" as the lowest category of risk, which implies the need of communitywide preventive, educational and policy initiatives to promote healthy lifestyles in the general population. Furthermore, the guidelines emphasize long-term overall CVD risk rather than short-term coronary risk. We also address several barriers and open questions in the evaluation and implementation of these guidelines, including how to increase the small proportion of women with ideal cardiovascular health; how to increase implementation and compliance with the recommendations; how to provide effectiveness-based recommendations for lifetime prevention goals based on short-term trials; how to obtain the best possible evidence in women; how to identify subgroups of women with different cardiovascular risk profiles or who may require tailored preventive strategies; and how to adapt current guidelines to international settings, particularly to low- and middle-income countries.

  12. Two rapidly evolving genes contribute to male fitness in Drosophila

    PubMed Central

    Reinhardt, Josephine A; Jones, Corbin D

    2013-01-01

    Purifying selection often results in conservation of gene sequence and function. The most functionally conserved genes are also thought to be among the most biologically essential. These observations have led to the use of sequence conservation as a proxy for functional conservation. Here we describe two genes that are exceptions to this pattern. We show that lack of sequence conservation among orthologs of CG15460 and CG15323 – herein named jean-baptiste (jb) and karr respectively – does not necessarily predict lack of functional conservation. These two Drosophila melanogaster genes are among the most rapidly evolving protein-coding genes in this species, being nearly as diverged from their D. yakuba orthologs as random sequences are. jb and karr are both expressed at an elevated level in larval males and adult testes, but they are not accessory gland proteins and their loss does not affect male fertility. Instead, knockdown of these genes in D. melanogaster via RNA interference caused male-biased viability defects. These viability effects occur prior to the third instar for jb and during late pupation for karr. We show that putative orthologs to jb and karr are also expressed strongly in the testes of other Drosophila species and have similar gene structure across species despite low levels of sequence conservation. While standard molecular evolution tests could not reject neutrality, other data hint at a role for natural selection. Together these data provide a clear case where a lack of sequence conservation does not imply a lack of conservation of expression or function. PMID:24221639

  13. Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

    PubMed Central

    2010-01-01

    Background In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past. Results Our analysis of the rapidly evolving trnK/matK, trnL-F and rps16 chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae) and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position. Conclusions Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales. The multiple independent evolution of the carnivorous syndrome, once in Lentibulariaceae and a second time in Byblidaceae, is strongly supported by all analyses and topological tests. The evolution of selected morphological characters such as flower symmetry is discussed. The addition of further sequence data from introns and spacers holds promise to eventually obtain a fully resolved plastid tree of

  14. Phylogenetic and epidemic modeling of rapidly evolving infectious diseases.

    PubMed

    Kühnert, Denise; Wu, Chieh-Hsi; Drummond, Alexei J

    2011-12-01

    Epidemic modeling of infectious diseases has a long history in both theoretical and empirical research. However the recent explosion of genetic data has revealed the rapid rate of evolution that many populations of infectious agents undergo and has underscored the need to consider both evolutionary and ecological processes on the same time scale. Mathematical epidemiology has applied dynamical models to study infectious epidemics, but these models have tended not to exploit--or take into account--evolutionary changes and their effect on the ecological processes and population dynamics of the infectious agent. On the other hand, statistical phylogenetics has increasingly been applied to the study of infectious agents. This approach is based on phylogenetics, molecular clocks, genealogy-based population genetics and phylogeography. Bayesian Markov chain Monte Carlo and related computational tools have been the primary source of advances in these statistical phylogenetic approaches. Recently the first tentative steps have been taken to reconcile these two theoretical approaches. We survey the Bayesian phylogenetic approach to epidemic modeling of infection diseases and describe the contrasts it provides to mathematical epidemiology as well as emphasize the significance of the future unification of these two fields. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. Rapidly evolving hypopituitarism in a boy with multiple autoimmune disorders.

    PubMed

    Jevalikar, Ganesh; Wong, Sze Choong; Zacharin, Margaret

    2013-09-01

    A 10-year-old boy with acute onset cranial diabetes insipidus and multiple autoimmune disorders had evolving panhypopituitarism, thought to be due to autoimmune hypophysitis. Over 18 months, a dramatic clinical course with progressive hypopituitarism and development of type 1 diabetes mellitus was evident. Serial brain imaging showed changes suggestive of germinoma.

  16. Rapidly Evolving Coronary Aneurysm in a Patient with Rheumatoid Arthritis

    PubMed Central

    Pappy, Reji; Wayangankar, Siddharth; Kalapura, Thomachan; Abu-Fadel, Mazen S.

    2011-01-01

    Coronary artery aneurysm (CAA) formation in the setting of an acute inflammatory state due to connective tissue disease is rare. We report a case of rapid progression from an ectatic to an aneursymatic left circumflex coronary artery leading to an acute coronary event in a patient with rheumatoid arthritis (RA). We report the accelerated growth of the aneurysm as it was temporally related to the lapse in treatment and the management strategies involved with this entity. PMID:21403892

  17. Rapidly evolving coronary aneurysm in a patient with rheumatoid arthritis.

    PubMed

    Pappy, Reji; Wayangankar, Siddharth; Kalapura, Thomachan; Abu-Fadel, Mazen S

    2011-02-21

    Coronary artery aneurysm (CAA) formation in the setting of an acute inflammatory state due to connective tissue disease is rare. We report a case of rapid progression from an ectatic to an aneursymatic left circumflex coronary artery leading to an acute coronary event in a patient with rheumatoid arthritis (RA). We report the accelerated growth of the aneurysm as it was temporally related to the lapse in treatment and the management strategies involved with this entity.

  18. Ultra-rapid formation of large volumes of evolved magma

    NASA Astrophysics Data System (ADS)

    Michaut, C.; Jaupart, C.

    2006-10-01

    We discuss evidence for, and evaluate the consequences of, the growth of magma reservoirs by small increments of thin (⋍ 1-2 m) sills. For such thin units, cooling proceeds faster than the nucleation and growth of crystals, which only allows a small amount of crystallization and leads to the formation of large quantities of glass. The heat balance equation for kinetic-controlled crystallization is solved numerically for a range of sill thicknesses, magma injection rates and crustal emplacement depths. Successive injections lead to the accumulation of poorly crystallized chilled magma with the properties of a solid. Temperatures increase gradually with each injection until they become large enough to allow a late phase of crystal nucleation and growth. Crystallization and latent heat release work in a positive feedback loop, leading to catastrophic heating of the magma pile, typically by 200 °C in a few decades. Large volumes of evolved melt are made available in a short time. The time for the catastrophic heating event varies as Q- 2 , where Q is the average magma injection rate, and takes values in a range of 10 5-10 6 yr for typical geological magma production rates. With this mechanism, storage of large quantities of magma beneath an active volcanic center may escape detection by seismic methods.

  19. Genetic basis for rapidly evolved tolerance in the wild ...

    EPA Pesticide Factsheets

    Atlantic killifish (Fundulus heteroclitus) residing in some urban and industrialized estuaries of the US eastern seaboard demonstrate recently evolved and extreme tolerance to toxic aryl hydrocarbon pollutants, characterized as dioxin-like compounds (DLCs). Here we provide an unusually comprehensive accounting (69%) through Quantitative Trait Locus (QTL) analysis of the genetic basis for DLC tolerance in killifish inhabiting an urban estuary contaminated with PCB congeners, the most toxic of which are DLCs. Consistent with mechanistic knowledge of DLC toxicity in fish and other vertebrates, the Aryl Hydrocarbon Receptor (ahr2) region accounts for 17% of trait variation; however, QTLs on independent linkage groups and their interactions have even greater explanatory power (44%). QTLs interpreted within the context of recently available Fundulus genomic resources and shared synteny among fish species suggest adaptation via inter-acting components of a complex stress response network. Some QTLs were also enriched in other killifish populations characterized as DLC tolerant and residing in distant urban estuaries contaminated with unique mixtures of pollutants. Together, our results suggest that DLC tolerance in killifish represents an emerging example of parallel contemporary evolution that has been driven by intense human-mediated selection on natural populations. This manuscript describes experimental studies that contribute to our understanding of the ecological

  20. Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

    PubMed Central

    Gottesman, Susan; Storz, Gisela

    2011-01-01

    Small RNA regulators (sRNAs) have been identified in a wide range of bacteria and found to play critical regulatory roles in many processes. The major families of sRNAs include true antisense RNAs, synthesized from the strand complementary to the mRNA they regulate, sRNAs that also act by pairing but have limited complementarity with their targets, and sRNAs that regulate proteins by binding to and affecting protein activity. The sRNAs with limited complementarity are akin to eukaryotic microRNAs in their ability to modulate the activity and stability of multiple mRNAs. In many bacterial species, the RNA chaperone Hfq is required to promote pairing between these sRNAs and their target mRNAs. Understanding the evolution of regulatory sRNAs remains a challenge; sRNA genes show evidence of duplication and horizontal transfer but also could be evolved from tRNAs, mRNAs or random transcription. PMID:20980440

  1. VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations.

    PubMed

    Petitjean, Michel; Vanet, Anne

    2014-02-15

    Daily, mutability and recombination of RNA viruses result in the production of million variants. All these rapid genomic changes directly influence the functional sites of the protein, its 3D structure or its drug resistances. Therefore, it is important to simulate these drastic switches to determine their effects on virus populations. Many computer programs are able to simulate specific variations in DNA genomes, but are generally non-adapted to RNA viruses. They simulate site-specific selection pressures, but rarely pressures on covariant or on higher order correlated sites and no at all on synthetic lethal groups. That is why we felt it important to create VIRAPOPS, a forward simulator that models specific RNA virus functions. It was designed for computational biologists, biologists and virologists. Free binaries are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.

  2. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes.

    PubMed

    Affaticati, Pierre E; Dai, Shao-Bo; Payongsri, Panwajee; Hailes, Helen C; Tittmann, Kai; Dalby, Paul A

    2016-10-21

    The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies.

  3. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes

    PubMed Central

    Affaticati, Pierre E.; Dai, Shao-Bo; Payongsri, Panwajee; Hailes, Helen C.; Tittmann, Kai; Dalby, Paul A.

    2016-01-01

    The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies. PMID:27767080

  4. A rapidly evolving secretome builds and patterns a sea shell

    PubMed Central

    Jackson, Daniel J; McDougall, Carmel; Green, Kathryn; Simpson, Fiona; Wörheide, Gert; Degnan, Bernard M

    2006-01-01

    Background Instructions to fabricate mineralized structures with distinct nanoscale architectures, such as seashells and coral and vertebrate skeletons, are encoded in the genomes of a wide variety of animals. In mollusks, the mantle is responsible for the extracellular production of the shell, directing the ordered biomineralization of CaCO3 and the deposition of architectural and color patterns. The evolutionary origins of the ability to synthesize calcified structures across various metazoan taxa remain obscure, with only a small number of protein families identified from molluskan shells. The recent sequencing of a wide range of metazoan genomes coupled with the analysis of gene expression in non-model animals has allowed us to investigate the evolution and process of biomineralization in gastropod mollusks. Results Here we show that over 25% of the genes expressed in the mantle of the vetigastropod Haliotis asinina encode secreted proteins, indicating that hundreds of proteins are likely to be contributing to shell fabrication and patterning. Almost 85% of the secretome encodes novel proteins; remarkably, only 19% of these have identifiable homologues in the full genome of the patellogastropod Lottia scutum. The spatial expression profiles of mantle genes that belong to the secretome is restricted to discrete mantle zones, with each zone responsible for the fabrication of one of the structural layers of the shell. Patterned expression of a subset of genes along the length of the mantle is indicative of roles in shell ornamentation. For example, Has-sometsuke maps precisely to pigmentation patterns in the shell, providing the first case of a gene product to be involved in molluskan shell pigmentation. We also describe the expression of two novel genes involved in nacre (mother of pearl) deposition. Conclusion The unexpected complexity and evolvability of this secretome and the modular design of the molluskan mantle enables diversification of shell strength and

  5. Rapid Target Modeling Through Genetic Inheritance Mechanism Genetically Evolved Target Prototypmg (GETP). Phase I

    DTIC Science & Technology

    1996-12-10

    Phase I Final Report Rapid Target Modeling Through Genetic Inheritance Mechanism Genetically Evolved Target Prototyping (GETP) Pbiai Dat December 10...COVERED 12/10/96 Final Report 5/7/96-12/10/96 A. TITE AND SUBTITU S. FUNDING NUMBERS Rapid Target Modeling Through Genetic Inheritance Mechanism... Genetically Evolved Target Prototyping (GETP) 6. AUTHOR(S) Dr. Jerzy Bala (P1) Dr. Peter Pachowicz (Co-P1) B.K. Gogia (PM) 7. PERFORMING ORGANIZATION

  6. A rapidly evolving genomic toolkit for Drosophila heterochromatin

    PubMed Central

    Levine, Mia T; Malik, Harmit S

    2013-01-01

    Heterochromatin is the enigmatic eukaryotic genome compartment found mostly at telomeres and centromeres. Conventional approaches to sequence assembly and genetic manipulation fail in this highly repetitive, gene-sparse, and recombinationally silent DNA. In contrast, genetic and molecular analyses of euchromatin-encoded proteins that bind, remodel, and propagate heterochromatin have revealed its vital role in numerous cellular and evolutionary processes. Utilizing the 12 sequenced Drosophila genomes, Levine et al1 took a phylogenomic approach to discover new such protein “surrogates” of heterochromatin function and evolution. This paper reported over 20 new members of what was traditionally believed to be a small and static Heterochromatin Protein 1 (HP1) gene family. The newly identified HP1 proteins are structurally diverse, lineage-restricted, and expressed primarily in the male germline. The birth and death of HP1 genes follows a “revolving door” pattern, where new HP1s appear to replace old HP1s. Here, we address alternative evolutionary models that drive this constant innovation. PMID:23519206

  7. Planetary Nebulae: Reviews and Previews of a Rapidly Evolving Field

    NASA Astrophysics Data System (ADS)

    Balick, Bruce

    2015-01-01

    Observational results from the ground and space in the past decade and covering the entire spectrum have jolted and energized research into the nature, the formation, and the evolution of planetary nebulae (PNs). The 101-level bubble structure of PNs turned out to be a pleasant but misleading fantasy as observations by HST and ALMA revealed basic details of their infancy. Some combination of close geriatric binary stars (the precusrors of SN Ia's) and magnetic fields dredged into the dusty winds appear to play vital roles in the ejection and collimation of AGB atmospheres. As a result, PNe and their antecedents, AGB stars and prePNs, are providing an array of new opportunities to study asymmetric wind formation, complex gas dynamics, CNO production rates in various galactic environments, and galaxy structure and evolution. I shall review the highlights of recent results, summarize their interpretations, and show some of the observational opportunities to monitor in the next decade, many of which couple strongly to research to related fields.This talk is dedicated to the career of Olivier Chesneau (1972-2014) who pioneered new high-resolution imaging methods that peered into the deep inner cores of nascent planetary nebulae. We remember Olivier as everyone's enthusiastic friend and colleague whose career ended in full stride.

  8. Shaping Outflows from Evolved Stars: Secrets Revealed by Chandra

    NASA Astrophysics Data System (ADS)

    Kastner, Joel H.

    2011-05-01

    Planetary nebulae (PNe), the near-endpoints of stellar evolution for intermediate-mass stars, exhibit a dizzying variety of optical/near-infrared morphologies: round; elliptical; bipolar; highly point-symmetric; chaotic and clumpy. The physical mechanisms responsible for this morphological menagerie are hotly debated. It is thought that the shape of a PN results from the sculpting of previously ejected, slow-moving (red giant) stellar envelope material by a fast wind from a (newly unveiled) white dwarf at the PN's core. But to explain the large fraction of nonspherical PNe -- which are presumably shaped by aspherical fast winds -- some models now further propose that many (perhaps most) PNe are the products of interacting binary systems. Chandra is yielding valuable insight into these stellar outflow shaping processes. Chandra imaging spectroscopy of PNe provides a unique means to determine the X-ray surface brightness distributions, temperatures, emission measures, and elemental abundances within the "hot bubbles" generated by fast wind shocks. Chandra observations of PNe have also revealed intriguing examples of unresolved X-ray sources that are too hard to be modeled as photospheric emission from hot white dwarfs. Such hard X-ray point sources are likely indicative of the presence of binary companions and/or accretion processes at PN central stars. I summarize the progress in these areas resulting from Chandra's first dozen years, and present early results from the first systematic Chandra survey of PNe in the solar neighborhood -- a survey designed to understand the formation and evolution of hot bubbles, and to establish the frequency and characteristics of point-like X-ray sources, within PNe with names like the Ring, the Dumbbell, the Owl, and Saturn. This work is supported by NASA Astrophysics Data Analysis Program and Chandra X-ray Center (CXC) grants to RIT. The CXC is operated by SAO for and on behalf of NASA under contract NAS8-03060.

  9. A rapidly evolving homeobox at the site of a hybrid sterility gene.

    PubMed

    Ting, C T; Tsaur, S C; Wu, M L; Wu, C I

    1998-11-20

    The homeodomain is a DNA binding motif that is usually conserved among diverse taxa. Rapidly evolving homeodomains are thus of interest because their divergence may be associated with speciation. The exact site of the Odysseus (Ods) locus of hybrid male sterility in Drosophila contains such a homeobox gene. In the past half million years, this homeodomain has experienced more amino acid substitutions than it did in the preceding 700 million years; during this period, it has also evolved faster than other parts of the protein or even the introns. Such rapid sequence divergence is driven by positive selection and may contribute to reproductive isolation.

  10. Licking Microstructure Reveals Rapid Attenuation of Neophobia

    PubMed Central

    Monk, Kevin J.; Rubin, Benjamin D.

    2014-01-01

    Many animals hesitate when initially consuming a novel food and increase their consumption of that food between the first and second sessions of access—a process termed attenuation of neophobia (AN). AN has received attention as a model of learning and memory; it has been suggested that plasticity resulting from an association of the novel tastant with “safe outcome” results in a change in the neural response to the tastant during the second session, such that consumption increases. Most studies have reported that AN emerges only an hour or more after the end of the first exposure to the tastant, consistent with what is known of learning-related plasticity. But these studies have typically measured consumption, rather than real-time behavior, and thus the possibility exists that a more rapidly developing AN remains to be discovered. Here, we tested this possibility, examining both consumption and individual lick times in a novel variant of a brief-access task (BAT). When quantified in terms of consumption, data from the BAT accorded well with the results of a classic one-bottle task—both revealed neophobia/AN specific to higher concentrations (for instance, 28mM) of saccharin. An analysis of licking microstructure, however, additionally revealed a real-time correlate of neophobia—an explicit tendency, similarly specific for 28-mM saccharin, to cut short the initial bout of licks in a single trial (compared with water). This relative hesitancy (i.e., the shortness of the first lick bout to 28-mM saccharin compared with water) that constitutes neophobia not only disappeared between sessions but also gradually declined in magnitude across session 1. These data demonstrate that the BAT accurately measures AN, and that aspects of AN—and the processes underlying familiarization—begin within minutes of the very first taste. PMID:24363269

  11. Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishes.

    PubMed

    Lee, Alison P; Kerk, Sze Yen; Tan, Yue Ying; Brenner, Sydney; Venkatesh, Byrappa

    2011-03-01

    Vertebrate genomes contain thousands of conserved noncoding elements (CNEs) that often function as tissue-specific enhancers. In this study, we have identified CNEs in human, dog, chicken, Xenopus, and four teleost fishes (zebrafish, stickleback, medaka, and fugu) using elephant shark, a cartilaginous vertebrate, as the base genome and investigated the evolution of these ancient vertebrate CNEs (aCNEs) in bony vertebrate lineages. Our analysis shows that aCNEs have been evolving at different rates in different bony vertebrate lineages. Although 78-83% of CNEs have diverged beyond recognition ("lost") in different teleost fishes, only 24% and 40% have been lost in the chicken and mammalian lineages, respectively. Relative rate tests of substitution rates in CNEs revealed that the teleost fish CNEs have been evolving at a significantly higher rate than those in other bony vertebrates. In the ray-finned fish lineage, 68% of aCNEs were lost before the divergence of the four teleosts. This implicates the "fish-specific" whole-genome duplication in the accelerated evolution and the loss of a large number of both copies of duplicated CNEs in teleost fishes. The aCNEs are rich in tissue-specific enhancers and thus many of them are likely to be evolutionarily constrained cis-regulatory elements. The rapid evolution of aCNEs might have affected the expression patterns driven by them. Transgenic zebrafish assay of some human CNE enhancers that have been lost in teleosts has indicated instances of conservation or changes in trans-acting factors between mammals and fishes.

  12. A fibre based triature interferometer for measuring rapidly evolving, ablatively driven plasma densities

    NASA Astrophysics Data System (ADS)

    Macdonald, J.; Bland, S. N.; Threadgold, J.

    2015-08-01

    We report on the first use of a fibre interferometer incorporating triature analysis for measuring rapidly evolving plasma densities of ne ˜ 1013/cm3 and above, such as those produced by simple coaxial plasma guns. The resultant system is extremely portable, easy to field in experiments, relatively cheap to produce, and—with the exception of a small open area in which the plasma is sampled—safe in operation as all laser light is enclosed.

  13. Pattern recognition algorithm reveals how birds evolve individual egg pattern signatures.

    PubMed

    Stoddard, Mary Caswell; Kilner, Rebecca M; Town, Christopher

    2014-06-18

    Pattern-based identity signatures are commonplace in the animal kingdom, but how they are recognized is poorly understood. Here we develop a computer vision tool for analysing visual patterns, NATUREPATTERNMATCH, which breaks new ground by mimicking visual and cognitive processes known to be involved in recognition tasks. We apply this tool to a long-standing question about the evolution of recognizable signatures. The common cuckoo (Cuculus canorus) is a notorious cheat that sneaks its mimetic eggs into nests of other species. Can host birds fight back against cuckoo forgery by evolving highly recognizable signatures? Using NATUREPATTERNMATCH, we show that hosts subjected to the best cuckoo mimicry have evolved the most recognizable egg pattern signatures. Theory predicts that effective pattern signatures should be simultaneously replicable, distinctive and complex. However, our results reveal that recognizable signatures need not incorporate all three of these features. Moreover, different hosts have evolved effective signatures in diverse ways.

  14. RAPIDLY EVOLVING AND LUMINOUS TRANSIENTS DRIVEN BY NEWLY BORN NEUTRON STARS

    SciTech Connect

    Yu, Yun-Wei; Li, Shao-Ze; Dai, Zi-Gao

    2015-06-10

    We provide a general analysis on the properties of the emitting material of some rapidly evolving and luminous transients discovered recently with the Pan-STARRS1 Medium Deep Survey. It was found that these transients are probably produced by a low-mass non-relativistic outflow that is continuously powered by a newly born, rapidly spinning, and highly magnetized neutron star (NS). Such a system could originate from an accretion-induced collapse of a white dwarf or a merger of an NS–NS binary. Therefore, observations of these transients would be helpful for constraining white dwarf and NS physics and/or for searching and identifying gravitational wave signals from the mergers.

  15. Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly.

    PubMed

    Aird, Steven D; Aggarwal, Shikha; Villar-Briones, Alejandro; Tin, Mandy Man-Ying; Terada, Kouki; Mikheyev, Alexander S

    2015-08-28

    While many studies have shown that extracellular proteins evolve rapidly, how selection acts on them remains poorly understood. We used snake venoms to understand the interaction between ecology, expression level, and evolutionary rate in secreted protein systems. Venomous snakes employ well-integrated systems of proteins and organic constituents to immobilize prey. Venoms are generally optimized to subdue preferred prey more effectively than non-prey, and many venom protein families manifest positive selection and rapid gene family diversification. Although previous studies have illuminated how individual venom protein families evolve, how selection acts on venoms as integrated systems, is unknown. Using next-generation transcriptome sequencing and mass spectrometry, we examined microevolution in two pitvipers, allopatrically separated for at least 1.6 million years, and their hybrids. Transcriptomes of parental species had generally similar compositions in regard to protein families, but for a given protein family, the homologs present and concentrations thereof sometimes differed dramatically. For instance, a phospholipase A2 transcript comprising 73.4 % of the Protobothrops elegans transcriptome, was barely present in the P. flavoviridis transcriptome (<0.05 %). Hybrids produced most proteins found in both parental venoms. Protein evolutionary rates were positively correlated with transcriptomic and proteomic abundances, and the most abundant proteins showed positive selection. This pattern holds with the addition of four other published crotaline transcriptomes, from two more genera, and also for the recently published king cobra genome, suggesting that rapid evolution of abundant proteins may be generally true for snake venoms. Looking more broadly at Protobothrops, we show that rapid evolution of the most abundant components is due to positive selection, suggesting an interplay between abundance and adaptation. Given log-scale differences in toxin

  16. Cross-Species Interaction between Rapidly Evolving Telomere-Specific Drosophila Proteins

    PubMed Central

    Vedelek, Balázs; Blastyák, András; Boros, Imre M.

    2015-01-01

    Telomere integrity in Drosophila melanogaster is maintained by a putative multisubunit complex called terminin that is believed to act in analogy to the mammalian shelterin complex in protecting chromosome ends from being recognized as sites of DNA damage. The five proteins supposed to form the terminin complex are HP1-ORC associated protein, HP1-HOAP interacting protein, Verrocchio, Drosophila Telomere Loss/Modigliani and Heterochromatic Protein 1. Four of these proteins evolve rapidly within the Drosophila genus. The accelerated evolution of terminin components may indicate the involvement of these proteins in the process by which new species arise, as the resulting divergence of terminin proteins might prevent hybrid formation, thus driving speciation. However, terminin is not an experimentally proven entity, and no biochemical studies have been performed to investigate its assembly and action in detail. Motivated by these facts in order to initiate biochemical studies on terminin function, we attempted to reconstitute terminin by co-expressing its subunits in bacteria and investigated the possible role of the fast-evolving parts of terminin components in complex assembly. Our results suggest formation of stable subcomplexes of terminin, but not of the whole complex in vitro. We found that the accelerated evolution is restricted to definable regions of terminin components, and that the divergence of D. melanogaster Drosophila Telomere Loss and D. yakuba Verrocchio proteins does not preclude their stable interaction. PMID:26566042

  17. Cross-Species Interaction between Rapidly Evolving Telomere-Specific Drosophila Proteins.

    PubMed

    Vedelek, Balázs; Blastyák, András; Boros, Imre M

    2015-01-01

    Telomere integrity in Drosophila melanogaster is maintained by a putative multisubunit complex called terminin that is believed to act in analogy to the mammalian shelterin complex in protecting chromosome ends from being recognized as sites of DNA damage. The five proteins supposed to form the terminin complex are HP1-ORC associated protein, HP1-HOAP interacting protein, Verrocchio, Drosophila Telomere Loss/Modigliani and Heterochromatic Protein 1. Four of these proteins evolve rapidly within the Drosophila genus. The accelerated evolution of terminin components may indicate the involvement of these proteins in the process by which new species arise, as the resulting divergence of terminin proteins might prevent hybrid formation, thus driving speciation. However, terminin is not an experimentally proven entity, and no biochemical studies have been performed to investigate its assembly and action in detail. Motivated by these facts in order to initiate biochemical studies on terminin function, we attempted to reconstitute terminin by co-expressing its subunits in bacteria and investigated the possible role of the fast-evolving parts of terminin components in complex assembly. Our results suggest formation of stable subcomplexes of terminin, but not of the whole complex in vitro. We found that the accelerated evolution is restricted to definable regions of terminin components, and that the divergence of D. melanogaster Drosophila Telomere Loss and D. yakuba Verrocchio proteins does not preclude their stable interaction.

  18. A volcano at work: the rapidly evolving landforms of Mt Etna documented through DEMs analysis

    NASA Astrophysics Data System (ADS)

    Tarquini, Simone; Favalli, Massimiliano; Fornaciai, Alessandro

    2016-04-01

    Volcanoes are characterized by rapid morphological changes in a continuously evolving landscape. In recent years, airborne LIDAR surveys have been repeatedly carried out to document the constructive and the destructive processes which modify the topography at Mount Etna (Italy), one of the most active volcanoes on Earth. In a few cases, time series of high resolution topographies have been acquired during ongoing effusive eruptions, and this extraordinary data allowed the systematic characterization of the morphology of active lava channels and the identification of a distinctive pulsating dynamic in lava flux. Furthermore, time series of topographies spaced several years allowed the quantification of the growth and of local collapses of summit craters, as well as the erosion of cinder cones formed during flank eruptions in 2001-2002. Overall, the availability of high resolution topographies boosted dramatically our understanding of volcanic processes, also allowing a better assessment of the related hazard. The present contribution is a review of several works spanning nearly a decade.

  19. Creating new knowledge for ruminant reproduction from rapidly expanding and evolving scientific databases.

    PubMed

    Bauersachs, S; Blum, H; Krebs, S; Fröhlich, T; Arnold, G J; Wolf, E

    2010-01-01

    Declining fertility is a major problem for the dairy industry. Recent developments of Omics-technologies facilitate a comprehensive analysis of molecular patters in gametes, embryos and tissues of the reproductive tract which may help to identify the reasons for impaired fertility. Large Omics-datasets require appropriate bioinformatics analysis in the context of rapidly expanding and evolving scientific databases. This overview summarizes the current status of ruminant genome projects, describes currently existing resources for ruminant genomics, transcriptomics and proteomics as well as databases and tools for the interpretation and exploitation of transcriptomics and proteomics datasets. Gene set enrichment analysis (GSEA) and transcription factor binding site (TFBS) analyses are strategies for the identification of regulatory genes. In general, the comprehensive analysis of molecular traits by Omics-technologies can enhance the interpretation of genome-wide association studies, providing insights into the biological pathways linking genotype and phenotype, and their modulation by endogenous and environmental factors.

  20. Broadly neutralizing antibodies against the rapidly evolving porcine reproductive and respiratory syndrome virus.

    PubMed

    Robinson, Sally R; Li, Juan; Nelson, Eric A; Murtaugh, Michael P

    2015-05-04

    Neutralizing antibodies are a critical part of the immune armory for defense against viruses, and the mechanism by which many effective vaccines work to protect against viral infections. However, infections by rapidly evolving and genetically diverse viruses are often characterized by ineffective neutralizing antibody responses. Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly genetically diverse RNA virus that causes PRRS, the most significant disease of pigs worldwide. The prevailing view of immunity to PRRSV is characterized by delayed and ineffectual production of neutralizing antibodies lacking cross-reactivity that is necessary for vaccine efficacy. Using an ELISA-based neutralizing assay developed to analyze PRRSV growth in porcine alveolar macrophages, the naturally permissive cell of PRRSV, we showed that sera from previously infected commercial sows had high levels of neutralizing activity against diverse PRRSV strains, including across distinct genotypes of PRRSV. Fifty percent cross-neutralization titers in excess of 1/1024 were observed. Neutralizing activity was dose-dependent and was maintained in the immunoglobulin fraction. Presence of high-titer, anti-PRRSV antibody activity that cross-neutralizes diverse strains of virus has prompted reevaluation of the role of neutralizing antibodies for cross-protection against PRRSV under field conditions. Understanding conditions that favor development of cross-neutralizing activity will be crucial for improved strategies to enhance cross-protection against PRRSV. More detailed studies are expected to elucidate mechanisms of neutralizing antibody production and maturation and to investigate conserved epitope targets of cross-neutralization in this rapidly evolving virus.

  1. Cancer immunotherapy: Opportunities and challenges in the rapidly evolving clinical landscape.

    PubMed

    Emens, Leisha A; Ascierto, Paolo A; Darcy, Phillip K; Demaria, Sandra; Eggermont, Alexander M M; Redmond, William L; Seliger, Barbara; Marincola, Francesco M

    2017-08-01

    Cancer immunotherapy is now established as a powerful way to treat cancer. The recent clinical success of immune checkpoint blockade (antagonists of CTLA-4, PD-1 and PD-L1) highlights both the universal power of treating the immune system across tumour types and the unique features of cancer immunotherapy. Immune-related adverse events, atypical clinical response patterns, durable responses, and clear overall survival benefit distinguish cancer immunotherapy from cytotoxic cancer therapy. Combination immunotherapies that transform non-responders to responders are under rapid development. Current challenges facing the field include incorporating immunotherapy into adjuvant and neoadjuvant cancer therapy, refining dose, schedule and duration of treatment and developing novel surrogate endpoints that accurately capture overall survival benefit early in treatment. As the field rapidly evolves, we must prioritise the development of biomarkers to guide the use of immunotherapies in the most appropriate patients. Immunotherapy is already transforming cancer from a death sentence to a chronic disease for some patients. By making smart, evidence-based decisions in developing next generation immunotherapies, cancer should become an imminently treatable, curable and even preventable disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. SN 2015U: a rapidly evolving and luminous Type Ibn supernova

    NASA Astrophysics Data System (ADS)

    Shivvers, Isaac; Zheng, Wei Kang; Mauerhan, Jon; Kleiser, Io K. W.; Van Dyk, Schuyler D.; Silverman, Jeffrey M.; Graham, Melissa L.; Kelly, Patrick L.; Filippenko, Alexei V.; Kumar, Sahana

    2016-09-01

    Supernova (SN) 2015U (also known as PSN J07285387+3349106) was discovered in NGC 2388 on 2015 Feb. 11. A rapidly evolving and luminous event, it showed effectively hydrogen-free spectra dominated by relatively narrow helium P-Cygni spectral features and it was classified as an SN Ibn. In this paper, we present photometric, spectroscopic, and spectropolarimetric observations of SN 2015U, including a Keck/DEIMOS spectrum (resolution ≈5000) which fully resolves the optical emission and absorption features. We find that SN 2015U is best understood via models of shock breakout from extended and dense circumstellar material (CSM), likely created by a history of mass-loss from the progenitor with an extreme outburst within ˜1-2 yr of core collapse (but we do not detect any outburst in our archival imaging of NGC 2388). We argue that the high luminosity of SN 2015U was powered not through 56Ni decay but via the deposition of kinetic energy into the ejecta/CSM shock interface. Though our analysis is hampered by strong host-galaxy dust obscuration (which likely exhibits multiple components), our data set makes SN 2015U one of the best-studied Type Ibn SNe and provides a bridge of understanding to other rapidly fading transients, both luminous and relatively faint.

  3. Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization.

    PubMed

    Kocot, Kevin M; Aguilera, Felipe; McDougall, Carmel; Jackson, Daniel J; Degnan, Bernard M

    2016-01-01

    An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes

  4. Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster.

    PubMed

    Burke, Molly K; Barter, Thomas T; Cabral, Larry G; Kezos, James N; Phillips, Mark A; Rutledge, Grant A; Phung, Kevin H; Chen, Richard H; Nguyen, Huy D; Mueller, Laurence D; Rose, Michael R

    2016-09-01

    Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  5. Rapidly evolving faint transients from stripped-envelope electron-capture supernovae

    NASA Astrophysics Data System (ADS)

    Moriya, Takashi J.; Eldridge, J. J.

    2016-09-01

    We investigate the expected rates and bolometric light-curve properties of stripped-envelope electron-capture supernovae (ECSNe) using stellar models from the Binary Population and Spectral Synthesis code. We find that 0.8 per cent (Z = 0.020) and 1.2 per cent (Z = 0.004) of core-collapse supernovae are stripped-envelope ECSNe. Their typical ejecta masses are estimated to be about 0.3 M⊙(Z = 0.020) and 0.6 M⊙ (Z = 0.004). Assuming ECSN explosion properties from numerical explosion simulations, an explosion energy of 1.5 × 1050 erg and a 56Ni mass of 2.5 × 10-3 M⊙, we find that stripped-envelope ECSNe have a typical rise time of around 7 d (Z = 0.020) or 13 d (Z = 0.004) and peak luminosity of around 1041 ergs-1 (-13.8 mag, Z = 0.020) or 7 × 1040 erg s-1 (-13.4 mag, Z = 0.004). Their typical ejecta velocities are around 7000 km s-1 (Z = 0.020) or 5000 km s-1 (Z = 0.004). Thus, stripped-envelope ECSNe are observed as rapidly evolving faint transients with relatively small velocities. SN 2008ha-like supernovae, which are the faintest kind of SN 2002cx-like (also known as Type Iax) supernovae, may be related to stripped-envelope ECSNe.

  6. Large, rapidly evolving gene families are at the forefront of host-parasite interactions in Apicomplexa.

    PubMed

    Reid, Adam J

    2015-02-01

    The Apicomplexa is a phylum of parasitic protozoa, which includes the malaria parasite Plasmodium, amongst other species that can devastate human and animal health. The past decade has seen the release of genome sequences for many of the most important apicomplexan species, providing an excellent basis for improving our understanding of their biology. One of the key features of each genome is a unique set of large, variant gene families. Although closely related species share the same families, even different types of malaria parasite have distinct families. In some species they tend to be found at the ends of chromosomes, which may facilitate aspects of gene expression regulation and generation of sequence diversity. In others they are scattered apparently randomly across chromosomes. For some families there is evidence they are involved in antigenic variation, immune regulation and immune evasion. For others there are no known functions. Even where function is unknown these families are most often predicted to be exposed to the host, contain much sequence diversity and evolve rapidly. Based on these properties it is clear that they are at the forefront of host-parasite interactions. In this review I compare and contrast the genomic context, gene structure, gene expression, protein localization and function of these families across different species.

  7. From Rapid to Delayed and Remote Postconditioning: the Evolving Concept of Ischemic Postconditioning in Brain Ischemia

    PubMed Central

    Zhao, Heng; Ren, Chuancheng; Chen, Xingmiao; Shen, Jiangang

    2012-01-01

    Ischemic postconditioning is a concept originally defined to contrast with that of ischemic preconditioning. While both preconditioning and postconditioning confer a neuroprotective effect on brain ischemia, preconditioning is a sublethal insult performed in advance of brain ischemia, and postconditioning, which conventionally refers to a series of brief occlusions and reperfusions of the blood vessels, is conducted after ischemia/reperfusion. In this article, we first briefly review the history of preconditioning, including the experimentation that initially uncovered its neuroprotective effects and later revealed its underlying mechanisms-of-action. We then discuss how preconditioning research evolved into that of postconditioning – a concept that now represents a broad range of stimuli or triggers, including delayed postconditioning, pharmacological postconditioning, remote postconditioning – and its underlying protective mechanisms involving the Akt, MAPK, PKC and KATP channel cell-signaling pathways. Because the concept of postconditioning is so closely associated with that of preconditioning, and both share some common protective mechanisms, we also discuss whether a combination of preconditioning and postconditioning offers greater protection than preconditioning or postconditioning alone. PMID:22204317

  8. Evaluating evolutionary constraint on the rapidly evolving gene matK using protein composition.

    PubMed

    Barthet, Michelle M; Hilu, Khidir W

    2008-02-01

    The rapidly evolving chloroplast matK gene has nucleotide and amino acid substitution rates suggestive of progression toward a pseudogene state. However, molecular evidence has demonstrated that matK is expressed and functional. We explore in this paper the underlying factors behind the mode and tempo of matK evolution that allow this protein coding gene to accommodate such elevated rates of substitution and yet maintain functionality. Conservative amino acid replacement may reconcile the fast evolutionary rate in matK with conservation in protein function. Based on this premise, we have examined putative amino acid sequences for MATK from across green plants to determine constraint on this protein as indicated by variation in composition of amino acid side chain category. Amino acids in the MATK ORF were divided into six categories based on chemical properties of their side chains: nonpolar, uncharged (pH 7), basic, acidic, aromatic, and "special" (amino acids that specifically affect protein structure, i.e., proline, glycine, and cysteine). The amount of standard deviation (SD) in side chain composition was used as a measure of variation and constraint, where a low SD implied high evolutionary constraint and a high SD implied low constraint. Further, we used secondary structure prediction to evaluate if conservation observed in side chain composition was reflected in stable predicted structure. The results of this study demonstrate evolutionary constraint on MATK, identify three regions of functional importance, show highly conserved secondary structure, and support the putative function of MATK as a group II intron maturase.

  9. The rapidly evolving centromere-specific histone has stringent functional requirements in Arabidopsis thaliana.

    PubMed

    Ravi, Maruthachalam; Kwong, Pak N; Menorca, Ron M G; Valencia, Joel T; Ramahi, Joseph S; Stewart, Jodi L; Tran, Robert K; Sundaresan, Venkatesan; Comai, Luca; Chan, Simon W-L

    2010-10-01

    Centromeres control chromosome inheritance in eukaryotes, yet their DNA structure and primary sequence are hypervariable. Most animals and plants have megabases of tandem repeats at their centromeres, unlike yeast with unique centromere sequences. Centromere function requires the centromere-specific histone CENH3 (CENP-A in human), which replaces histone H3 in centromeric nucleosomes. CENH3 evolves rapidly, particularly in its N-terminal tail domain. A portion of the CENH3 histone-fold domain, the CENP-A targeting domain (CATD), has been previously shown to confer kinetochore localization and centromere function when swapped into human H3. Furthermore, CENP-A in human cells can be functionally replaced by CENH3 from distantly related organisms including Saccharomyces cerevisiae. We have used cenh3-1 (a null mutant in Arabidopsis thaliana) to replace endogenous CENH3 with GFP-tagged variants. A H3.3 tail domain-CENH3 histone-fold domain chimera rescued viability of cenh3-1, but CENH3's lacking a tail domain were nonfunctional. In contrast to human results, H3 containing the A. thaliana CATD cannot complement cenh3-1. GFP-CENH3 from the sister species A. arenosa functionally replaces A. thaliana CENH3. GFP-CENH3 from the close relative Brassica rapa was targeted to centromeres, but did not complement cenh3-1, indicating that kinetochore localization and centromere function can be uncoupled. We conclude that CENH3 function in A. thaliana, an organism with large tandem repeat centromeres, has stringent requirements for functional complementation in mitosis.

  10. Biobanks in the United States: how to identify an undefined and rapidly evolving population.

    PubMed

    Boyer, Gregory J; Whipple, Warren; Cadigan, R Jean; Henderson, Gail E

    2012-12-01

    As part of a larger organizational study, we sought to survey biobanks in the United States. However, we encountered two problems with this population. First, no common definition of biobanks exists. Second, no census is available of these facilities from which to sample in order to implement a survey. In light of these problems, we employed a multifaceted approach using electronic searches of PubMed, RePORTER, and Google. In addition, we systematically searched for biobanks housed within universities that have NIH-designated Clinical and Translational Science Awards (CTSA). We expanded this part of the search by looking for biobanks among all members of the American Association of Medical Colleges (AAMC). Finally, we added banks to our database found previously by other researchers and banks found via correspondence with our colleagues. Our search strategy produced a database of 624 biobanks for which we were able to confirm contact information in order to conduct our online survey. Another 140 biobanks were identified but did not respond to our requests to confirm their existence or contact information. In order to maximize both the uniqueness of banks found and the greatest return on effort for each search, we suggest targeting resources that are already organized. In our work, these included the CTSA, AAMC, and part of the Google searches. We contend that our search provides a model for analysis of new fields of research and/or rapidly evolving industries. Furthermore, our approach demonstrates that with the appropriate tools it is possible to develop a systematic and comprehensive database to investigate undefined populations.

  11. Rapidly evolving conjunctivitis due to Pasteurella multocida, occurring after direct inoculation with animal droplets in an immuno-compromised host.

    PubMed

    Corchia, Anthony; Limelette, Anne; Hubault, Béatrice; Robbins, Ailsa; Quinquenel, Anne; Bani-Sadr, Firouze; N'Guyen, Yohan

    2015-03-08

    The rare descriptions, in the literature, of ocular infections due to Pasteurella multocida include: endophtalmitis, keratitis and corneal ulcers, Parinaud's oculoglandular syndrome, and conjunctivitis. Here, we report a rare case of rapidly evolving conjunctivitis due to Pasteurella multocida, occurring after direct inoculation with animal droplets in an immuno-compromised host. A 69-year-old, Caucasian male was referred to our department with purulent conjunctivitis, occurring five days after chemotherapy for an angioimmunoblastic-T-cell-lymphoma, and thirty-three hours after being struck in his right eye by his sneezing Dachshund dog. Physical examination revealed purulent conjunctivitis of the right eye associated with inflammatory edema of both lids. Direct bacteriological examination of conjunctival secretions showed gram-negative bacilli and regular, grey non-hemolytic colonies appearing the next day on blood agar. The oxidase test was positive for these colonies. An antibiotherapy associating intravenous amoxicillin and amoxicillin/clavulanate was administered. The outcome was favorable in the next three days allowing discharge of the patient with amoxicillin (2 g tid per os). This case report may be of interest for infectious diseases, ophthalmology or oncology specialists, especially nowadays with chemotherapy being administered in day care centres, where unusual home pathogens can be encountered in health related infections. In this case, previous animal contact and conjunctival samples showing Enterobacteriaceae like colonies with positive oxidase test were two important clues which could help clinicians to make the diagnosis of Pasteurella conjunctivitis in every day practice.

  12. Requirements for Efficient Correction of ΔF508 CFTR Revealed by Analyses of Evolved Sequences

    PubMed Central

    Mendoza, Juan L.; Schmidt, André; Li, Qin; Caspa, Emmanuel; Barrett, Tyler; Bridges, Robert J.; Feranchak, Andrew P.; Brautigam, Chad A.; Thomas, Philip J.

    2012-01-01

    SUMMARY Misfolding of ΔF508 CFTR underlies pathology in most CF patients. F508 resides in the first nucleotide binding domain (NBD1) of CFTR near a predicted interface with the fourth intracellular loop (ICL4). Efforts to identify small molecules that restore function by correcting the folding defect have revealed an apparent efficacy ceiling. To understand the mechanistic basis of this obstacle, positions statistically coupled to 508, in evolved sequences, were identified and assessed for their impact on both NBD1 and CFTR folding. The results indicate that both NBD1 folding and interaction with ICL4 are altered by the ΔF508 mutation and that correction of either individual process is only partially effective. By contrast, combination of mutations that counteract both defects restores ΔF508 maturation and function to wild type levels. These results provide a mechanistic rationale for the limited efficacy of extant corrector compounds and suggest approaches for identifying compounds that correct both defective steps. PMID:22265409

  13. BLASTIC PLASMACYTOID DENDRITIC CELL NEOPLASM --A RAPIDLY EVOLVING ENTITY. CASE REPORT.

    PubMed

    Andrese, Elena; Solovăstru, Laura Gheucă; Dimofte, G; Ferariu, D; Porumb, V; Vâţă, D; Iancul, Luminita Smaranda

    2015-01-01

    Blastic plasmacytoid dendritic cell neoplasm (BPDCN), CD4+/CD56+hematodermic neoplasm was formally known as blastic NK-cell lymphoma. It is in fact a form of acute myeloid leukemia notable for highly aggressive behavior with cutaneous, lymph node and bone marrow involvement. This entity is derived from plasmocytoid dendritic cells and has a predilection for extranodal sites, especially the skin. Elderly male patients are the most affected and the prognostic is poor. The first case was reported in 1994 and sice then, single cases and a few small series have been published. This article presents the case of a previously healthy 56-years-old man, who presented himself to a skin eruption consisting in multiple, large dermal ulcerated tumors, located on the trunk and scalp. The lesions were painless and grew in size rapidly. Physical examination was normal except for the skin lesions. Histological examination of a biopsy specimen and immunohistochemical studies (positive for next markers: CD4, CD 45, CD56, CD68, Ki 67) revealed the rare diagnostic-blastic plasmacytoid dendritic cell neoplasm.

  14. Rapid Evolving Environment and Exposure and Their Implication of New Risks in Mountainous Regions after Major Earthquake

    NASA Astrophysics Data System (ADS)

    Yang, Wentao; Wang, Ming; Shi, Peijun

    2014-05-01

    The Ms 8.0 Wenchuan Earthquake occurred in mountainous Sichuan Province triggered widespread coseismic landslides and heavy human casualties in the year 2008. Much attention has been focused on instantaneous hazards of seismicity and coseismic landslides, while few attentions are paid on the effects of the changed mountain environments caused by great earthquakes of this magnitude. Five years following the devastating Ms 8.0 Wenchuan Earthquake, new landslides, debris flow and flash floods are frequently reported and observed in the severely earthquake stricken regions. This indicates that the geological hazards after the major earthquake in a mountainous environment can be a long-term evolving threat. In this work, we combine image interpretation and extensive field reconnaissances to uncover the mechanism of the constant post-quake disasters that repeatedly destroyed rebuilt houses in Wenchuan Region. Based on high resolution image interpretations and field reconnaissance, coseismic landslides in 2008, post-quake landslide in 2011 and rural house footprints in 2002 and 2011 are interpreted manually in Shikan River Watershed of the heavily affected Pingwu County. Spatial analysis reveals that the spatial distributions of coseismic landslides mainly concentrated in steeper and high altitude slopes, while the post quake landslides evolves to gentle and lower slopes. Compared with pre-quake houses, more relocated houses are also concentrated on limited flat regions near riversides. The evolution of landslide debris and changing distribution of rebuilt houses after the Wenchuan Earthquake has shown quite similar moving trends to lower elevations and gentle slopes, and more post-disaster houses were relocated closer to expanded riverbed after the earthquake. Field reconnaissance also confirmed the downward movement of post-quake mass wasting, which fills up riverbed with debris, expanding river width and results in a catastrophic flash flood event in August 2013. Here

  15. What computational chemistry and magnetic resonance reveal concerning the oxygen evolving centre in Photosystem II.

    PubMed

    Terrett, Richard; Petrie, Simon; Stranger, Rob; Pace, Ron J

    2016-09-01

    Density Functional Theory (DFT) computational studies of the Mn4/Ca Oxygen Evolving Complex (OEC) region of Photosystem II in the paramagnetic S2 and S3 states of the water oxdizing catalytic cycle are described. These build upon recent advances in computationally understanding the detailed S1 state OEC geometries, revealed by the recent high resolution Photosystem II crystal structures of Shen et al., at 1.90Å and 1.95Å (Petrie et al., 2015, Angew. Chem. Int. Ed., 54, 7120). The models feature a 'Low Oxidation Paradigm' assumption for the mean Mn oxidation states in the functional enzyme, with the mean oxidation levels being 3.0, 3.25 and 3.5 in S1, S2 and S3, respectively. These calculations are used to infer magnetic exchange interactions within the coupled OEC cluster, particularly in the Electron Paramagnetic Resonance (EPR)-visible S2 and S3 states. Detailed computational estimates of the intrinsic magnitudes and molecular orientations of the (55)Mn hyperfine tensors in the S2 state are presented. These parameters, together with the resultant spin projected hyperfine values are compared with recent appropriate experimental EPR data (Continuous Wave (CW), Electron-Nuclear Double Resonance (ENDOR) and ELDOR (Electron-Electron Double Resonance)-Detected Nuclear Magnetic Resonance (EDNMR)) from the OEC. It is found that an effective Coupled Dimer magnetic organization of the four Mn in the OEC cluster in the S2 and S3 states is able to quantitatively rationalize the observed (55)Mn hyperfine data. This is consistent with structures we propose to represent the likely state of the OEC in the catalytically active form of the enzyme. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. THE FUTURE OF THE SUN: AN EVOLVED SOLAR TWIN REVEALED BY CoRoT

    SciTech Connect

    Do Nascimento, J.-D. Jr.; Da Costa, J. S.; Castro, M.; Takeda, Y.; Melendez, J.

    2013-07-10

    The question of whether the Sun is peculiar within the class of solar-type stars has been the subject of active investigation over the past three decades. Although several solar twins have been found with stellar parameters similar to those of the Sun (albeit in a range of Li abundances and with somewhat different compositions), their rotation periods are unknown, except for 18 Sco, which is younger than the Sun and with a rotation period shorter than solar. It is difficult to obtain rotation periods for stars of solar age from ground-based observations, as a low-activity level implies a shallow rotational modulation of their light curves. CoRoT has provided space-based long time series from which the rotation periods of solar twins as old as the Sun could be estimated. Based on high-signal-to-noise, high-resolution spectroscopic observations gathered at the Subaru Telescope, we show that the star CoRoT ID 102684698 is a somewhat evolved solar twin with a low Li abundance. Its rotation period is 29 {+-} 5 days, compatible with its age (6.7 Gyr) and low lithium content, A{sub Li} {approx}< 0.85 dex. Interestingly, our CoRoT solar twin seems to have enhanced abundances of the refractory elements with respect to the Sun, a typical characteristic of most nearby twins. With a magnitude V {approx_equal} 14.1, ID 102684698 is the first solar twin revealed by CoRoT, the farthest field solar twin so far known, and the only solar twin older than the Sun for which a rotation period has been determined.

  17. Ancient DNA from the extinct South American giant glyptodont Doedicurus sp. (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos.

    PubMed

    Mitchell, Kieren J; Scanferla, Agustin; Soibelzon, Esteban; Bonini, Ricardo; Ochoa, Javier; Cooper, Alan

    2016-07-01

    Glyptodonts were giant (some of them up to ~2400 kg), heavily armoured relatives of living armadillos, which became extinct during the Late Pleistocene/early Holocene alongside much of the South American megafauna. Although glyptodonts were an important component of Cenozoic South American faunas, their early evolution and phylogenetic affinities within the order Cingulata (armoured New World placental mammals) remain controversial. In this study, we used hybridization enrichment and high-throughput sequencing to obtain a partial mitochondrial genome from Doedicurus sp., the largest (1.5 m tall, and 4 m long) and one of the last surviving glyptodonts. Our molecular phylogenetic analyses revealed that glyptodonts fall within the diversity of living armadillos. Reanalysis of morphological data using a molecular 'backbone constraint' revealed several morphological characters that supported a close relationship between glyptodonts and the tiny extant fairy armadillos (Chlamyphorinae). This is surprising as these taxa are among the most derived cingulates: glyptodonts were generally large-bodied and heavily armoured, while the fairy armadillos are tiny (~9-17 cm) and adapted for burrowing. Calibration of our phylogeny with the first appearance of glyptodonts in the Eocene resulted in a more precise timeline for xenarthran evolution. The osteological novelties of glyptodonts and their specialization for grazing appear to have evolved rapidly during the Late Eocene to Early Miocene, coincident with global temperature decreases and a shift from wet closed forest towards drier open woodland and grassland across much of South America. This environmental change may have driven the evolution of glyptodonts, culminating in the bizarre giant forms of the Pleistocene. © 2016 John Wiley & Sons Ltd.

  18. Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity.

    PubMed

    Sperschneider, Jana; Gardiner, Donald M; Thatcher, Louise F; Lyons, Rebecca; Singh, Karam B; Manners, John M; Taylor, Jennifer M

    2015-05-19

    Pathogens and hosts are in an ongoing arms race and genes involved in host-pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host-pathogen interactions for experimental verification.

  19. Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity

    PubMed Central

    Sperschneider, Jana; Gardiner, Donald M.; Thatcher, Louise F.; Lyons, Rebecca; Singh, Karam B.; Manners, John M.; Taylor, Jennifer M.

    2015-01-01

    Pathogens and hosts are in an ongoing arms race and genes involved in host–pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host–pathogen interactions for experimental verification. PMID:25994930

  20. Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage

    PubMed Central

    Trapp, Paul; Miller, Christopher M.; Bazos, Ioannis

    2017-01-01

    Understanding mechanisms of coevolution between nuclear and mitochondrial (mt) genomes is a defining challenge in eukaryotic genetics. The angiosperm genus Silene is a natural system to investigate the causes and consequences of mt mutation rate variation because closely related species have highly divergent rates. In Silene species with fast-evolving mtDNA, nuclear genes that encode mitochondrially targeted proteins (N-mt genes) are also fast-evolving. This correlation could indicate positive selection to compensate for mt mutations, but might also result from a recent relaxation of selection. To differentiate between these interpretations, we used phylogenetic and population-genetic methods to test for positive and relaxed selection in three classes of N-mt genes (oxidative phosphorylation genes, ribosomal genes, and “RRR” genes involved in mtDNA recombination, replication, and repair). In all three classes, we found that species with fast-evolving mtDNA had: 1) elevated dN/dS, 2) an excess of nonsynonymous divergence relative to levels of intraspecific polymorphism, which is a signature of positive selection, and 3) no clear signals of relaxed selection. “Control” genes exhibited comparatively few signs of positive selection. These results suggest that high mt mutation rates can create selection on N-mt genes and that relaxed selection is an unlikely cause of recent accelerations in the evolution of N-mt genes. Because mt-RRR genes were found to be under positive selection, it is unlikely that elevated mt mutation rates in Silene were caused by inactivation of these mt-RRR genes. Therefore, the causes of extreme increases in angiosperm mt mutation rates remain uncertain. PMID:28164243

  1. Sensationalistic journalism and tales of snakebite: are rattlesnakes rapidly evolving more toxic venom?

    PubMed

    Hayes, William K; Mackessy, Stephen P

    2010-03-01

    Recent reports in the lay press have suggested that bites by rattlesnakes in the last several years have been more severe than those in the past. The explanation, often citing physicians, is that rattlesnakes are evolving more toxic venom, perhaps in response to anthropogenic causes. We suggest that other explanations are more parsimonious, including factors dependent on the snake and factors associated with the bite victim's response to envenomation. Although bites could become more severe from an increased proportion of bites from larger or more provoked snakes (ie, more venom injected), the venom itself evolves much too slowly to explain the severe symptoms occasionally seen. Increased snakebite severity could also result from a number of demographic changes in the victim profile, including age and body size, behavior toward the snake (provocation), anatomical site of bite, clothing, and general health including asthma prevalence and sensitivity to foreign antigens. Clinical management of bites also changes perpetually, rendering comparisons of snakebite severity over time tenuous. Clearly, careful study taking into consideration many factors will be essential to document temporal changes in snakebite severity or venom toxicity. Presently, no published evidence for these changes exists. The sensationalistic coverage of these atypical bites and accompanying speculation is highly misleading and can produce many detrimental results, such as inappropriate fear of the outdoors and snakes, and distraction from proven snakebite management needs, including a consistent supply of antivenom, adequate health care, and training. We urge healthcare providers to avoid propagating misinformation about snakes and snakebites. Copyright (c) 2010 Wilderness Medical Society. Published by Elsevier Inc. All rights reserved.

  2. Tau Spread, Apolipoprotein E, Inflammation, and More: Rapidly Evolving Basic Science in Alzheimer Disease.

    PubMed

    Gonzalez, Bianca; Abud, Edsel M; Abud, Abigail M; Poon, Wayne W; Gylys, Karen H

    2017-05-01

    To date, Alzheimer disease drug candidates have produced negative results in human trials, and progress in moving new targets out of the laboratory and into trials has been slow. However, based on 3 decades of previous work, there is reason to hope that amyloid-based and other novel therapies will move at a faster pace toward successful clinical trials. This article highlights selected preclinical research topics that are rapidly advancing in the laboratory. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite

    PubMed Central

    Mikheyev, Alexander S.; Tin, Mandy M. Y.; Arora, Jatin; Seeley, Thomas D.

    2015-01-01

    Understanding genetic changes caused by novel pathogens and parasites can reveal mechanisms of adaptation and genetic robustness. Using whole-genome sequencing of museum and modern specimens, we describe the genomic changes in a wild population of honey bees in North America following the introduction of the ectoparasitic mite, Varroa destructor. Even though colony density in the study population is the same today as in the past, a major loss of haplotypic diversity occurred, indicative of a drastic mitochondrial bottleneck, caused by massive colony mortality. In contrast, nuclear genetic diversity did not change, though hundreds of genes show signs of selection. The genetic diversity within each bee colony, particularly as a consequence of polyandry by queens, may enable preservation of genetic diversity even during population bottlenecks. These findings suggest that genetically diverse honey bee populations can recover from introduced diseases by evolving rapid tolerance, while maintaining much of the standing genetic variation. PMID:26246313

  4. Navigating the Perfect Storm: Research Strategies for Socialecological Systems in a Rapidly Evolving World

    NASA Astrophysics Data System (ADS)

    Dearing, John A.; Bullock, Seth; Costanza, Robert; Dawson, Terry P.; Edwards, Mary E.; Poppy, Guy M.; Smith, Graham M.

    2012-04-01

    The `Perfect Storm' metaphor describes a combination of events that causes a surprising or dramatic impact. It lends an evolutionary perspective to how social-ecological interactions change. Thus, we argue that an improved understanding of how social-ecological systems have evolved up to the present is necessary for the modelling, understanding and anticipation of current and future social-ecological systems. Here we consider the implications of an evolutionary perspective for designing research approaches. One desirable approach is the creation of multi-decadal records produced by integrating palaeoenvironmental, instrument and documentary sources at multiple spatial scales. We also consider the potential for improved analytical and modelling approaches by developing system dynamical, cellular and agent-based models, observing complex behaviour in social-ecological systems against which to test systems dynamical theory, and drawing better lessons from history. Alongside these is the need to find more appropriate ways to communicate complex systems, risk and uncertainty to the public and to policy-makers.

  5. Navigating the perfect storm: research strategies for socialecological systems in a rapidly evolving world.

    PubMed

    Dearing, John A; Bullock, Seth; Costanza, Robert; Dawson, Terry P; Edwards, Mary E; Poppy, Guy M; Smith, Graham M

    2012-04-01

    The 'Perfect Storm' metaphor describes a combination of events that causes a surprising or dramatic impact. It lends an evolutionary perspective to how social-ecological interactions change. Thus, we argue that an improved understanding of how social-ecological systems have evolved up to the present is necessary for the modelling, understanding and anticipation of current and future social-ecological systems. Here we consider the implications of an evolutionary perspective for designing research approaches. One desirable approach is the creation of multi-decadal records produced by integrating palaeoenvironmental, instrument and documentary sources at multiple spatial scales. We also consider the potential for improved analytical and modelling approaches by developing system dynamical, cellular and agent-based models, observing complex behaviour in social-ecological systems against which to test systems dynamical theory, and drawing better lessons from history. Alongside these is the need to find more appropriate ways to communicate complex systems, risk and uncertainty to the public and to policy-makers.

  6. ASASSN-15oi: a rapidly evolving, luminous tidal disruption event at 216 Mpc

    NASA Astrophysics Data System (ADS)

    Holoien, T. W.-S.; Kochanek, C. S.; Prieto, J. L.; Grupe, D.; Chen, Ping; Godoy-Rivera, D.; Stanek, K. Z.; Shappee, B. J.; Dong, Subo; Brown, J. S.; Basu, U.; Beacom, J. F.; Bersier, D.; Brimacombe, J.; Carlson, E. K.; Falco, E.; Johnston, E.; Madore, B. F.; Pojmanski, G.; Seibert, M.

    2016-12-01

    We present ground-based and Swift photometric and spectroscopic observations of the tidal disruption event (TDE) ASASSN-15oi, discovered at the centre of 2MASX J20390918-3045201 (d ≃ 216 Mpc) by the All-Sky Automated Survey for SuperNovae. The source peaked at a bolometric luminosity of L ≃ 1.3 × 1044 erg s-1 and radiated a total energy of E ≃ 6.6 × 1050 erg over the first ˜3.5 months of observations. The early optical/UV emission of the source can be fit by a blackbody with temperature increasing from T ˜ 2 × 104 K to T ˜ 4 × 104 K while the luminosity declines from L ≃ 1.3 × 1044 erg s-1 to L ≃ 2.3 × 1043 erg s-1, requiring the photosphere to be shrinking rapidly. The optical/UV luminosity decline during this period is most consistent with an exponential decline, L∝ e^{-(t-t_0)/τ}, with τ ≃ 46.5 d for t0 ≃ 57241.6 (MJD), while a power-law decline of L ∝ (t - t0)-α with t0 ≃ 57 212.3 and α = 1.62 provides a moderately worse fit. ASASSN-15oi also exhibits roughly constant soft X-ray emission that is significantly weaker than the optical/UV emission. Spectra of the source show broad helium emission lines and strong blue continuum emission in early epochs, although these features fade rapidly and are not present ˜3 months after discovery. The early spectroscopic features and colour evolution of ASASSN-15oi are consistent with a TDE, but the rapid spectral evolution is unique among optically selected TDEs.

  7. Cloning of novel rice blast resistance genes from two rapidly evolving NBS-LRR gene families in rice.

    PubMed

    Guo, Changjiang; Sun, Xiaoguang; Chen, Xiao; Yang, Sihai; Li, Jing; Wang, Long; Zhang, Xiaohui

    2016-01-01

    Most rice blast resistance genes (R-genes) encode proteins with nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. Our previous study has shown that more rice blast R-genes can be cloned in rapidly evolving NBS-LRR gene families. In the present study, two rapidly evolving R-gene families in rice were selected for cloning a subset of genes from their paralogs in three resistant rice lines. A total of eight functional blast R-genes were identified among nine NBS-LRR genes, and some of these showed resistance to three or more blast strains. Evolutionary analysis indicated that high nucleotide diversity of coding regions served as important parameters in the determination of gene resistance. We also observed that amino-acid variants (nonsynonymous mutations, insertions, or deletions) in essential motifs of the NBS domain contribute to the blast resistance capacity of NBS-LRR genes. These results suggested that the NBS regions might also play an important role in resistance specificity determination. On the other hand, different splicing patterns of introns were commonly observed in R-genes. The results of the present study contribute to improving the effectiveness of R-gene identification by using evolutionary analysis method and acquisition of novel blast resistance genes.

  8. Evolving Rapid Methicillin-resistant Staphylococcus aureus Detection: Cover All the Bases

    PubMed Central

    Bakthavatchalam, Yamuna Devi; Nabarro, Laura E B; Veeraraghavan, Balaji

    2017-01-01

    The dissemination of methicillin-resistant (MR) Staphylococcus aureus (SA) in community and health-care settings is of great concern and associated with high mortality and morbidity. Rapid detection of MRSA with short turnaround time can minimize the time to initiate appropriate therapy and further promote infection control. Early detection of MRSA directly from clinical samples is complicated by the frequent association of MRSA with methicillin-susceptible SA (MSSA) and coagulase-negative Staphylococcus (CoNS) species. Infection associated with true MRSA or MSSA is differentiated from CoNS, requires target specific primers for the presence of SA and mec A or nuc or fem A gene for confirmation of MR. Recently, livestock-associated MRSA carrying mec C variant complicates the epidemiology of MRSA further. Several commercial rapid molecular kits are available with a different combination of these targets for the detection of MRSA or MSSA. The claimed sensitivity and specificity of the currently available commercial kits is varying, because of the different target combination used for detection of SA and MR. PMID:28250621

  9. A resurrection study reveals rapid adaptive evolution within populations of an invasive plant.

    PubMed

    Sultan, Sonia E; Horgan-Kobelski, Tim; Nichols, Lauren M; Riggs, Charlotte E; Waples, Ryan K

    2013-02-01

    The future spread and impact of an introduced species will depend on how it adapts to the abiotic and biotic conditions encountered in its new range, so the potential for rapid evolution subsequent to species introduction is a critical, evolutionary dimension of invasion biology. Using a resurrection approach, we provide a direct test for change over time within populations in a species' introduced range, in the Asian shade annual Polygonum cespitosum. We document, over an 11-year period, the evolution of increased reproductive output as well as greater physiological and root-allocational plasticity in response to the more open, sunny conditions found in the North American range in which the species has become invasive. These findings show that extremely rapid adaptive modifications to ecologically-important traits and plastic expression patterns can evolve subsequent to a species' introduction, within populations established in its introduced range. This study is one of the first to directly document evolutionary change in adaptive plasticity. Such rapid evolutionary changes can facilitate the spread of introduced species into novel habitats and hence contribute to their invasive success in a new range. The data also reveal how evolutionary trajectories can differ among populations in ways that can influence invasion dynamics.

  10. A resurrection study reveals rapid adaptive evolution within populations of an invasive plant

    PubMed Central

    Sultan, Sonia E; Horgan-Kobelski, Tim; Nichols, Lauren M; Riggs, Charlotte E; Waples, Ryan K

    2013-01-01

    The future spread and impact of an introduced species will depend on how it adapts to the abiotic and biotic conditions encountered in its new range, so the potential for rapid evolution subsequent to species introduction is a critical, evolutionary dimension of invasion biology. Using a resurrection approach, we provide a direct test for change over time within populations in a species' introduced range, in the Asian shade annual Polygonum cespitosum. We document, over an 11-year period, the evolution of increased reproductive output as well as greater physiological and root-allocational plasticity in response to the more open, sunny conditions found in the North American range in which the species has become invasive. These findings show that extremely rapid adaptive modifications to ecologically-important traits and plastic expression patterns can evolve subsequent to a species' introduction, within populations established in its introduced range. This study is one of the first to directly document evolutionary change in adaptive plasticity. Such rapid evolutionary changes can facilitate the spread of introduced species into novel habitats and hence contribute to their invasive success in a new range. The data also reveal how evolutionary trajectories can differ among populations in ways that can influence invasion dynamics. PMID:23798976

  11. Proteins involved in motility and sperm-egg interaction evolve more rapidly in mouse spermatozoa.

    PubMed

    Vicens, Alberto; Lüke, Lena; Roldan, Eduardo R S

    2014-01-01

    Proteomic studies of spermatozoa have identified a large catalog of integral sperm proteins. Rapid evolution of these proteins may underlie adaptive changes of sperm traits involved in different events leading to fertilization, although the selective forces underlying such rapid evolution are not well understood. A variety of selective forces may differentially affect several steps ending in fertilization, thus resulting in a compartmentalized adaptation of sperm proteins. Here we analyzed the evolution of genes associated to various events in the sperm's life, from sperm formation to sperm-egg interaction. Evolutionary analyses were performed on gene sequences from 17 mouse strains whose genomes have been sequenced. Four of these are derived from wild Mus musculus, M. domesticus, M. castaneus and M. spretus. We found a higher proportion of genes exhibiting a signature of positive selection among those related to sperm motility and sperm-egg interaction. Furthermore, sperm proteins involved in sperm-egg interaction exhibited accelerated evolution in comparison to those involved in other events. Thus, we identified a large set of candidate proteins for future comparative analyses of genotype-phenotype associations in spermatozoa of species subjected to different sexual selection pressures. Adaptive evolution of proteins involved in motility could be driven by sperm competition, since this selective force is known to increase the proportion of motile sperm and their swimming velocity. On the other hand, sperm proteins involved in gamete interaction could be coevolving with their egg partners through episodes of sexual selection or sexual conflict resulting in species-specific sperm-egg interactions and barriers preventing interspecies fertilization.

  12. The Circumstellar Environment of Evolved Stars as Revealed by Studies of Circumstellar Water Masers

    NASA Astrophysics Data System (ADS)

    Marvel, K.

    1997-11-01

    This dissertation presents the results of a multi-epoch very long baseline interferometric (VLBI) study of water masers located in the extended atmospheres of seven evolved stars. The research was performed using the Very Long Baseline Array and Very Large Array of the National Radio Astronomy Observatory. Water masers are found to exist in the atmospheres of evolved, oxygen-rich stars where a population inversion of the rotational transition at 22 GHz can be maintained by collisional pumping. The masers are identified as individual pockets or filaments of gas, which have good velocity coherence and may be imaged using radio interferometry. Stellar winds are initiated in these sources by dust formation and acceleration of the gas through momentum coupling. The typical wind speeds in the region of the water masers are 10 to 20 \\kms. The water masers in several evolved stars (VY CMa, VX Sgr, S Per, U Her, IK Tau, RX Boo and NML Cyg) have been observed at three epochs and exhibit proper motions consistent with the assumed source distances and the measured outflow velocity in the water maser region. Estimates of the distance to the sources using statistical approximation are in agreement with the currently accepted distances to the stars. The following stars had reliable distances determined using proper motion data: S Per (2.3 +/- 0.5 kpc), VY CMa (1.4 +/- 0.2 kpc), VX Sgr (1.4 +/- 0.3 kpc). An upper limit for the distance of NML Cyg was obtained ( 3.5 kpc). The remaining stars had too few maser detections (RX BOO, IK Tau) or were not strong enough at all epochs (U Her) to self-calibrate using the VLBA. A detailed kinematic model was used to describe the flow motions of the gas in the maser region. The regions are found to be complex and not well modeled by uniform radial outflow, radial outflow with rotation, or radial outflow with acceleration. The reasons for this are explored and include the probable presence of anisotropic velocity fields induced through non

  13. Evolving the stimulus to fit the brain: a genetic algorithm reveals the brain's feature priorities in visual search.

    PubMed

    Van der Burg, Erik; Cass, John; Theeuwes, Jan; Alais, David

    2015-02-06

    How does the brain find objects in cluttered visual environments? For decades researchers have employed the classic visual search paradigm to answer this question using factorial designs. Although such approaches have yielded important information, they represent only a tiny fraction of the possible parametric space. Here we use a novel approach, by using a genetic algorithm (GA) to discover the way the brain solves visual search in complex environments, free from experimenter bias. Participants searched a series of complex displays, and those supporting fastest search were selected to reproduce (survival of the fittest). Their display properties (genes) were crossed and combined to create a new generation of "evolved" displays. Displays evolved quickly over generations towards a stable, efficiently searched array. Color properties evolved first, followed by orientation. The evolved displays also contained spatial patterns suggesting a coarse-to-fine search strategy. We argue that this behavioral performance-driven GA reveals the way the brain selects information during visual search in complex environments. We anticipate that our approach can be adapted to a variety of sensory and cognitive questions that have proven too intractable for factorial designs. © 2015 ARVO.

  14. Comparative transcriptomic analysis reveals phenol tolerance mechanism of evolved Chlorella strain.

    PubMed

    Zhou, Lin; Cheng, Dujia; Wang, Liang; Gao, Juan; Zhao, Quanyu; Wei, Wei; Sun, Yuhan

    2017-03-01

    The growth of microalgae is inhibited by high concentration phenol due to reactive oxygen species. An evolved strain tolerated to 500mg/L phenol, Chlorella sp. L5, was obtained in previous study. In this study, comparative transcriptomic analysis was performed for Chlorella sp. L5 and its original strain (Chlorella sp. L3). The tolerance mechanism of Chlorella sp. L5 for high concentration phenol was explored on genome scale. It was identified that the up-regulations of the related genes according to antioxidant enzymes (SOD, APX, CAT and GR) and carotenoids (astaxanthin, lutein and lycopene) biosynthesis had critical roles to tolerate high concentration phenol. In addition, most of genes of PS I, PS II, photosynthetic electron transport chain and starch biosynthesis were also up-regulated. It was consistent to the experimental results of total carbohydrate contents of Chlorella sp. L3 and Chlorella sp. L5 under 0mg/L and 500mg/L phenol.

  15. Brazilian Begomovirus Populations Are Highly Recombinant, Rapidly Evolving, and Segregated Based on Geographical Location

    PubMed Central

    Rocha, Carolina S.; Castillo-Urquiza, Gloria P.; Lima, Alison T. M.; Silva, Fábio N.; Xavier, Cesar A. D.; Hora-Júnior, Braz T.; Beserra-Júnior, José E. A.; Malta, Antonio W. O.; Martin, Darren P.; Varsani, Arvind; Alfenas-Zerbini, Poliane; Mizubuti, Eduardo S. G.

    2013-01-01

    The incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses. PMID:23487451

  16. Consumer Health Informatics: Past, Present, and Future of a Rapidly Evolving Domain.

    PubMed

    Demiris, G

    2016-05-20

    Consumer Health Informatics (CHI) is a rapidly growing domain within the field of biomedical and health informatics. The objective of this paper is to reflect on the past twenty five years and showcase informatics concepts and applications that led to new models of care and patient empowerment, and to predict future trends and challenges for the next 25 years. We discuss concepts and systems based on a review and analysis of published literature in the consumer health informatics domain in the last 25 years. The field was introduced with the vision that one day patients will be in charge of their own health care using informatics tools and systems. Scientific literature in the field originally focused on ways to assess the quality and validity of available printed health information, only to grow significantly to cover diverse areas such as online communities, social media, and shared decision-making. Concepts such as home telehealth, mHealth, and the quantified-self movement, tools to address transparency of health care organizations, and personal health records and portals provided significant milestones in the field. Consumers are able to actively participate in the decision-making process and to engage in health care processes and decisions. However, challenges such as health literacy and the digital divide have hindered us from maximizing the potential of CHI tools with a significant portion of underserved populations unable to access and utilize them. At the same time, at a global scale consumer tools can increase access to care for underserved populations in developing countries. The field continues to grow and emerging movements such as precision medicine and the sharing economy will introduce new opportunities and challenges.

  17. Gallus gallus NEU3 sialidase as model to study protein evolution mechanism based on rapid evolving loops

    PubMed Central

    2011-01-01

    Background Large surface loops contained within compact protein structures and not involved in catalytic process have been proposed as preferred regions for protein family evolution. These loops are subjected to lower sequence constraints and can evolve rapidly in novel structural variants. A good model to study this hypothesis is represented by sialidase enzymes. Indeed, the structure of sialidases is a β-propeller composed by anti-parallel β-sheets connected by loops that suit well with the rapid evolving loop hypothesis. These features prompted us to extend our studies on this protein family in birds, to get insights on the evolution of this class of glycohydrolases. Results Gallus gallus (Gg) genome contains one NEU3 gene encoding a protein with a unique 188 amino acid sequence mainly constituted by a peptide motif repeated six times in tandem with no homology with any other known protein sequence. The repeat region is located at the same position as the roughly 80 amino acid loop characteristic of mammalian NEU4. Based on molecular modeling, all these sequences represent a connecting loop between the first two highly conserved β-strands of the fifth blade of the sialidase β-propeller. Moreover this loop is highly variable in sequence and size in NEU3 sialidases from other vertebrates. Finally, we found that the general enzymatic properties and subcellular localization of Gg NEU3 are not influenced by the deletion of the repeat sequence. Conclusion In this study we demonstrated that sialidase protein structure contains a surface loop, highly variable both in sequence and size, connecting two conserved β-sheets and emerging on the opposite site of the catalytic crevice. These data confirm that sialidase family can serve as suitable model for the study of the evolutionary process based on rapid evolving loops, which may had occurred in sialidases. Giving the peculiar organization of the loop region identified in Gg NEU3, this protein can be considered of

  18. Single-Molecule Imaging of an in Vitro-Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics

    PubMed Central

    2009-01-01

    Many studies of RNA folding and catalysis have revealed conformational heterogeneity, metastable folding intermediates, and long-lived states with distinct catalytic activities. We have developed a single-molecule imaging approach for investigating the functional heterogeneity of in vitro-evolved RNA aptamers. Monitoring the association of fluorescently labeled ligands with individual RNA aptamer molecules has allowed us to record binding events over the course of multiple days, thus providing sufficient statistics to quantitatively define the kinetic properties at the single-molecule level. The ligand binding kinetics of the highly optimized RNA aptamer studied here displays a remarkable degree of uniformity and lack of memory. Such homogeneous behavior is quite different from the heterogeneity seen in previous single-molecule studies of naturally derived RNA and protein enzymes. The single-molecule methods we describe may be of use in analyzing the distribution of functional molecules in heterogeneous evolving populations or even in unselected samples of random sequences. PMID:19572753

  19. Linking rapid magma reservoir assembly and eruption trigger mechanisms at evolved Yellowstone-type supervolcanoes

    USGS Publications Warehouse

    Wotzlaw, J.F.; Bindeman, I.N.; Watts, Kathryn E.; Schmitt, A.K.; Caricchi, L.; Schaltegger, U.

    2014-01-01

    The geological record contains evidence of volcanic eruptions that were as much as two orders of magnitude larger than the most voluminous eruption experienced by modern civilizations, the A.D. 1815 Tambora (Indonesia) eruption. Perhaps nowhere on Earth are deposits of such supereruptions more prominent than in the Snake River Plain–Yellowstone Plateau (SRP-YP) volcanic province (northwest United States). While magmatic activity at Yellowstone is still ongoing, the Heise volcanic field in eastern Idaho represents the youngest complete caldera cycle in the SRP-YP, and thus is particularly instructive for current and future volcanic activity at Yellowstone. The Heise caldera cycle culminated 4.5 Ma ago in the eruption of the ∼1800 km3 Kilgore Tuff. Accessory zircons in the Kilgore Tuff display significant intercrystalline and intracrystalline oxygen isotopic heterogeneity, and the vast majority are 18O depleted. This suggests that zircons crystallized from isotopically distinct magma batches that were generated by remelting of subcaldera silicic rocks previously altered by low-δ18O meteoric-hydrothermal fluids. Prior to eruption these magma batches were assembled and homogenized into a single voluminous reservoir. U-Pb geochronology of isotopically diverse zircons using chemical abrasion–isotope dilution–thermal ionization mass spectrometry yielded indistinguishable crystallization ages with a weighted mean 206Pb/238U date of 4.4876 ± 0.0023 Ma (MSWD = 1.5; n = 24). These zircon crystallization ages are also indistinguishable from the sanidine 40Ar/39Ar dates, and thus zircons crystallized close to eruption. This requires that shallow crustal melting, assembly of isolated batches into a supervolcanic magma reservoir, homogenization, and eruption occurred extremely rapidly, within the resolution of our geochronology (103–104 yr). The crystal-scale image of the reservoir configuration, with several isolated magma batches, is very similar to the

  20. Sequential data assimilation strategies for utilizing ground deformation data to assess rapidly evolving magma reservoirs

    NASA Astrophysics Data System (ADS)

    Gregg, P. M.; Pettijohn, J. C.; Zhan, Y.

    2015-12-01

    Classic inversion and joint inversion schemes for analyzing ground deformation data are limited in their ability to provide model forecasts and track the temporal dynamics of a volcano experiencing unrest. Sequential data assimilation techniques, such as the Ensemble Kalman Filter (EnKF; Evensen, 1994), estimate the instantaneous state of a dynamic system in a time-forward fashion by updating the model of a system whenever observations become available. The EnKF method uses a Markov Chain Monte Carlo approach to estimate the covariance matrix in the Kalman filter and also tracks model parameters concurrently at a fraction of the computational cost of the Kalman filter (Kalman, 1960) and Extended Kalman Filter (Schmidt, 1966). In this investigation, we build upon Gregg and Pettijohn (2015) to test the performance of the EnKF for assimilating multiple, disparate ground deformation datasets (InSAR, GPS, leveling, and EDM) to provide model forecasts of a volcano exhibiting rapid variations in surface deformation. Specifically, the EnKF is applied to a hypothetical volcano experiencing both inflation and deflation to determine how quickly the EnKF is able to respond to changes in the magma chamber source given a particular set of surface observations. Of interest is how the EnKF responds to limitations imposed by the spatial and temporal resolution of the observations as well as data uncertainties. A series of synthetic tests is run to compare EnKF functionality with individual and multiple dataset assimilation. As the EnKF is model-independent, we test the performance of the EnKF with both time-forward viscoelastic finite element models as well as classic elastic analytical models. References: Evensen, G. (1994), Sequential data assimilation with a nonlinear quasi-geostrophic model using Monte Carlo methods to forecast error statistics, JGR, doi:10.1029/94jc00572. Gregg, P. M., and Pettijohn, J. C. (2015), A multi-data stream assimilation framework for the assessment

  1. An Initial Ultraviolet Investigation of Rapidly Evolving Short Period Eclipsing Binaries

    NASA Astrophysics Data System (ADS)

    Shaw, J. Scott

    A new class of short period, strongly interacting eclipsing binary systems undergoing rapid mass exchange and/or mass loss has been recently identified by one of us (JSS). This group of close binary systems is akin to W UMa-type systems but has somewhat longer orbital periods and components of very dissimilar temperatures. The systems SW Lyn, V1010 Oph, and RT Scl are the best known members of this class of binaries. These Systems appear to be in an early stage of case A binary evolution prior to becoming contact systems in which the more massive hotter (A to F) component is close to or at its Roche limiting surface. Analyses of their asymmetric light curves and period changes indicate substantial mass exchange and/or mass loss. Present groundbased spectra show variable asymmetric line profiles. The photometric studies indicate that the observed asymmetries in the light curves can be explained by the presence of a bright shock region ("hot spot") produced on the receding hemisphere of the cooler component, by the impact of a gas stream from the more massive component. In this initial UV study we propose to observe a small, but representative sample of these stars with the IUE satellite in the wavelength region 1175-3200 using the SWP and LWR cameras. Low dispersion SWP and LWR spectra will be taken during eclipses and at elongations to allow us to identify and map out gas flows and the interacting plasmas using resonance lines of Fe II and Mg II h and k in the near UV and lines such as CIII, CIV, NIV, NV, and SiIII and SiIV in the far UV. High dispersion UV spectra of the brightest member of the class, V1010 Oph, will be obtained for a detailed investigation of the velocities of the expected gas streaming as well as the thermal and mass flow properties of the interacting plasmas. We plan to obtain ground-based spectroscopic and photometric observations of V1010 Oph at or near the time the UV observations are made.

  2. Current and future antimicrobial treatment of gonorrhoea - the rapidly evolving Neisseria gonorrhoeae continues to challenge.

    PubMed

    Unemo, Magnus

    2015-08-21

    , randomized controlled clinical trials evaluating efficacy, ideal dose, toxicity, adverse effects, cost, and pharmacokinetic/pharmacodynamics data for anogenital and, importantly, also pharyngeal gonorrhoea, i.e. because treatment failures initially emerge at this anatomical site. Finally, in the future treatment at first health care visit will ideally be individually-tailored, i.e. by novel rapid phenotypic AMR tests and/or genetic point of care AMR tests, including detection of gonococci, which will improve the management and public health control of gonorrhoea and AMR. Nevertheless, now is certainly the right time to readdress the challenges of developing a gonococcal vaccine.

  3. Proteomic and UTR analyses of a rapidly evolving hypervariable family of vertebrate pheromones.

    PubMed

    Wilburn, Damien B; Bowen, Kathleen E; Gregg, Ronald G; Cai, Jian; Feldhoff, Pamela W; Houck, Lynne D; Feldhoff, Richard C

    2012-07-01

    During the annual mating season, the mental gland of male plethodontid salamanders diverts its protein synthesizing capacity to the production of courtship pheromones that increase female receptivity. Plethodontid modulating factor (PMF), a highly disulfide-bonded 7-kDa pheromone, shows unusual hypervariability with each male expressing >30 isoforms. Twenty-eight PMFs were purified and matched by proteomic analyses to cDNA sequences. In contrast to coding sequence hypervariability, the untranslated regions (UTRs) show extraordinary conservation, no predicted microRNA binding sites, and an overlapping triplet polyadenylation signal. Full-length cDNA sequencing revealed three PMF gene classes containing subclasses of clustered sequences that support ≥ 13 PMF gene duplications. The unusual phenomena of hypervariable coding regions embedded within extremely conserved UTRs is proposed to occur by a disjunctive evolutionary process. During the short courtship season, the UTRs are hypothesized to subsume and coordinate the transcriptional and translational regulatory mechanisms of the mental gland. PMF, as a secreted protein with limited metabolic feedback in the male, is under minimal mutational restraint and thus has experienced highly accelerated rates of evolution. Consequently, plethodontid salamanders may provide a unique model for furthering our understanding of the selective forces that determine differential rates of gene duplication and evolution in protein families. © 2012 The Author(s).

  4. MODIS-Aqua Reveals Evolving Phytoplankton Community Structure During the Arabian Sea Northeast Monsoon

    NASA Technical Reports Server (NTRS)

    Werdell, P. Jeremy; Roesler, Collin S.; Goes, Joaquim I.

    2016-01-01

    Applying a bio-optical model designed to identify the mixotrophic dinoflagellate Noctiluca miliaris to MODIS-Aqua revealed (1) patterns in its spatial distribution not previously seen (including its appearance in places not previously sampled), and (2) the surprising disassociation of total chlorophyll biomass with the presence of N. miliaris.

  5. The Genomics, Epigenomics, and Transcriptomics of HPV-Associated Oropharyngeal Cancer--Understanding the Basis of a Rapidly Evolving Disease.

    PubMed

    Lechner, M; Fenton, T R

    2016-01-01

    Human papillomavirus (HPV) has been shown to represent a major independent risk factor for head and neck squamous cell cancer, in particular for oropharyngeal carcinoma. This type of cancer is rapidly evolving in the Western world, with rising trends particularly in the young, and represents a distinct epidemiological, clinical, and molecular entity. It is the aim of this review to give a detailed description of genomic, epigenomic, transcriptomic, and posttranscriptional changes that underlie the phenotype of this deadly disease. The review will also link these changes and examine what is known about the interactions between the host genome and viral genome, and investigate changes specific for the viral genome. These data are then integrated into an updated model of HPV-induced head and neck carcinogenesis. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Evolving Notch polyQ tracts reveal possible solenoid interference elements.

    PubMed

    Erives, Albert J

    2017-01-01

    Polyglutamine (polyQ) tracts in regulatory proteins are extremely polymorphic. As functional elements under selection for length, triplet repeats are prone to DNA replication slippage and indel mutations. Many polyQ tracts are also embedded within intrinsically disordered domains, which are less constrained, fast evolving, and difficult to characterize. To identify structural principles underlying polyQ tracts in disordered regulatory domains, here I analyze deep evolution of metazoan Notch polyQ tracts, which can generate alleles causing developmental and neurogenic defects. I show that Notch features polyQ tract turnover that is restricted to a discrete number of conserved "polyQ insertion slots". Notch polyQ insertion slots are: (i) identifiable by an amphipathic "slot leader" motif; (ii) conserved as an intact C-terminal array in a 1-to-1 relationship with the N-terminal solenoid-forming ankyrin repeats (ARs); and (iii) enriched in carboxamide residues (Q/N), whose sidechains feature dual hydrogen bond donor and acceptor atoms. Correspondingly, the terminal loop and β-strand of each AR feature conserved carboxamide residues, which would be susceptible to folding interference by hydrogen bonding with residues outside the ARs. I thus suggest that Notch polyQ insertion slots constitute an array of AR interference elements (ARIEs). Notch ARIEs would dynamically compete with the delicate serial folding induced by adjacent ARs. Huntingtin, which harbors solenoid-forming HEAT repeats, also possesses a similar number of polyQ insertion slots. These results suggest that intrinsically disordered interference arrays featuring carboxamide and polyQ enrichment may constitute coupled proteodynamic modulators of solenoids.

  7. Evolving Notch polyQ tracts reveal possible solenoid interference elements

    PubMed Central

    2017-01-01

    Polyglutamine (polyQ) tracts in regulatory proteins are extremely polymorphic. As functional elements under selection for length, triplet repeats are prone to DNA replication slippage and indel mutations. Many polyQ tracts are also embedded within intrinsically disordered domains, which are less constrained, fast evolving, and difficult to characterize. To identify structural principles underlying polyQ tracts in disordered regulatory domains, here I analyze deep evolution of metazoan Notch polyQ tracts, which can generate alleles causing developmental and neurogenic defects. I show that Notch features polyQ tract turnover that is restricted to a discrete number of conserved “polyQ insertion slots”. Notch polyQ insertion slots are: (i) identifiable by an amphipathic “slot leader” motif; (ii) conserved as an intact C-terminal array in a 1-to-1 relationship with the N-terminal solenoid-forming ankyrin repeats (ARs); and (iii) enriched in carboxamide residues (Q/N), whose sidechains feature dual hydrogen bond donor and acceptor atoms. Correspondingly, the terminal loop and β-strand of each AR feature conserved carboxamide residues, which would be susceptible to folding interference by hydrogen bonding with residues outside the ARs. I thus suggest that Notch polyQ insertion slots constitute an array of AR interference elements (ARIEs). Notch ARIEs would dynamically compete with the delicate serial folding induced by adjacent ARs. Huntingtin, which harbors solenoid-forming HEAT repeats, also possesses a similar number of polyQ insertion slots. These results suggest that intrinsically disordered interference arrays featuring carboxamide and polyQ enrichment may constitute coupled proteodynamic modulators of solenoids. PMID:28319202

  8. Transcriptome analysis reveals molecular profiles associated with evolving steps of monoclonal gammopathies

    PubMed Central

    López-Corral, Lucía; Corchete, Luis Antonio; Sarasquete, María Eugenia; Mateos, María Victoria; García-Sanz, Ramón; Fermiñán, Encarna; Lahuerta, Juan-José; Bladé, Joan; Oriol, Albert; Teruel, Ana Isabel; Martino, María Luz; Hernández, José; Hernández-Rivas, Jesús María; Burguillo, Francisco Javier; San Miguel, Jesús F.; Gutiérrez, Norma C.

    2014-01-01

    A multistep model has been proposed of disease progression starting in monoclonal gammopathy of undetermined significance continuing through multiple myeloma, sometimes with an intermediate entity called smoldering myeloma, and ending in extramedullary disease. To gain further insights into the role of the transcriptome deregulation in the transition from a normal plasma cell to a clonal plasma cell, and from an indolent clonal plasma cell to a malignant plasma cell, we performed gene expression profiling in 20 patients with monoclonal gammopathy of undetermined significance, 33 with high-risk smoldering myeloma and 41 with multiple myeloma. The analysis showed that 126 genes were differentially expressed in monoclonal gammopathy of undetermined significance, smoldering myeloma and multiple myeloma as compared to normal plasma cell. Interestingly, 17 and 9 out of the 126 significant differentially expressed genes were small nucleolar RNA molecules and zinc finger proteins. Several proapoptotic genes (AKT1 and AKT2) were down-regulated and antiapoptotic genes (APAF1 and BCL2L1) were up-regulated in multiple myeloma, both symptomatic and asymptomatic, compared to monoclonal gammopathy of undetermined significance. When we looked for those genes progressively modulated through the evolving stages of monoclonal gammopathies, eight snoRNA showed a progressive increase while APAF1, VCAN and MEGF9 exhibited a progressive downregulation. In conclusion, our data show that although monoclonal gammopathy of undetermined significance, smoldering myeloma and multiple myeloma are not clearly distinguishable groups according to their gene expression profiling, several signaling pathways and genes were significantly deregulated at different steps of the transformation process. PMID:24816239

  9. Large number of replacement polymorphisms in rapidly evolving genes of Drosophila. Implications for genome-wide surveys of DNA polymorphism.

    PubMed Central

    Schmid, K J; Nigro, L; Aquadro, C F; Tautz, D

    1999-01-01

    We present a survey of nucleotide polymorphism of three novel, rapidly evolving genes in populations of Drosophila melanogaster and D. simulans. Levels of silent polymorphism are comparable to other loci, but the number of replacement polymorphisms is higher than that in most other genes surveyed in D. melanogaster and D. simulans. Tests of neutrality fail to reject neutral evolution with one exception. This concerns a gene located in a region of high recombination rate in D. simulans and in a region of low recombination rate in D. melanogaster, due to an inversion. In the latter case it shows a very low number of polymorphisms, presumably due to selective sweeps in the region. Patterns of nucleotide polymorphism suggest that most substitutions are neutral or nearly neutral and that weak (positive and purifying) selection plays a significant role in the evolution of these genes. At all three loci, purifying selection of slightly deleterious replacement mutations appears to be more efficient in D. simulans than in D. melanogaster, presumably due to different effective population sizes. Our analysis suggests that current knowledge about genome-wide patterns of nucleotide polymorphism is far from complete with respect to the types and range of nucleotide substitutions and that further analysis of differences between local populations will be required to understand the forces more completely. We note that rapidly diverging and nearly neutrally evolving genes cannot be expected only in the genome of Drosophila, but are likely to occur in large numbers also in other organisms and that their function and evolution are little understood so far. PMID:10581279

  10. High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains

    PubMed Central

    Woldring, Daniel R.; Holec, Patrick V.; Zhou, Hong; Hackel, Benjamin J.

    2015-01-01

    Discovering new binding function via a combinatorial library in small protein scaffolds requires balance between appropriate mutations to introduce favorable intermolecular interactions while maintaining intramolecular integrity. Sitewise constraints exist in a non-spatial gradient from diverse to conserved in evolved antibody repertoires; yet non-antibody scaffolds generally do not implement this strategy in combinatorial libraries. Despite the fact that biased amino acid distributions, typically elevated in tyrosine, serine, and glycine, have gained wider use in synthetic scaffolds, these distributions are still predominantly applied uniformly to diversified sites. While select sites in fibronectin domains and DARPins have shown benefit from sitewise designs, they have not been deeply evaluated. Inspired by this disparity between diversity distributions in natural libraries and synthetic scaffold libraries, we hypothesized that binders resulting from discovery and evolution would exhibit a non-spatial, sitewise gradient of amino acid diversity. To identify sitewise diversities consistent with efficient evolution in the context of a hydrophilic fibronectin domain, >105 binders to six targets were evolved and sequenced. Evolutionarily favorable amino acid distributions at 25 sites reveal Shannon entropies (range: 0.3–3.9; median: 2.1; standard deviation: 1.1) supporting the diversity gradient hypothesis. Sitewise constraints in evolved sequences are consistent with complementarity, stability, and consensus biases. Implementation of sitewise constrained diversity enables direct selection of nanomolar affinity binders validating an efficient strategy to balance inter- and intra-molecular interaction demands at each site. PMID:26383268

  11. Patient with rapidly evolving neurological disease with neuropathological lesions of Creutzfeldt-Jakob disease, Lewy body dementia, chronic subcortical vascular encephalopathy and meningothelial meningioma.

    PubMed

    Vita, Maria Gabriella; Tiple, Dorina; Bizzarro, Alessandra; Ladogana, Anna; Colaizzo, Elisa; Capellari, Sabina; Rossi, Marcello; Parchi, Piero; Masullo, Carlo; Pocchiari, Maurizio

    2017-04-01

    We report a case of rapidly evolving neurological disease in a patient with neuropathological lesions of Creutzfeldt-Jakob disease (CJD), Lewy body dementia (LBD), chronic subcortical vascular encephalopathy and meningothelial meningioma. The coexistence of severe multiple pathologies in a single patient strengthens the need to perform accurate clinical differential diagnoses in rapidly progressive dementias. © 2016 Japanese Society of Neuropathology.

  12. Artificial Selection on Relative Brain Size in the Guppy Reveals Costs and Benefits of Evolving a Larger Brain

    PubMed Central

    Kotrschal, Alexander; Rogell, Björn; Bundsen, Andreas; Svensson, Beatrice; Zajitschek, Susanne; Brännström, Ioana; Immler, Simone; Maklakov, Alexei A.; Kolm, Niclas

    2013-01-01

    Summary The large variation in brain size that exists in the animal kingdom has been suggested to have evolved through the balance between selective advantages of greater cognitive ability and the prohibitively high energy demands of a larger brain (the “expensive-tissue hypothesis” [1]). Despite over a century of research on the evolution of brain size, empirical support for the trade-off between cognitive ability and energetic costs is based exclusively on correlative evidence [2], and the theory remains controversial [3, 4]. Here we provide experimental evidence for costs and benefits of increased brain size. We used artificial selection for large and small brain size relative to body size in a live-bearing fish, the guppy (Poecilia reticulata), and found that relative brain size evolved rapidly in response to divergent selection in both sexes. Large-brained females outperformed small-brained females in a numerical learning assay designed to test cognitive ability. Moreover, large-brained lines, especially males, developed smaller guts, as predicted by the expensive-tissue hypothesis [1], and produced fewer offspring. We propose that the evolution of brain size is mediated by a functional trade-off between increased cognitive ability and reproductive performance and discuss the implications of these findings for vertebrate brain evolution. PMID:23290552

  13. Evolved Streptavidin Mutants Reveal Key Role of Loop Residue in High-affinity Binding

    SciTech Connect

    M Magalhaes; C Melo Czekster; R Guan; V Malashkevich; S Almo; M Levy

    2011-12-31

    We have performed a detailed analysis of streptavidin variants with altered specificity towards desthiobiotin. In addition to changes in key residues which widen the ligand binding pocket and accommodate the more structurally flexible desthiobiotin, the data revealed the role of a key, non-active site mutation at the base of the flexible loop (S52G) which slows dissociation of this ligand by approximately sevenfold. Our data suggest that this mutation results in the loss of a stabilizing contact which keeps this loop open and accessible in the absence of ligand. When this mutation was introduced into the wild-type protein, destabilization of the opened loop conferred a {approx}10-fold decrease in both the on-rate and off-rate for the ligand biotin-4-fluoroscein. A similar effect was observed when this mutation was added to a monomeric form of this protein. Our results provide key insight into the role of the streptavidin flexible loop in ligand binding and maintaining high affinity interactions.

  14. Dissection of Ire1 Functions Reveals Stress Response Mechanisms Uniquely Evolved in Candida glabrata

    PubMed Central

    Miyazaki, Taiga; Nakayama, Hironobu; Nagayoshi, Yohsuke; Kakeya, Hiroshi; Kohno, Shigeru

    2013-01-01

    Proper protein folding in the endoplasmic reticulum (ER) is vital in all eukaryotes. When misfolded proteins accumulate in the ER lumen, the transmembrane kinase/endoribonuclease Ire1 initiates splicing of HAC1 mRNA to generate the bZIP transcription factor Hac1, which subsequently activates its target genes to increase the protein-folding capacity of the ER. This cellular machinery, called the unfolded protein response (UPR), is believed to be an evolutionarily conserved mechanism in eukaryotes. In this study, we comprehensively characterized mutant phenotypes of IRE1 and other related genes in the human fungal pathogen Candida glabrata. Unexpectedly, Ire1 was required for the ER stress response independently of Hac1 in this fungus. C. glabrata Ire1 did not cleave mRNAs encoding Hac1 and other bZIP transcription factors identified in the C. glabrata genome. Microarray analysis revealed that the transcriptional response to ER stress is not mediated by Ire1, but instead is dependent largely on calcineurin signaling and partially on the Slt2 MAPK pathway. The loss of Ire1 alone did not confer increased antifungal susceptibility in C. glabrata contrary to UPR-defective mutants in other fungi. Taken together, our results suggest that the canonical Ire1-Hac1 UPR is not conserved in C. glabrata. It is known in metazoans that active Ire1 nonspecifically cleaves and degrades a subset of ER-localized mRNAs to reduce the ER load. Intriguingly, this cellular response could occur in an Ire1 nuclease-dependent fashion in C. glabrata. We also uncovered the attenuated virulence of the C. glabrata Δire1 mutant in a mouse model of disseminated candidiasis. This study has unveiled the unique evolution of ER stress response mechanisms in C. glabrata. PMID:23382685

  15. Phylogeny of ultra-rapidly evolving dinoflagellate chloroplast genes: a possible common origin for sporozoan and dinoflagellate plastids.

    PubMed

    Zhang, Z; Green, B R; Cavalier-Smith, T

    2000-07-01

    Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all. Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora) have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.

  16. Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs.

    PubMed

    Aagaard, Jan E; Yi, Xianhua; MacCoss, Michael J; Swanson, Willie J

    2006-11-14

    Proteins harboring a zona pellucida (ZP) domain are prominent components of vertebrate egg coats. Although less well characterized, the egg coat of the non-vertebrate marine gastropod abalone (Haliotis spp.) is also known to contain a ZP domain protein, raising the possibility of a common molecular basis of metazoan egg coat structures. Egg coat proteins from vertebrate as well as non-vertebrate taxa have been shown to evolve under positive selection. Studied most extensively in the abalone system, coevolution between adaptively diverging egg coat and sperm proteins may contribute to the rapid development of reproductive isolation. Thus, identifying the pattern of evolution among egg coat proteins is important in understanding the role these genes may play in the speciation process. The purpose of the present study is to characterize the constituent proteins of the egg coat [vitelline envelope (VE)] of abalone eggs and to provide preliminary evidence regarding how selection has acted on VE proteins during abalone evolution. A proteomic approach is used to match tandem mass spectra of peptides from purified VE proteins with abalone ovary EST sequences, identifying 9 of 10 ZP domain proteins as components of the VE. Maximum likelihood models of codon evolution suggest positive selection has acted among a subset of amino acids for 6 of these genes. This work provides further evidence of the prominence of ZP proteins as constituents of the egg coat, as well as the prominent role of positive selection in diversification of these reproductive proteins.

  17. Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs

    PubMed Central

    Aagaard, Jan E.; Yi, Xianhua; MacCoss, Michael J.; Swanson, Willie J.

    2006-01-01

    Proteins harboring a zona pellucida (ZP) domain are prominent components of vertebrate egg coats. Although less well characterized, the egg coat of the non-vertebrate marine gastropod abalone (Haliotis spp.) is also known to contain a ZP domain protein, raising the possibility of a common molecular basis of metazoan egg coat structures. Egg coat proteins from vertebrate as well as non-vertebrate taxa have been shown to evolve under positive selection. Studied most extensively in the abalone system, coevolution between adaptively diverging egg coat and sperm proteins may contribute to the rapid development of reproductive isolation. Thus, identifying the pattern of evolution among egg coat proteins is important in understanding the role these genes may play in the speciation process. The purpose of the present study is to characterize the constituent proteins of the egg coat [vitelline envelope (VE)] of abalone eggs and to provide preliminary evidence regarding how selection has acted on VE proteins during abalone evolution. A proteomic approach is used to match tandem mass spectra of peptides from purified VE proteins with abalone ovary EST sequences, identifying 9 of 10 ZP domain proteins as components of the VE. Maximum likelihood models of codon evolution suggest positive selection has acted among a subset of amino acids for 6 of these genes. This work provides further evidence of the prominence of ZP proteins as constituents of the egg coat, as well as the prominent role of positive selection in diversification of these reproductive proteins. PMID:17085584

  18. Semantic elaboration: ERPs reveal rapid transition from novel to known

    PubMed Central

    Bauer, Patricia J.; Jackson, Felicia L.

    2014-01-01

    Like language, semantic memory is productive: It extends itself through self-derivation of new information through logical processes such as analogy, deduction, and induction, for example. Though it is clear these productive processes occur, little is known about the time course over which newly self-derived information becomes incorporated into semantic knowledge. In the present research, we used event-related potentials (ERPs) to examine this dynamic process. Subjects were presented with separate but related facts that when integrated with one another, supported generation of new information (Integration facts). After two 400 ms presentations, P600 responses to Integration facts differed from responses to Novel facts and did not differ from responses to Well-known facts, suggesting that the newly self-derived information had been incorporated into the knowledge base. The finding of rapid transition from newly self-derived to well-known helps explain the richness of semantic memory. By implication, it also may contribute to the absence of episodic information specifying when and where semantic contents were acquired. PMID:25089741

  19. Rapid loss of glacial ice reveals stream community assembly processes

    PubMed Central

    Brown, Lee E; Milner, Alexander M

    2012-01-01

    Glacial retreat creates new habitat which is colonized and developed by plants and animals during the process of primary succession. While there has been much debate about the relative role of deterministic and stochastic processes during terrestrial succession, evidence from freshwater ecosystems remains minimal and a general consensus is lacking. Using a unique 27 years record of community assembly following glacial recession in southeast Alaska, we demonstrate significant change in the trait composition of stream invertebrate communities as catchment glacial cover decreased from ∼70% to zero. Functional diversity increased significantly as glacier cover decreased and taxonomic richness increased. Null modelling approaches led to a key finding that niche filtering processes were dominant when glacial cover was extensive, reflecting water temperature and dispersal constraints. Thereafter the community shifted towards co-occurrence of stochastic and deterministic assembly processes. A further novel discovery was that intrinsic functional redundancy developed throughout the study, particularly because new colonizers possessed similar traits to taxa already present. Rapid glacial retreat is occurring in Arctic and alpine environments worldwide and the assembly processes observed in this study provide new fundamental insights into how glacially influenced stream ecosystems will respond. The findings support tolerance as a key primary successional mechanism in this system, and have broader value for developing our understanding of how biological communities in river ecosystems assemble or restructure in response to environmental change.

  20. Semantic elaboration: ERPs reveal rapid transition from novel to known.

    PubMed

    Bauer, Patricia J; Jackson, Felicia L

    2015-01-01

    Like language, semantic memory is productive: It extends itself through self-derivation of new information through logical processes such as analogy, deduction, and induction, for example. Though it is clear these productive processes occur, little is known about the time course over which newly self-derived information becomes incorporated into semantic knowledge. In the present research, we used event-related potentials to examine this dynamic process. Subjects were presented with separate but related facts that, when integrated with one another, supported generation of new information (Integration facts). After 2 400-ms presentations, P600 responses to Integration facts differed from responses to Novel facts and did not differ from responses to Well-known facts, suggesting that the newly self-derived information had been incorporated into the knowledge base. The finding of rapid transition from newly self-derived to well known helps explain the richness of semantic memory. By implication, it also may contribute to the absence of episodic information specifying when and where semantic contents were acquired.

  1. Transient Creep of a Composite Lower Crust. 2; A Polymineralic Basis for Rapidly Evolving Postseismic Deformation Modes

    NASA Technical Reports Server (NTRS)

    Ivins, Erik R.

    1996-01-01

    Postseismic horizontal strain and displacement following the June 28, 1992, Landers, California, earthquake (M(sub W) 7.3) is broad scale and cannot be explained solely by delayed afterslip located at the rupturing fault trace. Both the observed strain at Pifion Flat Observatory (PFO) and observed Global Positioning System receiver velocities evolve rapidly after the Landers-Big Bear earthquake sequence. The observed exponential decay of these motions, with timescales of 4-34 days, may reflect a soft creep rheology in the lower crust and brittle-ductile transition zone or even within the seismogenic crust itself. Here a simple model of a two-dimensional screw dislocation in a layered Maxwell viscoelastic Earth is employed in conjunction with a composite rheology to demonstrate that the short timescale transient response modes (approx. = 4-34 days) are consistent with the behavior of a biviscous lower crust. The lowest viscosity of this system is derivable from laboratory experimental data on the long-term creep of natural quarztites, and the highest viscosity is consistent with isostasy-related lower crustal flow in a continental extensional tectonic environment. The model predicts significant stress relaxation at the base of the seismogenic crust. Near the base of the seismogenic zone, and about 4 km away from the mainshock, the rate of predicted relaxation is of the order of 0.01 MPa/ d during the first 20 days of postseismic flow. Oblate spheroidal inclusions at 5% concentration levels that are both aligned and fairly flat in shape and that have a viscosity of 3-4 x 10(exp 15) Pa s are consistent with both the amplitude and decay time of horizontal crustal strain observed at PFO after the Landers mainshock. It is speculated that the structures exposed in cross sections and in seismic reflection profiles of the lower crust that have mylonitic associations are, in part, the cause of such rapid postseismic evolution in southeastern California. Unmylonitized quartz

  2. Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F, and rbcL in basal angiosperms.

    PubMed

    Müller, Kai F; Borsch, Thomas; Hilu, Khidir W

    2006-10-01

    The prevailing view in molecular systematics is that relationships among distantly related taxa should be inferred using DNA segments with low rates of evolution. However, recent analyses of sequences from the rapidly evolving matK and trnT-trnF regions yielded well resolved and highly supported trees for early diverging angiosperms. We compare here the phylogenetic structure in matK, trnT-F, and rbcL datasets for the same 42, primarily basal angiosperm taxa. Phylogenetic trees based on matK or trnT-F are far more robust than those based on rbcL. Combined analysis of the rapidly evolving regions provides support for higher-level relationships stronger than that derived from analyses of multi-gene datasets of up to several fold the number of characters analyzed here. In addition to displaying a higher percentage of parsimony-informative characters, the average phylogenetic signal per informative character is significantly higher in the datasets from rapidly evolving DNA than in the more slowly evolving rbcL, as detected using resampling of identical numbers of parsimony-informative characters from the data matrices and subjecting different statistics for overall tree robustness and phylogenetic signal to significance tests. Automated via a set of scripts, the method used here should be easily extendable to comparisons of a broader range of genomic regions for varying taxon samplings. The relative performance of markers correlates not only with a lower mean homoplasy in matK and trnT-trnF compared to rbcL, but in particular correlates negatively with the percentage of sites exhibiting maximum or close to maximum homoplasy. A likelihood ratio test confirms that the rapidly evolving gene matK evolves significantly closer to neutrality, which may be one of the underlying factors for lower levels of overall homoplasy. Our results are in line with evidence from simulation studies suggesting that the deleterious effect of multiple hits in using rapidly evolving DNA at

  3. High resolution spectroscopy of the high latitude rapidly evolving post-AGB star SAO 85766 (= IRAS 18062+2410)

    NASA Astrophysics Data System (ADS)

    Parthasarathy, M.; García-Lario, P.; Sivarani, T.; Manchado, A.; Sanz Fernández de Córdoba, L.

    2000-05-01

    SAO 85766 (b = +20o) is an IRAS source with far-infrared colours similar to planetary nebulae. According to the HDE catalogue, its spectrum in 1940 was that of an A5 star. The UV fluxes and colours derived from data obtained by the TD1 satellite in 1972 also indicate that SAO 85766 was an A-type supergiant at that epoch. However, high resolution spectra of SAO 85766 obtained in 1993 in the wavelength interval 4350Ä to 8820Ä shows that now it is similar to that of an early B type post-AGB supergiant. In addition to the absorptions lines typical of a B1I type star, the spectrum of SAO 85766 is found to show numerous permitted and forbidden emission lines of several elements, typically observed in the spectra of young high density low excitation planetary nebulae. From an analysis of the absorption lines we have estimated Teff=22000+/-500 K, log g=3.0+/-0.5, xi t=15+/-2km s-1 and [M/H]=-0.6. Carbon is found to be strongly underabundant ([C/Fe] = -1.0), similarly to what has been observed in other high galactic latitude hot post-AGB stars. The underabundance of carbon and metals, high galactic latitude, high radial velocity (46 km s-1), the presence of planetary nebula type detached cold circumstellar dust shell and also the presence of low excitation nebular emission lines in the spectrum indicate that SAO 85766 is a low mass star in the post-AGB stage of evolution. The above mentioned characteristics and the variations observed in the spectrum of SAO 85766 suggest that it has rapidly evolved during the past 50 years and it is now in the early stages of the planetary nebula phase. The central star may just have become hot enough to photoionize the circumstellar envelope ejected during the previous AGB phase. >From an analysis of the nebular emission lines we find Te=10000+/- 500K and Ne=2.5 104 cm-3. The nebula also shows an abundance pattern similar to that of the central star. The rapid post-AGB evolution of SAO 85766 appears to be similar to that observed in the

  4. Rapid evolution and gene expression: a rapidly evolving Mendelian trait that silences field crickets has widespread effects on mRNA and protein expression.

    PubMed

    Pascoal, S; Liu, X; Ly, T; Fang, Y; Rockliffe, N; Paterson, S; Shirran, S L; Botting, C H; Bailey, N W

    2016-06-01

    A major advance in modern evolutionary biology is the ability to start linking phenotypic evolution in the wild with genomic changes that underlie that evolution. We capitalized on a rapidly evolving Hawaiian population of crickets (Teleogryllus oceanicus) to test hypotheses about the genomic consequences of a recent Mendelian mutation of large effect which disrupts the development of sound-producing structures on male forewings. The resulting silent phenotype, flatwing, persists because of natural selection imposed by an acoustically orienting parasitoid, but it interferes with mate attraction. We examined gene expression differences in developing wing buds of wild-type and flatwing male crickets using RNA-seq and quantitative proteomics. Most differentially expressed (DE) transcripts were down-regulated in flatwing males (625 up vs. 1716 down), whereas up- and down-regulated proteins were equally represented (30 up and 34 down). Differences between morphs were clearly not restricted to a single pathway, and we recovered annotations associated with a broad array of functions that would not be predicted a priori. Using a candidate gene detection test based on homology, we identified 30% of putative Drosophila wing development genes in the cricket transcriptome, but only 10% were DE. In addition to wing-related annotations, endocrine pathways and several biological processes such as reproduction, immunity and locomotion were DE in the mutant crickets at both biological levels. Our results illuminate the breadth of genetic pathways that are potentially affected in the early stages of adaptation. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  5. Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species

    EPA Science Inventory

    Atlantic killifish (Fundulus heteroclitus) residing in some urban and industrialized estuaries of the US eastern seaboard demonstrate recently evolved and extreme tolerance to toxic aryl hydrocarbon pollutants, characterized as dioxin-like compounds (DLCs). Here we provide an unu...

  6. Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species

    EPA Science Inventory

    Atlantic killifish (Fundulus heteroclitus) residing in some urban and industrialized estuaries of the US eastern seaboard demonstrate recently evolved and extreme tolerance to toxic aryl hydrocarbon pollutants, characterized as dioxin-like compounds (DLCs). Here we provide an unu...

  7. Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus tobamovirus.

    PubMed

    Pagán, Israel; Firth, Cadhla; Holmes, Edward C

    2010-10-01

    Early studies on the evolutionary dynamics of plant RNA viruses suggested that they may evolve more slowly than their animal counterparts, sometimes dramatically so. However, these estimates were often based on an assumption of virus-host codivergence over time-scales of many millions of years that is difficult to verify. An important example are viruses of the genus Tobamovirus, where the assumption of host-virus codivergence over 100 million years has led to rate estimates in the range of ~1 × 10(-8) nucleotide substitutions per site, per year. Such a low evolutionary rate is in apparent contradiction with the ability of some tobamoviruses to quickly overcome inbred genetic resistance. To resolve how rapidly molecular evolution proceeds in the tobomaviruses, we estimated rates of nucleotide substitution, times to common ancestry, and the extent of congruence between virus and host phylogenies. Using Bayesian coalescent methods applied to time-stamped sequences, we estimated mean evolutionary rates at the nucleotide and amino acid levels of between 1 × 10(-5) and 1.3 × 10(-3) substitutions per site, per year, and hence similar to those seen in a broad range of animal and plant RNA viruses. Under these rates, a conservative estimate for the time of origin of the sampled tobamoviruses is within the last 100,000 years, and hence a far more recently than proposed assuming codivergence. This is supported by our cophylogeny analysis which revealed significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect.

  8. Fast and Furious: Analysis of the Luminous and Rapidly-Evolving Type Ic-BL Supernova iPTF16asu

    NASA Astrophysics Data System (ADS)

    Whitesides, Lindsey; Lunnan, Ragnhild; Kasliwal, Mansi M.; Corsi, Alessandra; Cenko, Stephen B.

    2017-01-01

    Wide-field surveys have discovered a growing number of rapidly-evolving supernovae and transients in the luminosity gap between regular core-collapse and super-luminous supernovae. The physical origin of these events is not yet well understood. Here, we present data and analysis of iPTF16asu, a rapidly-evolving Type Ic-BL supernova in this luminosity gap. With a rest-frame rise-time of just 4 days and a peak absolute magnitude of -20.4 mag, iPTF16asu's light curve is somewhat more luminous but otherwise similar to previous events, including SN2011kl which was associated with an ultra-long gamma-ray burst. The spectrum of iPTF16asu near peak shows a featureless, blue continuum, again similar to previous events, and develops into a Ic-BL spectrum on the decline. Combining information from the light curve, spectroscopy, and X-ray and radio upper limits, we compare iPTF16asu to other events in this part of transient phase-space, and also to physical models proposed to explain rapidly-evolving supernovae.

  9. Highly differentiated ZW sex microchromosomes in the Australian Varanus species evolved through rapid amplification of repetitive sequences.

    PubMed

    Matsubara, Kazumi; Sarre, Stephen D; Georges, Arthur; Matsuda, Yoichi; Marshall Graves, Jennifer A; Ezaz, Tariq

    2014-01-01

    Transitions between sex determination systems have occurred in many lineages of squamates and it follows that novel sex chromosomes will also have arisen multiple times. The formation of sex chromosomes may be reinforced by inhibition of recombination and the accumulation of repetitive DNA sequences. The karyotypes of monitor lizards are known to be highly conserved yet the sex chromosomes in this family have not been fully investigated. Here, we compare male and female karyotypes of three Australian monitor lizards, Varanus acanthurus, V. gouldii and V. rosenbergi, from two different clades. V. acanthurus belongs to the acanthurus clade and the other two belong to the gouldii clade. We applied C-banding and comparative genomic hybridization to reveal that these species have ZZ/ZW sex micro-chromosomes in which the W chromosome is highly differentiated from the Z chromosome. In combination with previous reports, all six Varanus species in which sex chromosomes have been identified have ZZ/ZW sex chromosomes, spanning several clades on the varanid phylogeny, making it likely that the ZZ/ZW sex chromosome is ancestral for this family. However, repetitive sequences of these ZW chromosome pairs differed among species. In particular, an (AAT)n microsatellite repeat motif mapped by fluorescence in situ hybridization on part of W chromosome in V. acanthurus only, whereas a (CGG)n motif mapped onto the W chromosomes of V. gouldii and V. rosenbergi. Furthermore, the W chromosome probe for V. acanthurus produced hybridization signals only on the centromeric regions of W chromosomes of the other two species. These results suggest that the W chromosome sequences were not conserved between gouldii and acanthurus clades and that these repetitive sequences have been amplified rapidly and independently on the W chromosome of the two clades after their divergence.

  10. Highly Differentiated ZW Sex Microchromosomes in the Australian Varanus Species Evolved through Rapid Amplification of Repetitive Sequences

    PubMed Central

    Matsubara, Kazumi; Sarre, Stephen D.; Georges, Arthur; Matsuda, Yoichi; Marshall Graves, Jennifer A.; Ezaz, Tariq

    2014-01-01

    Transitions between sex determination systems have occurred in many lineages of squamates and it follows that novel sex chromosomes will also have arisen multiple times. The formation of sex chromosomes may be reinforced by inhibition of recombination and the accumulation of repetitive DNA sequences. The karyotypes of monitor lizards are known to be highly conserved yet the sex chromosomes in this family have not been fully investigated. Here, we compare male and female karyotypes of three Australian monitor lizards, Varanus acanthurus, V. gouldii and V. rosenbergi, from two different clades. V. acanthurus belongs to the acanthurus clade and the other two belong to the gouldii clade. We applied C-banding and comparative genomic hybridization to reveal that these species have ZZ/ZW sex micro-chromosomes in which the W chromosome is highly differentiated from the Z chromosome. In combination with previous reports, all six Varanus species in which sex chromosomes have been identified have ZZ/ZW sex chromosomes, spanning several clades on the varanid phylogeny, making it likely that the ZZ/ZW sex chromosome is ancestral for this family. However, repetitive sequences of these ZW chromosome pairs differed among species. In particular, an (AAT)n microsatellite repeat motif mapped by fluorescence in situ hybridization on part of W chromosome in V. acanthurus only, whereas a (CGG)n motif mapped onto the W chromosomes of V. gouldii and V. rosenbergi. Furthermore, the W chromosome probe for V. acanthurus produced hybridization signals only on the centromeric regions of W chromosomes of the other two species. These results suggest that the W chromosome sequences were not conserved between gouldii and acanthurus clades and that these repetitive sequences have been amplified rapidly and independently on the W chromosome of the two clades after their divergence. PMID:24743344

  11. Can maternally inherited endosymbionts adapt to a novel host? Direct costs of Spiroplasma infection, but not vertical transmission efficiency, evolve rapidly after horizontal transfer into D. melanogaster.

    PubMed

    Nakayama, S; Parratt, S R; Hutchence, K J; Lewis, Z; Price, T A R; Hurst, G D D

    2015-06-01

    Maternally inherited symbionts are common in arthropods and many have important roles in host adaptation. The observation that specific symbiont lineages infect distantly related host species implies new interactions are commonly established by lateral transfer events. However, studies have shown that symbionts often perform poorly in novel hosts. We hypothesized selection on the symbiont may be sufficiently rapid that poor performance in a novel host environment is rapidly ameliorated, permitting symbiont maintenance. Here, we test this prediction for a Spiroplasma strain transinfected into the novel host Drosophila melanogaster. In the generations immediately following transinfection, the symbiont had low transmission efficiency to offspring and imposed severe fitness costs on its host. We observed that effects on host fitness evolved rapidly, being undetectable after 17 generations in the novel host, whereas vertical transmission efficiency was poorly responsive over this period. Our results suggest that long-term symbiosis may more readily be established in cases where symbionts perform poorly in just one aspect of symbiosis.

  12. Comparison of conference abstracts and presentations with full-text articles in the health technology assessments of rapidly evolving technologies.

    PubMed

    Dundar, Y; Dodd, S; Dickson, R; Walley, T; Haycox, A; Williamson, P R

    2006-02-01

    , they would only consider the data in the full publication. Conversely, if data were only available in conference abstract/presentation, all but two groups reported that they would extract and use the data from the abstract/presentation. In total, 63 HTA reports for NICE were identified. In 20 of 63 TARs (32%) explicit statements were made with regards to inclusion and assessment of data from abstracts/presentations. Thirty-eight (60%) identified at least one randomised controlled trial (RCT) available as a conference abstract or presentation. Of these, 26 (68%) included trials available as abstracts/presentations. About 80% (20/26) of the 26 TARs that included RCTs in abstract/presentation form carried out an assessment of the methodological quality of such trials. In 16 TARs full reports of these trials were used for quality assessment where both abstracts/presentations and subsequent full publications were available. Twenty-three of 63 TARs (37%) carried out a quantitative analysis of results. Of these, ten (43%) included trials that were available as abstracts/presentations in the review; however, only 60% (6/10) of these included data from abstracts/presentations in the data analysis of results. Thirteen TARs evaluated rapidly evolving technologies and only three of these identified and included trial data from conference abstracts/presentations and carried out a quantitative analysis where abstract/presentation data were used. These three TARs were used as case studies. In all three case studies the overall quality of reporting in abstracts/presentations was generally poor. In all case studies abstracts and presentations failed to describe the method of randomisation or allocation concealment. Overall, there was no mention of blinding in 66% (25/38) of the abstracts and in 26% (7/27) of the presentations included in case studies, and one presentation (4%) explicitly stated use of intention-to-treat analysis. Results from one case study demonstrated discrepancies

  13. Rapidly evolving genes in pathogens: methods for detecting positive selection and examples among fungi, bacteria, viruses and protists.

    PubMed

    Aguileta, Gabriela; Refrégier, Guislaine; Yockteng, Roxana; Fournier, Elisabeth; Giraud, Tatiana

    2009-07-01

    The ongoing coevolutionary struggle between hosts and pathogens, with hosts evolving to escape pathogen infection and pathogens evolving to escape host defences, can generate an 'arms race', i.e., the occurrence of recurrent selective sweeps that each favours a novel resistance or virulence allele that goes to fixation. Host-pathogen coevolution can alternatively lead to a 'trench warfare', i.e., balancing selection, maintaining certain alleles at loci involved in host-pathogen recognition over long time scales. Recently, technological and methodological progress has enabled detection of footprints of selection directly on genes, which can provide useful insights into the processes of coevolution. This knowledge can also have practical applications, for instance development of vaccines or drugs. Here we review the methods for detecting genes under positive selection using divergence data (i.e., the ratio of nonsynonymous to synonymous substitution rates, d(N)/d(S)). We also review methods for detecting selection using polymorphisms, such as methods based on F(ST) measures, frequency spectrum, linkage disequilibrium and haplotype structure. In the second part, we review examples where targets of selection have been identified in pathogens using these tests. Genes under positive selection in pathogens have mostly been sought among viruses, bacteria and protists, because of their paramount importance for human health. Another focus is on fungal pathogens owing to their agronomic importance. We finally discuss promising directions in pathogen studies, such as detecting selection in non-coding regions.

  14. Rapid emergence and predominance of a broadly recognizing and fast-evolving norovirus GII.17 variant in late 2014

    PubMed Central

    Chan, Martin C. W.; Lee, Nelson; Hung, Tin-Nok; Kwok, Kirsty; Cheung, Kelton; Tin, Edith K. Y.; Lai, Raymond W. M.; Nelson, E. Anthony S.; Leung, Ting F.; Chan, Paul K. S.

    2015-01-01

    Norovirus genogroup II genotype 4 (GII.4) has been the predominant cause of viral gastroenteritis since 1996. Here we show that during the winter of 2014–2015, an emergent variant of a previously rare norovirus GII.17 genotype, Kawasaki 2014, predominated in Hong Kong and outcompeted contemporary GII.4 Sydney 2012 in hospitalized cases. GII.17 cases were significantly older than GII.4 cases. Root-to-tip and Bayesian BEAST analyses estimate GII.17 viral protein 1 (VP1) evolves one order of magnitude faster than GII.4 VP1. Residue substitutions and insertion occur in four of five inferred antigenic epitopes, suggesting immune evasion. Sequential GII.4-GII.17 infections are noted, implicating a lack of cross-protection. Virus bound to saliva of secretor histo-blood groups A, B and O, indicating broad susceptibility. This fast-evolving, broadly recognizing and probably immune-escaped emergent GII.17 variant causes severe gastroenteritis and hospitalization across all age groups, including populations who were previously less vulnerable to GII.4 variants; therefore, the global spread of GII.17 Kawasaki 2014 needs to be monitored. PMID:26625712

  15. Evidence of positive selection and concerted evolution in the rapidly evolving PRDM9 zinc finger domain in goats and sheep.

    PubMed

    Ahlawat, S; Sharma, P; Sharma, R; Arora, R; Verma, N K; Brahma, B; Mishra, P; De, S

    2016-12-01

    Meiotic recombination contributes to augmentation of genetic diversity, exclusion of deleterious alleles and proper segregation of chromatids. PRDM9 has been identified as the gene responsible for specifying the location of recombination hotspots during meiosis and is also the only known vertebrate gene associated with reproductive isolation between species. PRDM9 encodes a protein with a highly variable zinc finger (ZF) domain that varies between as well as within species. In the present study, the ZF domain of PRDM9 on chromosome 1 was characterized for the first time in 15 goat breeds and 25 sheep breeds of India. A remarkable variation in the number and sequence of ZF domains was observed. The number of ZF repeats in the ZF array varied from eight to 12 yielding five homozygous and 10 heterozygous genotypes. The number of different ZF domains was 84 and 52 producing 36 and 26 unique alleles in goats and sheep respectively. The posterior mean of dN/dS or omega values were calculated using the codeml tool of pamlx to identify amino acids that are evolving positively in goats and sheep, as positions -1, +3 and +6 in the ZF domain have been reported to experience strong positive selection across different lineages. Our study identified sites -5, -1, +3, +4 and +6 to be experiencing positive selection. Small ruminant zinc fingers were also found to be evolving under concerted evolution. Our results demonstrate the existence of a vast diversity of PRDM9 in goats and sheep, which is in concert with reports in many metazoans.

  16. Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species.

    PubMed

    Nacci, Diane; Proestou, Dina; Champlin, Denise; Martinson, John; Waits, Eric R

    2016-11-01

    Atlantic killifish (Fundulus heteroclitus) residing in some urban and industrialized estuaries of the US eastern seaboard demonstrate recently evolved and extreme tolerance to toxic aryl hydrocarbon pollutants, characterized as dioxin-like compounds (DLCs). Here, we provide an unusually comprehensive accounting (69%) through quantitative trait locus (QTL) analysis of the genetic basis for DLC tolerance in killifish inhabiting an urban estuary contaminated with PCB congeners, the most toxic of which are DLCs. Consistent with mechanistic knowledge of DLC toxicity in fish and other vertebrates, the aryl hydrocarbon receptor (ahr2) region accounts for 17% of trait variation; however, QTL on independent linkage groups and their interactions have even greater explanatory power (44%). QTL interpreted within the context of recently available Fundulus genomic resources and shared synteny among fish species suggest adaptation via interacting components of a complex stress response network. Some QTL were also enriched in other killifish populations characterized as DLC-tolerant and residing in distant urban estuaries contaminated with unique mixtures of pollutants. Together, our results suggest that DLC tolerance in killifish represents an emerging example of parallel contemporary evolution that has been driven by intense human-mediated selection on natural populations.

  17. Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

    PubMed Central

    Raychoudhury, Rhitoban; Lavrov, Dennis V.; Werren, John H.

    2008-01-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a “Compensation-Draft Feedback”; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus

  18. Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae).

    PubMed

    Oliveira, Deodoro C S G; Raychoudhury, Rhitoban; Lavrov, Dennis V; Werren, John H

    2008-10-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a "Compensation-Draft Feedback"; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus

  19. Volcanic lightning and plume behavior reveal evolving hazards during the April 2015 eruption of Calbuco volcano, Chile

    USGS Publications Warehouse

    Van Eaton, Alexa; Amigo, Álvaro; Bertin, Daniel; Mastin, Larry G.; Giacosa, Raúl E; González, Jerónimo; Valderrama, Oscar; Fontijn, Karen; Behnke, Sonja A

    2016-01-01

    Soon after the onset of an eruption, model forecasts of ash dispersal are used to mitigate the hazards to aircraft, infrastructure and communities downwind. However, it is a significant challenge to constrain the model inputs during an evolving eruption. Here we demonstrate that volcanic lightning may be used in tandem with satellite detection to recognize and quantify changes in eruption style and intensity. Using the eruption of Calbuco volcano in southern Chile on 22-23 April 2015, we investigate rates of umbrella cloud expansion from satellite observations, occurrence of lightning, and mapped characteristics of the fall deposits. Our remote-sensing analysis gives a total erupted volume that is within uncertainty of the mapped volume (0.56 ±0.28 km3 bulk). Observations and volcanic plume modeling further suggest that electrical activity was enhanced both by ice formation in the ash clouds >10 km asl and development of a low-level charge layer from ground-hugging currents.

  20. Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving.

    PubMed

    Sealey, Katie L; Harris, Simon R; Fry, Norman K; Hurst, Laurence D; Gorringe, Andrew R; Parkhill, Julian; Preston, Andrew

    2015-07-15

    A major outbreak of whooping cough, or pertussis, occurred in 2012 in the United Kingdom (UK), with nearly 10 000 laboratory-confirmed cases and 14 infant deaths attributed to pertussis. A worldwide resurgence of pertussis has been linked to switch to the use of acellular pertussis vaccines and the evolution of Bordetella pertussis away from vaccine-mediated immunity. We have conducted genomic analyses of multiple strains from the UK outbreak. We show that the UK outbreak was polyclonal in nature, caused by multiple distinct but closely related strains. Importantly, we demonstrate that acellular vaccine antigen-encoding genes are evolving at higher rates than other surface protein-encoding genes. This was true even prior to the introduction of pertussis vaccines but has become more pronounced since the introduction of the current acellular vaccines. The fast evolution of vaccine antigen-encoding genes has serious consequences for the ability of current vaccines to continue to control pertussis.

  1. Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola).

    PubMed

    Poppe, Stephan; Dorsheimer, Lena; Happel, Petra; Stukenbrock, Eva Holtgrewe

    2015-07-01

    The speciation of pathogens can be driven by divergent host specialization. Specialization to a new host is possible via the acquisition of advantageous mutations fixed by positive selection. Comparative genome analyses of closely related species allows for the identification of such key substitutions via inference of genome-wide signatures of positive selection. We previously used a comparative genomics framework to identify genes that have evolved under positive selection during speciation of the prominent wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola). In this study, we conducted functional analyses of four genes exhibiting strong signatures of positive selection in Z. tritici. We deleted the four genes in Z. tritici and confirm a virulence-related role of three of the four genes ΔZt80707, ΔZt89160 and ΔZt103264. The two mutants ΔZt80707 and ΔZt103264 show a significant reduction in virulence during infection of wheat; the ΔZt89160 mutant causes a hypervirulent phenotype in wheat. Mutant phenotypes of ΔZt80707, ΔZt89160 and ΔZt103264 can be restored by insertion of the wild-type genes. However, the insertion of the Zt80707 and Zt89160 orthologs from Z. pseudotritici and Z. ardabiliae do not restore wild-type levels of virulence, suggesting that positively selected substitutions in Z. tritici may relate to divergent host specialization. Interestingly, the gene Zt80707 encodes also a secretion signal that targets the protein for cell secretion. This secretion signal is however only transcribed in Z. tritici, suggesting that Z. tritici-specific substitutions relate to a new function of the protein in the extracellular space of the wheat-Z. tritici interaction. Together, the results presented here highlight that Zt80707, Zt103264 and Zt89160 represent key genes involved in virulence and host-specific disease development of Z. tritici. Our findings illustrate that evolutionary predictions provide a powerful tool for the

  2. Light-induced nuclear export reveals rapid dynamics of epigenetic modifications

    PubMed Central

    Yumerefendi, Hayretin; Lerner, Andrew Michael; Zimmerman, Seth Parker; Hahn, Klaus; Bear, James E; Strahl, Brian D.; Kuhlman, Brian

    2016-01-01

    We engineered a photoactivatable system for rapidly and reversibly exporting proteins from the nucleus by embedding a nuclear export signal in the LOV2 domain from phototropin 1. Fusing the chromatin modifier Bre1 to the photoswitch, we achieved light-dependent control of histone H2B monoubiquitylation in yeast, revealing fast turnover of the ubiquitin mark. Moreover, this inducible system allowed us to dynamically monitor the status of epigenetic modifications dependent on H2B ubiquitylation. PMID:27089030

  3. Volcanic lightning and plume behavior reveal evolving hazards during the April 2015 eruption of Calbuco Volcano, Chile

    SciTech Connect

    Van Eaton, Alexa R.; Behnke, Sonja Ann; Amigo, Alvaro; Bertin, Daniel; Mastin, Larry G.; Giacosa, Raul E.; Gonzalez, Jeronimo; Valderrama, Oscar; Fontijn, Karen

    2016-04-12

    Soon after the onset of an eruption, model forecasts of ash dispersal are used to mitigate the hazards to aircraft, infrastructure, and communities downwind. However, it is a significant challenge to constrain the model inputs during an evolving eruption. Here we demonstrate that volcanic lightning may be used in tandem with satellite detection to recognize and quantify changes in eruption style and intensity. Using the eruption of Calbuco volcano in southern Chile on 22 and 23 April 2015, we investigate rates of umbrella cloud expansion from satellite observations, occurrence of lightning, and mapped characteristics of the fall deposits. Our remote sensing analysis gives a total erupted volume that is within uncertainty of the mapped volume (0.56 ± 0.28 km3 bulk). Furthermore, observations and volcanic plume modeling further suggest that electrical activity was enhanced both by ice formation in the ash clouds >10 km above sea level and development of a low-level charge layer from ground-hugging currents.

  4. Volcanic lightning and plume behavior reveal evolving hazards during the April 2015 eruption of Calbuco Volcano, Chile

    DOE PAGES

    Van Eaton, Alexa R.; Behnke, Sonja Ann; Amigo, Alvaro; ...

    2016-04-12

    Soon after the onset of an eruption, model forecasts of ash dispersal are used to mitigate the hazards to aircraft, infrastructure, and communities downwind. However, it is a significant challenge to constrain the model inputs during an evolving eruption. Here we demonstrate that volcanic lightning may be used in tandem with satellite detection to recognize and quantify changes in eruption style and intensity. Using the eruption of Calbuco volcano in southern Chile on 22 and 23 April 2015, we investigate rates of umbrella cloud expansion from satellite observations, occurrence of lightning, and mapped characteristics of the fall deposits. Our remotemore » sensing analysis gives a total erupted volume that is within uncertainty of the mapped volume (0.56 ± 0.28 km3 bulk). Furthermore, observations and volcanic plume modeling further suggest that electrical activity was enhanced both by ice formation in the ash clouds >10 km above sea level and development of a low-level charge layer from ground-hugging currents.« less

  5. Hagfish and lancelet fibrillar collagens reveal that type II collagen-based cartilage evolved in stem vertebrates

    PubMed Central

    Zhang, GuangJun; Cohn, Martin J.

    2006-01-01

    The origin of vertebrates was defined by evolution of a skeleton; however, little is known about the developmental mechanisms responsible for this landmark evolutionary innovation. In jawed vertebrates, cartilage matrix consists predominantly of type II collagen (Col2α1), whereas that of jawless fishes has long been thought to be noncollagenous. We recently showed that Col2α1 is present in lamprey cartilage, indicating that type II collagen-based cartilage evolved earlier than previously recognized. Here, we investigate the origin of vertebrate cartilage, and we report that hagfishes, the sister group to lampreys, also have Col2α1-based cartilage, suggesting its presence in the common ancestor of crown-group vertebrates. We go on to show that lancelets, a sister group to vertebrates, possess an ancestral clade A fibrillar collagen (ColA) gene that is expressed in the notochord. Together, these results suggest that duplication and diversification of ColA genes at the chordate–vertebrate transition may underlie the evolutionary origin of vertebrate skeletal tissues. PMID:17077149

  6. Hagfish and lancelet fibrillar collagens reveal that type II collagen-based cartilage evolved in stem vertebrates.

    PubMed

    Zhang, Guangjun; Cohn, Martin J

    2006-11-07

    The origin of vertebrates was defined by evolution of a skeleton; however, little is known about the developmental mechanisms responsible for this landmark evolutionary innovation. In jawed vertebrates, cartilage matrix consists predominantly of type II collagen (Col2alpha1), whereas that of jawless fishes has long been thought to be noncollagenous. We recently showed that Col2alpha1 is present in lamprey cartilage, indicating that type II collagen-based cartilage evolved earlier than previously recognized. Here, we investigate the origin of vertebrate cartilage, and we report that hagfishes, the sister group to lampreys, also have Col2alpha1-based cartilage, suggesting its presence in the common ancestor of crown-group vertebrates. We go on to show that lancelets, a sister group to vertebrates, possess an ancestral clade A fibrillar collagen (ColA) gene that is expressed in the notochord. Together, these results suggest that duplication and diversification of ColA genes at the chordate-vertebrate transition may underlie the evolutionary origin of vertebrate skeletal tissues.

  7. A two-tiered model for simulating the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza.

    PubMed

    Koelle, Katia; Khatri, Priya; Kamradt, Meredith; Kepler, Thomas B

    2010-09-06

    Understanding the epidemiological and evolutionary dynamics of rapidly evolving pathogens is one of the most challenging problems facing disease ecologists today. To date, many mathematical and individual-based models have provided key insights into the factors that may regulate these dynamics. However, in many of these models, abstractions have been made to the simulated sequences that limit an effective interface with empirical data. This is especially the case for rapidly evolving viruses in which de novo mutations result in antigenically novel variants. With this focus, we present a simple two-tiered 'phylodynamic' model whose purpose is to simulate, along with case data, sequence data that will allow for a more quantitative interface with observed sequence data. The model differs from previous approaches in that it separates the simulation of the epidemiological dynamics (tier 1) from the molecular evolution of the virus's dominant antigenic protein (tier 2). This separation of phenotypic dynamics from genetic dynamics results in a modular model that is computationally simpler and allows sequences to be simulated with specifications such as sequence length, nucleotide composition and molecular constraints. To illustrate its use, we apply the model to influenza A (H3N2) dynamics in humans, influenza B dynamics in humans and influenza A (H3N8) dynamics in equine hosts. In all three of these illustrative examples, we show that the model can simulate sequences that are quantitatively similar in pattern to those empirically observed. Future work should focus on statistical estimation of model parameters for these examples as well as the possibility of applying this model, or variants thereof, to other host-virus systems.

  8. A broadly neutralizing anti-influenza antibody reveals ongoing capacity of haemagglutinin-specific memory B cells to evolve

    PubMed Central

    Fu, Ying; Zhang, Zhen; Sheehan, Jared; Avnir, Yuval; Ridenour, Callie; Sachnik, Thomas; Sun, Jiusong; Hossain, M. Jaber; Chen, Li-Mei; Zhu, Quan; Donis, Ruben O.; Marasco, Wayne A.

    2016-01-01

    Understanding the natural evolution and structural changes involved in broadly neutralizing antibody (bnAb) development holds great promise for improving the design of prophylactic influenza vaccines. Here we report an haemagglutinin (HA) stem-directed bnAb, 3I14, isolated from human memory B cells, that utilizes a heavy chain encoded by the IGHV3-30 germline gene. MAb 3I14 binds and neutralizes groups 1 and 2 influenza A viruses and protects mice from lethal challenge. Analysis of VH and VL germline back-mutants reveals binding to H3 and H1 but not H5, which supports the critical role of somatic hypermutation in broadening the bnAb response. Moreover, a single VLD94N mutation improves the affinity of 3I14 to H5 by nearly 10-fold. These data provide evidence that memory B cell evolution can expand the HA subtype specificity. Our results further suggest that establishing an optimized memory B cell pool should be an aim of ‘universal' influenza vaccine strategies. PMID:27619409

  9. TYPE-I X-RAY BURSTS REVEAL A FAST CO-EVOLVING BEHAVIOR OF THE CORONA IN AN X-RAY BINARY

    SciTech Connect

    Chen, Yu-Peng; Zhang, Shu; Zhang, Shuang-Nan; Li, Jian; Wang, Jian-Min E-mail: szhang@ihep.ac.cn

    2012-06-20

    The coronae in X-ray binaries (XRBs) still remain poorly understood, although they have been believed for a long time to play a key role in modeling the characteristic outbursts of XRBs. Type-I X-ray bursts, the thermonuclear flashes happening on the surface of a neutron star (NS), can be used as a probe to the innermost region of an NS XRB, where the corona is believed to be located very close to the NS. We report the discovery of a tiny life cycle of the corona that is promptly co-evolved with the type-I bursts superimposed on the outburst of the NS XRB IGR J17473-2721. This finding may serve as the first evidence of directly seeing the rapid disappearance and formation of a corona in an XRB with a cooling/heating timescale of less than a second, which can strongly constrain the accretion models in XRBs at work.

  10. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.

    PubMed

    Mackelprang, Rachel; Waldrop, Mark P; DeAngelis, Kristen M; David, Maude M; Chavarria, Krystle L; Blazewicz, Steven J; Rubin, Edward M; Jansson, Janet K

    2011-11-06

    Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.

  11. Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins.

    PubMed

    Grosser, Stefanie; Rawlence, Nicolas J; Anderson, Christian N K; Smith, Ian W G; Scofield, R Paul; Waters, Jonathan M

    2016-02-10

    The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional 'cryptic' invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts.

  12. Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins

    PubMed Central

    Rawlence, Nicolas J.; Anderson, Christian N. K.; Smith, Ian W. G.; Scofield, R. Paul; Waters, Jonathan M.

    2016-01-01

    The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional ‘cryptic’ invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts. PMID:26842575

  13. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

    PubMed Central

    2011-01-01

    Background A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. Results An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Conclusions Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic

  14. Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates.

    PubMed

    King, Benedict; Qiao, Tuo; Lee, Michael S Y; Zhu, Min; Long, John A

    2017-07-01

    The phylogeny of early gnathostomes provides an important framework for understanding one of the most significant evolutionary events, the origin and diversification of jawed vertebrates. A series of recent cladistic analyses have suggested that the placoderms, an extinct group of armoured fish, form a paraphyletic group basal to all other jawed vertebrates. We revised and expanded this morphological data set, most notably by sampling autapomorphies in a similar way to parsimony-informative traits, thus ensuring this data (unlike most existing morphological data sets) satisfied an important assumption of Bayesian tip-dated morphological clock approaches. We also found problems with characters supporting placoderm paraphyly, including character correlation and incorrect codings. Analysis of this data set reveals that paraphyly and monophyly of core placoderms (excluding maxillate forms) are essentially equally parsimonious. The two alternative topologies have different root positions for the jawed vertebrates but are otherwise similar. However, analysis using tip-dated clock methods reveals strong support for placoderm monophyly, due to this analysis favoring trees with more balanced rates of evolution. Furthermore, enforcing placoderm paraphyly results in higher levels and unusual patterns of rate heterogeneity among branches, similar to that generated from simulated trees reconstructed with incorrect root positions. These simulations also show that Bayesian tip-dated clock methods outperform parsimony when the outgroup is largely uninformative (e.g., due to inapplicable characters), as might be the case here. The analysis also reveals that gnathostomes underwent a rapid burst of evolution during the Silurian period which declined during the Early Devonian. This rapid evolution during a period with few articulated fossils might partly explain the difficulty in ascertaining the root position of jawed vertebrates. © The Author(s) 2016. Published by Oxford University

  15. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences.

    PubMed

    Chen, Zhuo; Xu, Shixia; Zhou, Kaiya; Yang, Guang

    2011-10-27

    A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future.

  16. A Rapid Colorimetric Method Reveals Fraudulent Substitutions in Sea Urchin Roe Marketed in Sardinia (Italy)

    PubMed Central

    Meloni, Domenico; Spina, Antonio; Satta, Gianluca; Chessa, Vittorio

    2016-01-01

    In recent years, besides the consumption of fresh sea urchin specimens, the demand of minimally-processed roe has grown considerably. This product has made frequent consumption in restaurants possible and frauds are becoming widespread with the partial replacement of sea urchin roe with surrogates that are similar in colour. One of the main factors that determines the quality of the roe is its colour and small differences in colour scale cannot be easily discerned by the consumers. In this study we have applied a rapid colorimetric method for reveal the fraudulent partial substitution of semi-solid sea urchin roe with liquid egg yolk. Objective assessment of whiteness (L*), redness (a*), yellowness (b*), hue (h*), and chroma (C*) was carried out with a digital spectrophotometer using the CIE L*a*b* colour measurement system. The colorimetric method highlighted statistically significant differences among sea urchin roe and liquid egg yolk that could be easily discerned quantitatively. PMID:28231142

  17. A Rapid Colorimetric Method Reveals Fraudulent Substitutions in Sea Urchin Roe Marketed in Sardinia (Italy).

    PubMed

    Meloni, Domenico; Spina, Antonio; Satta, Gianluca; Chessa, Vittorio

    2016-06-25

    In recent years, besides the consumption of fresh sea urchin specimens, the demand of minimally-processed roe has grown considerably. This product has made frequent consumption in restaurants possible and frauds are becoming widespread with the partial replacement of sea urchin roe with surrogates that are similar in colour. One of the main factors that determines the quality of the roe is its colour and small differences in colour scale cannot be easily discerned by the consumers. In this study we have applied a rapid colorimetric method for reveal the fraudulent partial substitution of semi-solid sea urchin roe with liquid egg yolk. Objective assessment of whiteness (L*), redness (a*), yellowness (b*), hue (h*), and chroma (C*) was carried out with a digital spectrophotometer using the CIE L*a*b* colour measurement system. The colorimetric method highlighted statistically significant differences among sea urchin roe and liquid egg yolk that could be easily discerned quantitatively.

  18. Dynamic habitat suitability modelling reveals rapid poleward distribution shift in a mobile apex predator.

    PubMed

    Hill, Nicholas J; Tobin, Andrew J; Reside, April E; Pepperell, Julian G; Bridge, Tom C L

    2016-03-01

    Many taxa are undergoing distribution shifts in response to anthropogenic climate change. However, detecting a climate signal in mobile species is difficult due to their wide-ranging, patchy distributions, often driven by natural climate variability. For example, difficulties associated with assessing pelagic fish distributions have rendered fisheries management ill-equipped to adapt to the challenges posed by climate change, leaving pelagic species and ecosystems vulnerable. Here, we demonstrate the value of citizen science data for modelling the dynamic habitat suitability of a mobile pelagic predator (black marlin, Istiompax indica) within the south-west Pacific Ocean. The extensive spatial and temporal coverage of our occurrence data set (n = 18 717), collected at high resolution (~1.85 km(2) ), enabled identification of suitable habitat at monthly time steps over a 16-year period (1998-2013). We identified considerable monthly, seasonal and interannual variability in the extent and distribution of suitable habitat, predominately driven by chlorophyll a and sea surface height. Interannual variability correlated with El Nino Southern Oscillation (ENSO) events, with suitable habitat extending up to ~300 km further south during La Nina events. Despite the strong influence of ENSO, our model revealed a rapid poleward shift in the geometric mean of black marlin habitat, occurring at 88.2 km decade(-1) . By incorporating multiple environmental factors at monthly time steps, we were able to demonstrate a rapid distribution shift in a mobile pelagic species. Our findings suggest that the rapid velocity of climate change in the south-west Pacific Ocean is likely affecting mobile pelagic species, indicating that they may be more vulnerable to climate change than previously thought. © 2015 John Wiley & Sons Ltd.

  19. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

    USGS Publications Warehouse

    MacKelprang, R.; Waldrop, M.P.; Deangelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

    2011-01-01

    Permafrost contains an estimated 1672????????Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 ??C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost. ?? 2011 Macmillan Publishers Limited. All rights reserved.

  20. Revealing the inner accretion flow around black holes using rapid variability

    NASA Astrophysics Data System (ADS)

    Axelsson, Magnus

    2015-08-01

    The geometry of the inner accretion flow of X-ray binaries is complex, with multiple regions contributing to the observed emission. Frequency-resolved spectroscopy is a powerful tool in breaking this spectral degeneracy. We have extracted the spectra of the strong low-frequency quasi-periodic oscillation (QPO) and its harmonic in GX339-4 and XTE J1550-564. We compare these to the time-averaged spectrum and the spectrum of the rapid (< 0.1s) variability. Our results support the picture where the QPO arises from vertical (Lense-Thirring) precession of an inhomogeneous hot flow, so that it is softer at larger radii closer to the truncated disc, and harder in the innermost parts of the flow where the rapid variability is produced. This coupling between variability and spectra allows us to constrain the soft Comptonization component, breaking the degeneracy plaguing the time-averaged spectrum and revealing the geometry of the accretion flow close to the black hole. We further show how the upcoming launch of ASTRO-H will allow even more specific regions in the accretion flow to be probed.

  1. Rapid Holocene coastal change revealed by high-resolution micropaleontological analysis, Pamlico Sound, North Carolina, USA

    NASA Astrophysics Data System (ADS)

    Grand Pre, Candace; Culver, Stephen J.; Mallinson, David J.; Farrell, Kathleen M.; Corbett, D. Reide; Horton, Benjamin P.; Hillier, Caroline; Riggs, Stanley R.; Snyder, Scott W.; Buzas, Martin A.

    2011-11-01

    Foraminiferal analyses of 404 contiguous samples, supported by diatom, lithologic, geochronologic and seismic data, reveal both rapid and gradual Holocene paleoenvironmental changes in an 8.21-m vibracore taken from southern Pamlico Sound, North Carolina. Data record initial flooding of a latest Pleistocene river drainage and the formation of an estuary 9000 yr ago. Estuarine conditions were punctuated by two intervals of marine influence from approximately 4100 to 3700 and 1150 to 500 cal yr BP. Foraminiferal assemblages in the muddy sand facies that accumulated during these intervals contain many well-preserved benthic foraminiferal species, which occur today in open marine settings as deep as the mid shelf, and significant numbers of well-preserved planktonic foraminifera, some typical of Gulf Stream waters. We postulate that these marine-influenced units resulted from temporary destruction of the southern Outer Banks barrier islands by hurricanes. The second increase in marine influence is coeval with increased rate of sea-level rise and a peak in Atlantic tropical cyclone activity during the Medieval Climate Anomaly. This high-resolution analysis demonstrates the range of environmental variability and the rapidity of coastal change that can result from the interplay of changing climate, sea level and geomorphology in an estuarine setting.

  2. Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes.

    PubMed

    Walker, Olivia S; Elsässer, Simon J; Mahesh, Mohan; Bachman, Martin; Balasubramanian, Shankar; Chin, Jason W

    2016-01-27

    Isocitrate dehydrogenase is mutated at a key active site arginine residue (Arg172 in IDH2) in many cancers, leading to the synthesis of the oncometabolite (R)-2-hydroxyglutarate (2HG). To investigate the early events following acquisition of this mutation in mammalian cells we created a photoactivatable version of IDH2(R172K), in which K172 is replaced with a photocaged lysine (PCK), via genetic code expansion. Illumination of cells expressing this mutant protein led to a rapid increase in the levels of 2HG, with 2HG levels reaching those measured in patient tumor samples, within 8 h. 2HG accumulation is closely followed by a global decrease in 5-hydroxymethylcytosine (5-hmC) in DNA, demonstrating that perturbations in epigenetic DNA base modifications are an early consequence of mutant IDH2 in cells. Our results provide a paradigm for rapidly and synchronously uncloaking diverse oncogenic mutations in live cells to reveal the sequence of events through which they may ultimately cause transformation.

  3. Photoactivation of Mutant Isocitrate Dehydrogenase 2 Reveals Rapid Cancer-Associated Metabolic and Epigenetic Changes

    PubMed Central

    2016-01-01

    Isocitrate dehydrogenase is mutated at a key active site arginine residue (Arg172 in IDH2) in many cancers, leading to the synthesis of the oncometabolite (R)-2-hydroxyglutarate (2HG). To investigate the early events following acquisition of this mutation in mammalian cells we created a photoactivatable version of IDH2(R172K), in which K172 is replaced with a photocaged lysine (PCK), via genetic code expansion. Illumination of cells expressing this mutant protein led to a rapid increase in the levels of 2HG, with 2HG levels reaching those measured in patient tumor samples, within 8 h. 2HG accumulation is closely followed by a global decrease in 5-hydroxymethylcytosine (5-hmC) in DNA, demonstrating that perturbations in epigenetic DNA base modifications are an early consequence of mutant IDH2 in cells. Our results provide a paradigm for rapidly and synchronously uncloaking diverse oncogenic mutations in live cells to reveal the sequence of events through which they may ultimately cause transformation. PMID:26761588

  4. Rapid Holocene coastal change revealed by high-resolution micropaleontological analysis, Pamlico Sound, North Carolina, USA

    USGS Publications Warehouse

    Grand, Pre C.; Culver, S.J.; Mallinson, D.J.; Farrell, K.M.; Corbett, D.R.; Horton, B.P.; Hillier, C.; Riggs, S.R.; Snyder, S.W.; Buzas, M.A.

    2011-01-01

    Foraminiferal analyses of 404 contiguous samples, supported by diatom, lithologic, geochronologic and seismic data, reveal both rapid and gradual Holocene paleoenvironmental changes in an 8.21-m vibracore taken from southern Pamlico Sound, North Carolina. Data record initial flooding of a latest Pleistocene river drainage and the formation of an estuary 9000. yr ago. Estuarine conditions were punctuated by two intervals of marine influence from approximately 4100 to 3700 and 1150 to 500. cal. yr BP. Foraminiferal assemblages in the muddy sand facies that accumulated during these intervals contain many well-preserved benthic foraminiferal species, which occur today in open marine settings as deep as the mid shelf, and significant numbers of well-preserved planktonic foraminifera, some typical of Gulf Stream waters. We postulate that these marine-influenced units resulted from temporary destruction of the southern Outer Banks barrier islands by hurricanes. The second increase in marine influence is coeval with increased rate of sea-level rise and a peak in Atlantic tropical cyclone activity during the Medieval Climate Anomaly. This high-resolution analysis demonstrates the range of environmental variability and the rapidity of coastal change that can result from the interplay of changing climate, sea level and geomorphology in an estuarine setting. ?? 2011 University of Washington.

  5. A discrete event simulation to model the cost-utility of fingolimod and natalizumab in rapidly evolving severe relapsing-remitting multiple sclerosis in the UK.

    PubMed

    Montgomery, Stephen M; Maruszczak, Maciej J; Slater, David; Kusel, Jeanette; Nicholas, Richard; Adlard, Nicholas

    2017-05-01

    Two disease-modifying therapies are licensed in the EU for use in rapidly-evolving severe (RES) relapsing-remitting multiple sclerosis (RRMS), fingolimod and natalizumab. Here a discrete event simulation (DES) model to analyze the cost-effectiveness of natalizumab and fingolimod in the RES population, from the perspective of the National Health Service (NHS) in the UK, is reported. A DES model was developed to track individual RES patients, based on Expanded Disability Status Scale scores. Individual patient characteristics were taken from the RES sub-groups of the pivotal trials for fingolimod. Utility data were in line with previous models. Published costs were inflated to NHS cost year 2015. Owing to the confidential patient access scheme (PAS) discount applied to fingolimod in the UK, a range of discount levels were applied to the fingolimod list price, to capture the likelihood of natalizumab being cost-effective in a real-world setting. At the lower National Institute of Health and Care Excellence (NICE) threshold of £20,000/quality-adjusted life year (QALY), fingolimod only required a discount greater than 0.8% of list price to be cost-effective. At the upper threshold of £30,000/QALY employed by the NICE, fingolimod was cost-effective if the confidential discount is greater than 2.5%. Sensitivity analyses conducted using fingolimod list-price showed the model to be most sensitive to changes in the cost of each drug, particularly fingolimod. The DES model shows that only a modest discount to the UK fingolimod list-price is required to make fingolimod a more cost-effective option than natalizumab in RES RRMS.

  6. Case study of the comparison of data from conference abstracts and full-text articles in health technology assessment of rapidly evolving technologies: does it make a difference?

    PubMed

    Dundar, Yenal; Dodd, Susanna; Williamson, Paula; Dickson, Rumona; Walley, Tom

    2006-01-01

    The aim of this study was to examine (i) the consistency of reporting research findings presented in conference abstracts and presentations and subsequent full publications, (ii) the ability to judge methodological quality of trials from conference abstracts and presentations, and (iii) the effect of inclusion or exclusion of data from these sources on the pooled effect estimates in a meta-analysis. This report is a case study of a selected health technology assessment review (TAR) of a rapidly evolving technology that had identified and included a meta-analysis of trial data from conference abstracts and presentations. The overall quality of reporting in abstracts and presentations was poor, especially in abstracts. There was incomplete or inconsistent reporting of data in the abstract/presentations. Most often inconsistencies were between conference slide presentations and data reported in published full-text articles. Sensitivity analyses indicated that using data only from published papers would not have altered the direction of any of the results when compared with those using published and abstract data. However, the statistical significance of three of ten results would have changed. If conference abstracts and presentations were excluded from the early analysis, the direction of effect and statistical significance would have changed in one result. The overall conclusions of the original analysis would not have been altered. There are inconsistencies in data presented as conference abstracts/presentations and those reported in subsequent published reports. These inconsistencies could impact the final assessment results. Data discrepancies identified across sources included in TARs should be highlighted and their impact assessed and discussed. Sensitivity analyses should be carried out with and without abstract/presentation data included in the analysis. Incomplete reporting in conference abstracts and presentations limits the ability of reviewers to assess

  7. Systematic literature review and network meta-analysis in highly active relapsing–remitting multiple sclerosis and rapidly evolving severe multiple sclerosis

    PubMed Central

    Huisman, Eline; Papadimitropoulou, Katerina; Jarrett, James; Bending, Matthew; Firth, Zoe; Allen, Felicity; Adlard, Nick

    2017-01-01

    Objective Multiple sclerosis (MS) is a chronic, neurodegenerative autoimmune disorder affecting the central nervous system. Relapsing–remitting MS (RRMS) is the most common clinical form of MS and affects ∼85% of cases at onset. Highly active (HA) and rapidly evolving severe (RES) RRMS are 2 forms of RRMS amenable to disease-modifying therapies (DMT). This study explored the efficacy of fingolimod relative to other DMTs for the treatment of HA and RES RRMS. Methods A systematic literature review (SLR) was conducted to identify published randomised controlled trials in HA and RES RRMS. Identified evidence was vetted, and a Bayesian network meta-analysis (NMA) was performed to evaluate the relative efficacy of fingolimod versus dimethyl fumarate (DMF) in HA RRMS and versus natalizumab in RES RRMS. Results For HA RRMS, the SLR identified 2 studies with relevant patient subgroup data: 1 comparing fingolimod with placebo and the other comparing DMF with placebo. 3 studies were found for RES RRMS: 1 comparing fingolimod with placebo and 2 studies comparing natalizumab with placebo. NMA results in the HA population showed a favourable numerical trend of fingolimod versus DMF assessed for annualised relapse rate (ARR) and 3-month confirmed disability progression. For the RES population, the results identified an increase of ARR and 3-month confirmed disability progression for fingolimod versus natalizumab (not statistically significant). Sparse study data and the consequently high uncertainty around the estimates restricted our ability to demonstrate statistical significance in the studied subgroups. Conclusions Data limitations are apparent when conducting an informative indirect comparison for the HA and RES RRMS subgroups as the subgroups analyses were retrospective analyses of studies powered to indicate differences across entire study populations. Comparisons across treatments in HA or RES RRMS will be associated with high levels of uncertainty until new data are

  8. Bactericidal mechanisms revealed for rapid water disinfection by superabsorbent cryogels decorated with silver nanoparticles.

    PubMed

    Loo, Siew-Leng; Krantz, William B; Fane, Anthony G; Gao, Yiben; Lim, Teik-Thye; Hu, Xiao

    2015-02-17

    The authors have recently reported the fabrication of superabsorbent cryogels decorated with silver nanoparticles (PSA/AgNP cryogels) that demonstrate rapid water disinfection. This paper provides a systematic elucidation of the bactericidal mechanisms of AgNPs (silver nanoparticles), both generally and in the specific context of cryogels. Direct contact between the PSA/AgNP cryogel interface and the bacterial cells is required to accomplish disinfection. Specifically, the disinfection efficacy is closely correlated to the cell-bound Ag concentration, which constitutes >90% of the Ag released. Cells exposed to PSA/AgNP cryogels show a significant depletion of intracellular adenosine triphosphate (ATP) content and cell-membrane lesions. A positive ROS (reactive oxygen species) scavenging test confirms the involvement of ROS (·O2(-), H2O2, and ·OH) in the bactericidal mechanism. Furthermore, exposed bacterial cells show an enhanced level of thiobarbituric acid reactive substances, indicating the occurrence of cell-membrane peroxidation mediated by ROS. In addition, this study reveals that both Ag(+) and Ag(0) are involved in the bactericidal mechanism of AgNPs via tests conducted using PSA cryogels with bound Ag(+) ions (or PSA/Ag(+) cryogels without reducing Ag(+) to Ag(0)). Significantly, bacterial cells exposed to PSA/Ag(+) cryogels did not show any cell-membrane damage even though the former had a higher cell-bound Ag concentration than that of the PSA/AgNP cryogels, thus indicating the differential action of Ag(+) and Ag(0).

  9. Rapid ester biosynthesis screening reveals a high activity alcohol-O-acyltransferase (AATase) from tomato fruit.

    PubMed

    Lin, Jyun-Liang; Zhu, Jie; Wheeldon, Ian

    2016-05-01

    Ethyl and acetate esters are naturally produced in various yeasts, plants, and bacteria. The biosynthetic pathways that produce these esters share a common reaction step, the condensation of acetyl/acyl-CoA with an alcohol by alcohol-O-acetyl/acyltransferase (AATase). Recent metabolic engineering efforts exploit AATase activity to produce fatty acid ethyl esters as potential diesel fuel replacements as well as short- and medium-chain volatile esters as fragrance and flavor compounds. These efforts have been limited by the lack of a rapid screen to quantify ester biosynthesis. Enzyme engineering efforts have also been limited by the lack of a high throughput screen for AATase activity. Here, we developed a high throughput assay for AATase activity and used this assay to discover a high activity AATase from tomato fruit, Solanum lycopersicum (Atf-S.l). Atf1-S.l exhibited broad specificity towards acyl-CoAs with chain length from C4 to C10 and was specific towards 1-pentanol. The AATase screen also revealed new acyl-CoA substrate specificities for Atf1, Atf2, Eht1, and Eeb1 from Saccharomyces cerevisiae, and Atf-C.m from melon fruit, Cucumis melo, thus increasing the pool of characterized AATases that can be used in ester biosynthesis of ester-based fragrance and flavor compounds as well as fatty acid ethyl ester biofuels.

  10. Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives

    PubMed Central

    Iwata-Otsubo, Aiko; Radke, Brittany; Findley, Seth; Abernathy, Brian; Vallejos, C. Eduardo; Jackson, Scott A.

    2016-01-01

    Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species. PMID:26865698

  11. An international survey and modified Delphi approach revealed numerous rapid review methods.

    PubMed

    Tricco, Andrea C; Zarin, Wasifa; Antony, Jesmin; Hutton, Brian; Moher, David; Sherifali, Diana; Straus, Sharon E

    2016-02-01

    To solicit experiences with and perceptions of rapid reviews from stakeholders, including researchers, policy makers, industry, journal editors, and health care providers. An international survey of rapid review producers and modified Delphi. Forty rapid review producers responded on our survey (63% response rate). Eighty-eight rapid reviews with 31 different names were reported. Rapid review commissioning organizations were predominantly government (78%) and health care (58%) organizations. Several rapid review approaches were identified, including updating the literature search of previous reviews (92%); limiting the search strategy by date of publication (88%); and having only one reviewer screen (85%), abstract data (84%), and assess the quality of studies (86%). The modified Delphi included input from 113 stakeholders on the rapid review approaches from the survey. Approach 1 (search limited by date and language; study selection by one reviewer only, and data abstraction and quality appraisal conducted by one reviewer and one verifier) was ranked the most feasible (72%, 81/113 responses), with the lowest perceived risk of bias (12%, 12/103); it also ranked second in timeliness (37%, 38/102) and fifth in comprehensiveness (5%, 5/100). Rapid reviews have many names and approaches, and some methods might be more desirable than others. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Emergence and Transmission Pathways of Rapidly Evolving Evolutionary Branch C4a Strains of Human Enterovirus 71 in the Central Plain of China

    PubMed Central

    Wang, Haiyan; Zhu, Shuangli; Wang, Dongyan; Bai, Ruyin; Li, Xingle; Yan, Dongmei; Wang, Huiling; Zhang, Yan; Zhu, Zhen; Tan, Xiaojuan; An, Hongqiu; Xu, Aiqiang; Xu, Wenbo

    2011-01-01

    Background Large-scale outbreaks of hand, foot, and mouth disease (HFMD) occurred repeatedly in the Central Plain of China (Shandong, Anhui, and Henan provinces) from 2007 until now. These epidemics have increased in size and severity each year and are a major public health concern in mainland China. Principal Findings Phylogenetic analysis was performed and a Bayesian Markov chain Monte Carlo tree was constructed based on the complete VP1 sequences of HEV71 isolates. These analyses showed that the HFMD epidemic in the Central Plain of China was caused by at least 5 chains of HEV71 transmission and that the virus continued to circulate and evolve over the winter seasons between outbreaks. Between 1998 and 2010, there were 2 stages of HEV71 circulation in mainland China, with a shift from evolutionary branch C4b to C4a in 2003–2004. The evolution rate of C4a HEV71 was 4.99×10-3 substitutions per site per year, faster than the mean of all HEV71 genotypes. The most recent common ancestor estimates for the Chinese clusters dated to October 1994 and November 1993 for the C4a and C4b evolutionary branches, respectively. Compared with all C4a HEV71 strains, a nucleotide substitution in all C4b HEV71 genome (A to C reversion at nt2503 in the VP1 coding region, which caused amino acid substitution of VP1–10: Gln to His) had reverted. Conclusions The data suggest that C4a HEV71 strains introduced into the Central Plain of China are responsible for the recent outbreaks. The relationships among HEV71 isolates determined from the combined sequence and epidemiological data reveal the underlying seasonal dynamics of HEV71 circulation. At least 5 HEV71 lineages circulated in the Central Plain of China from 2007 to 2009, and the Shandong and Anhui lineages were found to have passed through a genetic bottleneck during the low-transmission winter season. PMID:22125635

  13. Relationships between the sarcoplasmic reticulum and sarcolemmal calcium transport revealed by rapidly cooling rabbit ventricular muscle

    PubMed Central

    1986-01-01

    Rabbit right ventricular papillary muscles were cooled from 30 to approximately 1 degree C immediately after discontinuing electrical stimulation (0.5 Hz). This produced a contracture that was 30-50% of the preceding twitch magnitude and required 20-30 s to develop. The contractures were identical in cooling solutions with normal (144 mM) or low (2.0 mM) Na. They were therefore not Na-withdrawal contractures. Contracture activation was considerably slower than muscle cooling (approximately 2.5 s to cool below 2 degrees C). Cooling contractures were suppressed by caffeine treatment (10.0 mM). Rapid cooling did not cause sufficient membrane depolarization (16.5 +/- 1.2 mV after 30 s of cooling) to produce either a voltage-dependent activation of contracture or a gated entry of Ca from the extracellular space. Contractures induced by treating resting muscles with 5 X 10(-5) M strophanthidin at 30 degrees C exhibited pronounced tension noise. The Fourier spectrum of this noise revealed a periodic component (2-3 Hz) that disappeared when the muscle was cooled. Cooling contractures decayed with rest (t1/2 = 71.0 +/- 9.3 s). This decay accelerated in the presence of 10.0 mM caffeine and was prevented and to some extent reversed when extracellular Na was reduced to 2.0 mM. 20 min of rest resulted in a net decline in intracellular Ca content of 1.29 +/- 0.38 mmol/kg dry wt. I infer that cooling contractures are principally activated by Ca from the sarcoplasmic reticulum (SR). The properties of these contractures suggest that they may provide a convenient relative index of the availability of SR Ca for contraction. The rest decay of cooling contractures (and hence the decay in the availability of activating Ca) is consistent with the measured loss in analytic Ca during rest. The results suggest that contraction in heart muscle can be regulated by an interaction between sarcolemmal and SR Ca transport. PMID:3783123

  14. Electronic structure of the oxygen evolving complex in photosystem II, as revealed by 55Mn Davies ENDOR studies at 2.5 K.

    PubMed

    Jin, Lu; Smith, Paul; Noble, Christopher J; Stranger, Rob; Hanson, Graeme R; Pace, Ron J

    2014-05-07

    We report the first (55)Mn pulsed ENDOR studies on the S2 state multiline spin ½ centre of the oxygen evolving complex (OEC) in Photosystem II (PS II), at temperatures below 4.2 K. These were performed on highly active samples of spinach PS II core complexes, developed previously in our laboratories for photosystem spectroscopic use, at temperatures down to 2.5 K. Under these conditions, relaxation effects which have previously hindered observation of most of the manganese ENDOR resonances from the OEC coupled Mn cluster are suppressed. (55)Mn ENDOR hyperfine couplings ranging from ∼50 to ∼680 MHz are now seen on the S2 state multiline EPR signal. These, together with complementary high resolution X-band CW EPR measurements and detailed simulations, reveal that at least two and probably three Mn hyperfine couplings with large anisotropy are seen, indicating that three Mn(III) ions are likely present in the functional S2 state of the enzyme. This suggests a low oxidation state paradigm for the OEC (mean Mn oxidation level 3.0 in the S1 state) and unexpected Mn exchange coupling in the S2 state, with two Mn ions nearly magnetically silent. Our results rationalize a number of previous ligand ESEEM/ENDOR studies and labelled water exchange experiments on the S2 state of the photosystem, in a common picture which is closely consistent with recent photo-assembly (Kolling et al., Biophys. J. 2012, 103, 313-322) and large scale computational studies on the OEC (Gatt et al., Angew. Chem., Int. Ed. 2012, 51, 12025-12028, Kurashige et al. Nat. Chem. 2013, 5, 660-666).

  15. Diversity and Evolution of Bacterial Twin Arginine Translocase Protein, TatC, Reveals a Protein Secretion System That Is Evolving to Fit Its Environmental Niche

    PubMed Central

    Simone, Domenico; Bay, Denice C.; Leach, Thorin; Turner, Raymond J.

    2013-01-01

    Background The twin-arginine translocation (Tat) protein export system enables the transport of fully folded proteins across a membrane. This system is composed of two integral membrane proteins belonging to TatA and TatC protein families and in some systems a third component, TatB, a homolog of TatA. TatC participates in substrate protein recognition through its interaction with a twin arginine leader peptide sequence. Methodology/Principal Findings The aim of this study was to explore TatC diversity, evolution and sequence conservation in bacteria to identify how TatC is evolving and diversifying in various bacterial phyla. Surveying bacterial genomes revealed that 77% of all species possess one or more tatC loci and half of these classes possessed only tatC and tatA genes. Phylogenetic analysis of diverse TatC homologues showed that they were primarily inherited but identified a small subset of taxonomically unrelated bacteria that exhibited evidence supporting lateral gene transfer within an ecological niche. Examination of bacilli tatCd/tatCy isoform operons identified a number of known and potentially new Tat substrate genes based on their frequent association to tatC loci. Evolutionary analysis of these Bacilli isoforms determined that TatCy was the progenitor of TatCd. A bacterial TatC consensus sequence was determined and highlighted conserved and variable regions within a three dimensional model of the Escherichia coli TatC protein. Comparative analysis between the TatC consensus sequence and Bacilli TatCd/y isoform consensus sequences revealed unique sites that may contribute to isoform substrate specificity or make TatA specific contacts. Synonymous to non-synonymous nucleotide substitution analyses of bacterial tatC homologues determined that tatC sequence variation differs dramatically between various classes and suggests TatC specialization in these species. Conclusions/Significance TatC proteins appear to be diversifying within particular bacterial

  16. Radiocarbon-dating and ancient DNA reveal rapid replacement of extinct prehistoric penguins

    NASA Astrophysics Data System (ADS)

    Rawlence, Nicolas J.; Perry, George L. W.; Smith, Ian W. G.; Scofield, R. Paul; Tennyson, Alan J. D.; Matisoo-Smith, Elizabeth A.; Boessenkool, Sanne; Austin, Jeremy J.; Waters, Jonathan M.

    2015-03-01

    Prehistoric faunal extinctions dramatically reshaped biological assemblages around the world. However, the timing of such biotic shifts is often obscured by the fragmentary nature and limited temporal resolution of fossil records. We use radiocarbon-dating and ancient-DNA analysis of prehistoric (ca A.D. 1450-1834) Megadyptes penguin specimens to assess the time-frame of biological turnover in coastal New Zealand following human settlement. These data suggest that the final extirpation of the endemic Megadyptes waitaha, and subsequent replacement by the previously sub-Antarctic-limited Megadyptes antipodes, likely occurred within a narrow temporal window (e.g. a century or less). This transition represents one of the most rapid prehistoric faunal turnover events documented, and is likely linked to human demographic and cultural transitions during the 15th Century. Our results suggest that anthropogenic forces can trigger rapid biogeographic shifts.

  17. β-Arrestin biosensors reveal a rapid, receptor-dependent activation/deactivation cycle

    PubMed Central

    Nuber, Susanne; Zabel, Ulrike; Lorenz, Kristina; Nuber, Andreas; Milligan, Graeme; Tobin, Andrew B.; Lohse, Martin J.; Hoffmann, Carsten

    2016-01-01

    (β-)Arrestins are important regulators of G-protein-coupled receptors (GPCRs)1–3. They bind to active, phosphorylated GPCRs and thereby shut off ‘classical’ signalling to G proteins3,4, trigger internalization of GPCRs via interaction with the clathrin machinery5–7 and mediate signalling via ‘non-classical’ pathways1,2. In addition to two visual arrestins that bind to rod and cone photoreceptors (termed arrestin1 and arrestin4), there are only two (non-visual) β-arrestin proteins (β-arrestin1 and β-arrestin2, also termed arrestin2 and arrestin3), which regulate hundreds of different (non-visual) GPCRs. Binding of these proteins to GPCRs usually requires the active form of the receptors plus their phosphorylation by G-protein-coupled receptor kinases (GRKs)1,3,4. The binding of receptors or their carboxy terminus as well as certain truncations induce active conformations of (β-)arrestins that have recently been solved by X-ray crystallography8–10. Here we investigate both the interaction of β-arrestin with GPCRs, and the β-arrestin conformational changes in real time and in living human cells, using a series of fluorescence resonance energy transfer (FRET)-based β-arrestin2 biosensors. We observe receptor-specific patterns of conformational changes in β-arrestin2 that occur rapidly after the receptor–β-arrestin2 interaction. After agonist removal, these changes persist for longer than the direct receptor interaction. Our data indicate a rapid, receptor-type-specific, two-step binding and activation process between GPCRs and β-arrestins. They further indicate that β-arrestins remain active after dissociation from receptors, allowing them to remain at the cell surface and presumably signal independently. Thus, GPCRs trigger a rapid, receptor-specific activation/deactivation cycle of β-arrestins, which permits their active signalling. PMID:27007855

  18. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes.

    PubMed

    Macaulay, Vincent; Hill, Catherine; Achilli, Alessandro; Rengo, Chiara; Clarke, Douglas; Meehan, William; Blackburn, James; Semino, Ornella; Scozzari, Rosaria; Cruciani, Fulvio; Taha, Adi; Shaari, Norazila Kassim; Raja, Joseph Maripa; Ismail, Patimah; Zainuddin, Zafarina; Goodwin, William; Bulbeck, David; Bandelt, Hans-Jürgen; Oppenheimer, Stephen; Torroni, Antonio; Richards, Martin

    2005-05-13

    A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia approximately 65,000 years ago was rapid, most likely taking only a few thousand years.

  19. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation.

    PubMed

    Pease, James B; Haak, David C; Hahn, Matthew W; Moyle, Leonie C

    2016-02-01

    Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.

  20. Rapid emotional processing in relation to trauma-related symptoms as revealed by magnetic source imaging

    PubMed Central

    2014-01-01

    Background Traumatic stress leads to functional reorganization in the brain and may trigger an alarm response. However, when the traumatic event produces severe helplessness, the predominant peri-traumatic response may instead be marked by a dissociative shutdown reaction. The neural correlates of this dissociative shutdown were investigated by presenting rapidly presented affective pictures to female participants with posttraumatic stress disorder (PTSD), and comparing responses to a Non-PTSD control group. Methods Event-related-magnetic-fields were recorded during rapid visual serial presentation of emotionally arousing stimuli (unpleasant or pleasant), which alternated with pictures with low affective content (neutral). Neural sources, based on the L2-surface-minimum-norm, correlated with the severity of the symptom clusters: PTSD, depression and shutdown dissociation. Results For the early cortical response (60 to 110 ms), dissociation and PTSD symptom severity show similar spatial distributions of correlates for unpleasant stimuli. Cortical networks that could be involved in the relationships seem to be widespread. Conclusion We conclude that shutdown dissociation, PTSD and depression all have distinct effects on early processing of emotional stimuli. PMID:24997778

  1. Quantitative Phosphoproteomics Reveals Signaling Mechanisms Associated with Rapid Cold Hardening in a Chill-Tolerant Fly.

    PubMed

    Teets, Nicholas M; Denlinger, David L

    2016-08-05

    Rapid cold hardening (RCH) is a physiological adaptation in which brief chilling (minutes to hours) significantly enhances the cold tolerance of insects. RCH allows insects to cope with sudden cold snaps and diurnal variation in temperature, but the mechanistic basis of this rapid stress response is poorly understood. Here, we used phosphoproteomics to identify phosphorylation-mediated signaling events that are regulated by chilling that induces RCH. Phosphoproteomic changes were measured in both brain and fat bodies, two tissues that are essential for sensing cold and coordinating RCH at the organismal level. Tissues were chilled ex vivo, and changes in phosphoprotein abundance were measured using 2D electrophoresis coupled with Pro-Q diamond labeling of phosphoproteins followed by protein identification via LC-MS/MS. In both tissues, we observed an abundance of protein phosphorylation events in response to chilling. Some of the proteins regulated by RCH-inducing chilling include proteins involved in cytoskeletal reorganization, heat shock proteins, and proteins involved in the degradation of damaged cellular components via the proteasome and autophagosome. Our results suggest that phosphorylation-mediated signaling cascades are major drivers of RCH and enhance our mechanistic understanding of this complex phenotype.

  2. Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

    PubMed Central

    Pease, James B.; Haak, David C.; Hahn, Matthew W.; Moyle, Leonie C.

    2016-01-01

    Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a “PhyloGWAS” approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations. PMID:26871574

  3. Genome Scale Evolution of Myxoma Virus Reveals Host-Pathogen Adaptation and Rapid Geographic Spread

    PubMed Central

    Kerr, Peter J.; Rogers, Matthew B.; Fitch, Adam; DePasse, Jay V.; Cattadori, Isabella M.; Twaddle, Alan C.; Hudson, Peter J.; Tscharke, David C.; Read, Andrew F.; Holmes, Edward C.

    2013-01-01

    The evolutionary interplay between myxoma virus (MYXV) and the European rabbit (Oryctolagus cuniculus) following release of the virus in Australia in 1950 as a biological control is a classic example of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within individual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified. PMID:24067966

  4. Genome scale evolution of myxoma virus reveals host-pathogen adaptation and rapid geographic spread.

    PubMed

    Kerr, Peter J; Rogers, Matthew B; Fitch, Adam; Depasse, Jay V; Cattadori, Isabella M; Twaddle, Alan C; Hudson, Peter J; Tscharke, David C; Read, Andrew F; Holmes, Edward C; Ghedin, Elodie

    2013-12-01

    The evolutionary interplay between myxoma virus (MYXV) and the European rabbit (Oryctolagus cuniculus) following release of the virus in Australia in 1950 as a biological control is a classic example of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within individual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified.

  5. Intoxication of a Young Girl Reveals the Pitfalls of GHB Rapid Screening.

    PubMed

    Franken, Linda G; Andrews, Louise M; Slooff, Valerie D; de Wildt, Saskia N; Koch, Birgit C P

    2016-02-01

    The authors discuss the case of a 14-year-old girl who was transferred to the ICU of our hospital with ethanol intoxication (3.3 g/L), loss of consciousness (E5M3V1), and severe amnesia on recovery that was suspected of gamma-hydroxybutyric acid (GHB) intoxication. STAT toxicology screening may be necessary, when sexual assault under GHB intoxication is suspected. Therefore, the initial analysis of a urine sample was performed with a new enzymatic assay analysis for GHB. The enzymatic assay reported a GHB concentration of 26 mg/L, which is above the cut-off value of 10 mg/L. This cut-off value is to differentiate endogenous and exogenous levels because low levels of GHB occur naturally in the body. However, confirmation of these results by gas chromatography, which is common practice to confirm a positive GHB, gave a negative result. This discrepancy is probably contributed to interference of ethanol with the assay. This is a substantial downside of the GHB rapid screening, since the combination of GHB and ethanol is common. It is therefore advised to confirm that the positive GHB results are lower than 50 mg/L by gas chromatography, when using the rapid screening. This way the false-positive results and consequent inappropriate social and legal actions may be avoided.

  6. Neural evidence reveals the rapid effects of reward history on selective attention.

    PubMed

    MacLean, Mary H; Giesbrecht, Barry

    2015-05-05

    Selective attention is often framed as being primarily driven by two factors: task-relevance and physical salience. However, factors like selection and reward history, which are neither currently task-relevant nor physically salient, can reliably and persistently influence visual selective attention. The current study investigated the nature of the persistent effects of irrelevant, physically non-salient, reward-associated features. These features affected one of the earliest reliable neural indicators of visual selective attention in humans, the P1 event-related potential, measured one week after the reward associations were learned. However, the effects of reward history were moderated by current task demands. The modulation of visually evoked activity supports the hypothesis that reward history influences the innate salience of reward associated features, such that even when no longer relevant, nor physically salient, these features have a rapid, persistent, and robust effect on early visual selective attention.

  7. Forward Genetics by Genome Sequencing Reveals That Rapid Cyanide Release Deters Insect Herbivory of Sorghum bicolor

    PubMed Central

    Krothapalli, Kartikeya; Buescher, Elizabeth M.; Li, Xu; Brown, Elliot; Chapple, Clint; Dilkes, Brian P.; Tuinstra, Mitchell R.

    2013-01-01

    Whole genome sequencing has allowed rapid progress in the application of forward genetics in model species. In this study, we demonstrated an application of next-generation sequencing for forward genetics in a complex crop genome. We sequenced an ethyl methanesulfonate-induced mutant of Sorghum bicolor defective in hydrogen cyanide release and identified the causal mutation. A workflow identified the causal polymorphism relative to the reference BTx623 genome by integrating data from single nucleotide polymorphism identification, prior information about candidate gene(s) implicated in cyanogenesis, mutation spectra, and polymorphisms likely to affect phenotypic changes. A point mutation resulting in a premature stop codon in the coding sequence of dhurrinase2, which encodes a protein involved in the dhurrin catabolic pathway, was responsible for the acyanogenic phenotype. Cyanogenic glucosides are not cyanogenic compounds but their cyanohydrins derivatives do release cyanide. The mutant accumulated the glucoside, dhurrin, but failed to efficiently release cyanide upon tissue disruption. Thus, we tested the effects of cyanide release on insect herbivory in a genetic background in which accumulation of cyanogenic glucoside is unchanged. Insect preference choice experiments and herbivory measurements demonstrate a deterrent effect of cyanide release capacity, even in the presence of wild-type levels of cyanogenic glucoside accumulation. Our gene cloning method substantiates the value of (1) a sequenced genome, (2) a strongly penetrant and easily measurable phenotype, and (3) a workflow to pinpoint a causal mutation in crop genomes and accelerate in the discovery of gene function in the postgenomic era. PMID:23893483

  8. Jumping Stand Apparatus Reveals Rapidly Specific Age-Related Cognitive Impairments in Mouse Lemur Primates

    PubMed Central

    Picq, Jean-Luc; Villain, Nicolas; Gary, Charlotte; Pifferi, Fabien; Dhenain, Marc

    2015-01-01

    The mouse lemur (Microcebus murinus) is a promising primate model for investigating normal and pathological cerebral aging. The locomotor behavior of this arboreal primate is characterized by jumps to and from trunks and branches. Many reports indicate insufficient adaptation of the mouse lemur to experimental devices used to evaluate its cognition, which is an impediment to the efficient use of this animal in research. In order to develop cognitive testing methods appropriate to the behavioral and biological traits of this species, we adapted the Lashley jumping stand apparatus, initially designed for rats, to the mouse lemur. We used this jumping stand apparatus to compare performances of young (n = 12) and aged (n = 8) adults in acquisition and long-term retention of visual discriminations. All mouse lemurs completed the tasks and only 25 trials, on average, were needed to master the first discrimination problem with no age-related differences. A month later, all mouse lemurs made progress for acquiring the second discrimination problem but only the young group reached immediately the criterion in the retention test of the first discrimination problem. This study shows that the jumping stand apparatus allows rapid and efficient evaluation of cognition in mouse lemurs and demonstrates that about half of the old mouse lemurs display a specific deficit in long-term retention but not in acquisition of visual discrimination. PMID:26716699

  9. Impaired Intracellular Ca2+ Dynamics in Live Cardiomyocytes Revealed by Rapid Line Scan Confocal Microscopy

    NASA Astrophysics Data System (ADS)

    Plank, David M.; Sussman, Mark A.

    2005-06-01

    Altered intracellular Ca2+ dynamics are characteristically observed in cardiomyocytes from failing hearts. Studies of Ca2+ handling in myocytes predominantly use Fluo-3 AM, a visible light excitable Ca2+ chelating fluorescent dye in conjunction with rapid line-scanning confocal microscopy. However, Fluo-3 AM does not allow for traditional ratiometric determination of intracellular Ca2+ concentration and has required the use of mathematic correction factors with values obtained from separate procedures to convert Fluo-3 AM fluorescence to appropriate Ca2+ concentrations. This study describes methodology to directly measure intracellular Ca2+ levels using inactivated, Fluo-3-AM-loaded cardiomyocytes equilibrated with Ca2+ concentration standards. Titration of Ca2+ concentration exhibits a linear relationship to increasing Fluo-3 AM fluorescence intensity. Images obtained from individual myocyte confocal scans were recorded, average pixel intensity values were calculated, and a plot is generated relating the average pixel intensity to known Ca2+ concentrations. These standard plots can be used to convert transient Ca2+ fluorescence obtained with experimental cells to Ca2+ concentrations by linear regression analysis. Standards are determined on the same microscope used for acquisition of unknown Ca2+ concentrations, simplifying data interpretation and assuring accuracy of conversion values. This procedure eliminates additional equipment, ratiometric imaging, and mathematic correction factors and should be useful to investigators requiring a straightforward method for measuring Ca2+ concentrations in live cells using Ca2+-chelating dyes exhibiting variable fluorescence intensity.

  10. Jumping Stand Apparatus Reveals Rapidly Specific Age-Related Cognitive Impairments in Mouse Lemur Primates.

    PubMed

    Picq, Jean-Luc; Villain, Nicolas; Gary, Charlotte; Pifferi, Fabien; Dhenain, Marc

    2015-01-01

    The mouse lemur (Microcebus murinus) is a promising primate model for investigating normal and pathological cerebral aging. The locomotor behavior of this arboreal primate is characterized by jumps to and from trunks and branches. Many reports indicate insufficient adaptation of the mouse lemur to experimental devices used to evaluate its cognition, which is an impediment to the efficient use of this animal in research. In order to develop cognitive testing methods appropriate to the behavioral and biological traits of this species, we adapted the Lashley jumping stand apparatus, initially designed for rats, to the mouse lemur. We used this jumping stand apparatus to compare performances of young (n = 12) and aged (n = 8) adults in acquisition and long-term retention of visual discriminations. All mouse lemurs completed the tasks and only 25 trials, on average, were needed to master the first discrimination problem with no age-related differences. A month later, all mouse lemurs made progress for acquiring the second discrimination problem but only the young group reached immediately the criterion in the retention test of the first discrimination problem. This study shows that the jumping stand apparatus allows rapid and efficient evaluation of cognition in mouse lemurs and demonstrates that about half of the old mouse lemurs display a specific deficit in long-term retention but not in acquisition of visual discrimination.

  11. Rapid scavenging of jellyfish carcasses reveals the importance of gelatinous material to deep-sea food webs.

    PubMed

    Sweetman, Andrew K; Smith, Craig R; Dale, Trine; Jones, Daniel O B

    2014-12-07

    Jellyfish blooms are common in many oceans, and anthropogenic changes appear to have increased their magnitude in some regions. Although mass falls of jellyfish carcasses have been observed recently at the deep seafloor, the dense necrophage aggregations and rapid consumption rates typical for vertebrate carrion have not been documented. This has led to a paradigm of limited energy transfer to higher trophic levels at jelly falls relative to vertebrate organic falls. We show from baited camera deployments in the Norwegian deep sea that dense aggregations of deep-sea scavengers (more than 1000 animals at peak densities) can rapidly form at jellyfish baits and consume entire jellyfish carcasses in 2.5 h. We also show that scavenging rates on jellyfish are not significantly different from fish carrion of similar mass, and reveal that scavenging communities typical for the NE Atlantic bathyal zone, including the Atlantic hagfish, galatheid crabs, decapod shrimp and lyssianasid amphipods, consume both types of carcasses. These rapid jellyfish carrion consumption rates suggest that the contribution of gelatinous material to organic fluxes may be seriously underestimated in some regions, because jelly falls may disappear much more rapidly than previously thought. Our results also demonstrate that the energy contained in gelatinous carrion can be efficiently incorporated into large numbers of deep-sea scavengers and food webs, lessening the expected impacts (e.g. smothering of the seafloor) of enhanced jellyfish production on deep-sea ecosystems and pelagic-benthic coupling.

  12. Rapid scavenging of jellyfish carcasses reveals the importance of gelatinous material to deep-sea food webs

    PubMed Central

    Sweetman, Andrew K.; Smith, Craig R.; Dale, Trine; Jones, Daniel O. B.

    2014-01-01

    Jellyfish blooms are common in many oceans, and anthropogenic changes appear to have increased their magnitude in some regions. Although mass falls of jellyfish carcasses have been observed recently at the deep seafloor, the dense necrophage aggregations and rapid consumption rates typical for vertebrate carrion have not been documented. This has led to a paradigm of limited energy transfer to higher trophic levels at jelly falls relative to vertebrate organic falls. We show from baited camera deployments in the Norwegian deep sea that dense aggregations of deep-sea scavengers (more than 1000 animals at peak densities) can rapidly form at jellyfish baits and consume entire jellyfish carcasses in 2.5 h. We also show that scavenging rates on jellyfish are not significantly different from fish carrion of similar mass, and reveal that scavenging communities typical for the NE Atlantic bathyal zone, including the Atlantic hagfish, galatheid crabs, decapod shrimp and lyssianasid amphipods, consume both types of carcasses. These rapid jellyfish carrion consumption rates suggest that the contribution of gelatinous material to organic fluxes may be seriously underestimated in some regions, because jelly falls may disappear much more rapidly than previously thought. Our results also demonstrate that the energy contained in gelatinous carrion can be efficiently incorporated into large numbers of deep-sea scavengers and food webs, lessening the expected impacts (e.g. smothering of the seafloor) of enhanced jellyfish production on deep-sea ecosystems and pelagic–benthic coupling. PMID:25320167

  13. Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice

    PubMed Central

    Ter-Voskanyan, Hasmik; Allgaier, Martin; Borsch, Thomas

    2014-01-01

    Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae)—a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC–trnV, trnR–atpA, ndhF–rpl32, psbM–trnD, and trnQ–rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters). Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid), Olea (asterids) and Cymbidium (monocots) showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF–rpl32 and trnK–rps16) were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations

  14. Online Stimulus Optimization Rapidly Reveals Multidimensional Selectivity in Auditory Cortical Neurons

    PubMed Central

    Hancock, Kenneth E.; Sen, Kamal

    2014-01-01

    Neurons in sensory brain regions shape our perception of the surrounding environment through two parallel operations: decomposition and integration. For example, auditory neurons decompose sounds by separately encoding their frequency, temporal modulation, intensity, and spatial location. Neurons also integrate across these various features to support a unified perceptual gestalt of an auditory object. At higher levels of a sensory pathway, neurons may select for a restricted region of feature space defined by the intersection of multiple, independent stimulus dimensions. To further characterize how auditory cortical neurons decompose and integrate multiple facets of an isolated sound, we developed an automated procedure that manipulated five fundamental acoustic properties in real time based on single-unit feedback in awake mice. Within several minutes, the online approach converged on regions of the multidimensional stimulus manifold that reliably drove neurons at significantly higher rates than predefined stimuli. Optimized stimuli were cross-validated against pure tone receptive fields and spectrotemporal receptive field estimates in the inferior colliculus and primary auditory cortex. We observed, from midbrain to cortex, increases in both level invariance and frequency selectivity, which may underlie equivalent sparseness of responses in the two areas. We found that onset and steady-state spike rates increased proportionately as the stimulus was tailored to the multidimensional receptive field. By separately evaluating the amount of leverage each sound feature exerted on the overall firing rate, these findings reveal interdependencies between stimulus features as well as hierarchical shifts in selectivity and invariance that may go unnoticed with traditional approaches. PMID:24990917

  15. Rapid regional perturbations to the recent global geomagnetic decay revealed by a new Hawaiian record

    PubMed Central

    de Groot, L. V.; Biggin, A. J.; Dekkers, M. J.; Langereis, C. G.; Herrero-Bervera, E.

    2013-01-01

    The dominant dipolar component of the Earth’s magnetic field has been steadily weakening for at least the last 170 years. Prior to these direct measurements, archaeomagnetic records show short periods of significantly elevated geomagnetic intensity. These striking phenomena are not captured by current field models and their relationship to the recent dipole decay is highly unclear. Here we apply a novel multi-method archaeomagnetic approach to produce a new high-quality record of geomagnetic intensity variations for Hawaii, a crucial locality in the central Pacific. It reveals a short period of high intensity occurring ~1,000 years ago, qualitatively similar to behaviour observed 200 years earlier in Europe and 500 years later in Mesoamerica. We combine these records with one from Japan to produce a coherent picture that includes the dipole decaying steadily over the last millennium. Strong, regional, short-term intensity perturbations are superimposed on this global trend; their asynchronicity necessitates a highly non-dipolar nature. PMID:24177390

  16. Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics

    PubMed Central

    von Wulffen, Joachim; Ulmer, Andreas; Jäger, Günter; Sawodny, Oliver; Feuer, Ronny

    2017-01-01

    Escherichia coli is able to shift between anaerobic and aerobic metabolism by adapting its gene expression, e.g., of metabolic genes, to the new environment. The dynamics of gene expression that result from environmental shifts are limited, amongst others, by the time needed for regulation and transcription elongation. In this study, we examined gene expression dynamics after an anaerobic-to-aerobic shift on a short time scale (0.5, 1, 2, 5, and 10 min) by RNA sequencing with emphasis on delay times and transcriptional elongation rates (TER). Transient expression patterns and timing of differential expression, characterized by delay and elongation, were identified as key features of the dataset. Gene ontology enrichment analysis revealed early upregulation of respiratory and iron-related gene sets. We inferred specific TERs of 89 operons with a mean TER of 42.0 nt/s and mean delay time of 22.4 s. TERs correlate with sequence features, such as codon bias, whereas delay times correlate with the involvement of regulators. The presented data illustrate that at very short times after a shift in oxygenation, extensional changes of the transcriptome, such as temporary responses, can be observed. Besides regulation, TERs contribute to the dynamics of gene expression. PMID:28264512

  17. Rapid regional perturbations to the recent global geomagnetic decay revealed by a new Hawaiian record

    NASA Astrophysics Data System (ADS)

    de Groot, L. V.; Biggin, A. J.; Dekkers, M. J.; Langereis, C. G.; Herrero-Bervera, E.

    2013-10-01

    The dominant dipolar component of the Earth’s magnetic field has been steadily weakening for at least the last 170 years. Prior to these direct measurements, archaeomagnetic records show short periods of significantly elevated geomagnetic intensity. These striking phenomena are not captured by current field models and their relationship to the recent dipole decay is highly unclear. Here we apply a novel multi-method archaeomagnetic approach to produce a new high-quality record of geomagnetic intensity variations for Hawaii, a crucial locality in the central Pacific. It reveals a short period of high intensity occurring ~1,000 years ago, qualitatively similar to behaviour observed 200 years earlier in Europe and 500 years later in Mesoamerica. We combine these records with one from Japan to produce a coherent picture that includes the dipole decaying steadily over the last millennium. Strong, regional, short-term intensity perturbations are superimposed on this global trend; their asynchronicity necessitates a highly non-dipolar nature.

  18. Online stimulus optimization rapidly reveals multidimensional selectivity in auditory cortical neurons.

    PubMed

    Chambers, Anna R; Hancock, Kenneth E; Sen, Kamal; Polley, Daniel B

    2014-07-02

    Neurons in sensory brain regions shape our perception of the surrounding environment through two parallel operations: decomposition and integration. For example, auditory neurons decompose sounds by separately encoding their frequency, temporal modulation, intensity, and spatial location. Neurons also integrate across these various features to support a unified perceptual gestalt of an auditory object. At higher levels of a sensory pathway, neurons may select for a restricted region of feature space defined by the intersection of multiple, independent stimulus dimensions. To further characterize how auditory cortical neurons decompose and integrate multiple facets of an isolated sound, we developed an automated procedure that manipulated five fundamental acoustic properties in real time based on single-unit feedback in awake mice. Within several minutes, the online approach converged on regions of the multidimensional stimulus manifold that reliably drove neurons at significantly higher rates than predefined stimuli. Optimized stimuli were cross-validated against pure tone receptive fields and spectrotemporal receptive field estimates in the inferior colliculus and primary auditory cortex. We observed, from midbrain to cortex, increases in both level invariance and frequency selectivity, which may underlie equivalent sparseness of responses in the two areas. We found that onset and steady-state spike rates increased proportionately as the stimulus was tailored to the multidimensional receptive field. By separately evaluating the amount of leverage each sound feature exerted on the overall firing rate, these findings reveal interdependencies between stimulus features as well as hierarchical shifts in selectivity and invariance that may go unnoticed with traditional approaches.

  19. Genomic medicine: evolving science, evolving ethics

    PubMed Central

    Soden, Sarah E; Farrow, Emily G; Saunders, Carol J; Lantos, John D

    2012-01-01

    Genomic medicine is rapidly evolving. Next-generation sequencing is changing the diagnostic paradigm by allowing genetic testing to be carried out more quickly, less expensively and with much higher resolution; pushing the envelope on existing moral norms and legal regulations. Early experience with implementation of next-generation sequencing to diagnose rare genetic conditions in symptomatic children suggests ways that genomic medicine might come to be used and some of the ethical issues that arise, impacting test design, patient selection, consent, sequencing analysis and communication of results. The ethical issues that arise from use of new technologies cannot be satisfactorily analyzed until they are understood and they cannot be understood until the technologies are deployed in the real world. PMID:23173007

  20. Nanophase Carbonates on Mars: Does Evolved Gas Analysis of Nanophase Carbonates Reveal a Large Organic Carbon Budget in Near-Surface Martian Materials?

    NASA Technical Reports Server (NTRS)

    Archer, P. Douglas, Jr.; Niles, Paul B.; Ming, Douglas W.; Sutter, Brad; Eigenbrode, Jen

    2015-01-01

    Evolved Gas Analysis (EGA), which involves heating a sample and monitoring the gases released, has been performed on Mars by the Viking gas chromatography/mass spectrometry instruments, the Thermal and Evolved Gas Analyzer (TEGA) on the Phoenix lander, and the Sample Analysis at Mars (SAM) instrument on the Mars Science Laboratory. All of these instruments detected CO2 released during sample analysis at abundances of approx. 0.1 to 5 wt% assuming a carbonate source. The source of the CO2 can be constrained by evaluating the temperature of the gas release, a capability of both the TEGA and SAM instruments. The samples analyzed by SAM show that the majority of the CO2 is released below 400C, much lower than traditional carbonate decomposition temperatures which can be as low as 400C for some siderites, with magnesites and calcites decomposing at even higher temperatures. In addition to mineralogy, decomposition temperature can depend on particle size (among other factors). If carbonates formed on Mars under low temperature and relative humidity conditions, the resulting small particle size (nanophase) carbonates could have low decomposition temperatures. We have found that calcite can be synthesized by exposing CaO to water vapor and CO2 and that the resulting mineral has an EGA peak of approx. 550C for CO2, which is about 200C lower than for other calcites. Work is ongoing to produce Fe and Mg-bearing carbonates using the same process. Current results suggest that nanophase calcium carbonates cannot explain the CO2 released from martian samples. If the decomposition temperatures of Mg and Fe-bearing nanophase carbonates are not significantly lower than 400C, other candidate sources include oxalates and carboxylated organic molecules. If present, the abundance of organic carbon in these samples could be greater than 0.1 wt % (1000s of ppm), a signficant departure from the paradigm of the organic-poor Mars based on Viking results.

  1. Nanophase Carbonates on Mars: Does Evolved Gas Analysis of Nanophase Carbonates Reveal a Large Organic Carbon Budget in Near-surface Martian Materials?

    NASA Astrophysics Data System (ADS)

    Archer, P. D., Jr.; Ming, D. W.; Sutter, B.; Niles, P. B.; Eigenbrode, J. L.

    2015-12-01

    Evolved Gas Analysis (EGA), which involves heating a sample and monitoring the gases released, has been performed on Mars by the Viking gas chromatography/mass spectrometry instruments, the Thermal and Evolved Gas Analyzer (TEGA) on the Phoenix lander, and the Sample Analysis at Mars (SAM) instrument on the Mars Science Laboratory. All of these instruments detected CO2 released during sample analysis at abundances of ~0.1 to 5 wt% assuming a carbonate source. The source of the CO2 can be constrained by evaluating the temperature of the gas release, a capability of both the TEGA and SAM instruments. The samples analyzed by SAM show that the majority of the CO2is released below 400 °C, much lower than traditional carbonate decomposition temperatures which can be as low as 400 °C for some siderites, with magnesites and calcites decomposing at even higher temperatures. In addition to mineralogy, decomposition temperature can depend on particle size (among other factors). If carbonates formed on Mars under low temperature and relative humidity conditions, the resulting small particle size (nanophase) carbonates could have low decomposition temperatures. We have found that calcite can be synthesized by exposing CaO to water vapor and CO2 and that the resulting mineral has an EGA peak of ~550 °C for CO2, which is about 200 °C lower than for other calcites. Work is ongoing to produce Fe and Mg-bearing carbonates using the same process. Current results suggest that nanophase calcium carbonates cannot explain the CO2 released from martian samples. If the decomposition temperatures of Mg and Fe-bearing nanophase carbonates are not significantly lower than 400 °C, other candidate sources include oxalates and carboxylated organic molecules. If present, the abundance of organic carbon in these samples could be > 0.1 wt % (1000s of ppm), a signficant departure from the paradigm of the organic-poor Mars based on Viking results.

  2. Culture evolves

    PubMed Central

    Whiten, Andrew; Hinde, Robert A.; Laland, Kevin N.; Stringer, Christopher B.

    2011-01-01

    Culture pervades human lives and has allowed our species to create niches all around the world and its oceans, in ways quite unlike any other primate. Indeed, our cultural nature appears so distinctive that it is often thought to separate humanity from the rest of nature and the Darwinian forces that shape it. A contrary view arises through the recent discoveries of a diverse range of disciplines, here brought together to illustrate the scope of a burgeoning field of cultural evolution and to facilitate cross-disciplinary fertilization. Each approach emphasizes important linkages between culture and evolutionary biology rather than quarantining one from the other. Recent studies reveal that processes important in cultural transmission are more widespread and significant across the animal kingdom than earlier recognized, with important implications for evolutionary theory. Recent archaeological discoveries have pushed back the origins of human culture to much more ancient times than traditionally thought. These developments suggest previously unidentified continuities between animal and human culture. A third new array of discoveries concerns the later diversification of human cultures, where the operations of Darwinian-like processes are identified, in part, through scientific methods borrowed from biology. Finally, surprising discoveries have been made about the imprint of cultural evolution in the predispositions of human minds for cultural transmission. PMID:21357216

  3. Culture evolves.

    PubMed

    Whiten, Andrew; Hinde, Robert A; Laland, Kevin N; Stringer, Christopher B

    2011-04-12

    Culture pervades human lives and has allowed our species to create niches all around the world and its oceans, in ways quite unlike any other primate. Indeed, our cultural nature appears so distinctive that it is often thought to separate humanity from the rest of nature and the Darwinian forces that shape it. A contrary view arises through the recent discoveries of a diverse range of disciplines, here brought together to illustrate the scope of a burgeoning field of cultural evolution and to facilitate cross-disciplinary fertilization. Each approach emphasizes important linkages between culture and evolutionary biology rather than quarantining one from the other. Recent studies reveal that processes important in cultural transmission are more widespread and significant across the animal kingdom than earlier recognized, with important implications for evolutionary theory. Recent archaeological discoveries have pushed back the origins of human culture to much more ancient times than traditionally thought. These developments suggest previously unidentified continuities between animal and human culture. A third new array of discoveries concerns the later diversification of human cultures, where the operations of Darwinian-like processes are identified, in part, through scientific methods borrowed from biology. Finally, surprising discoveries have been made about the imprint of cultural evolution in the predispositions of human minds for cultural transmission.

  4. Effects of ammonia on the structure of the oxygen-evolving complex in photosystem II as revealed by light-induced FTIR difference spectroscopy.

    PubMed

    Hou, Li-Hsiu; Wu, Chia-Ming; Huang, Hsin-Ho; Chu, Hsiu-An

    2011-11-01

    NH(3) is a structural analogue of substrate H(2)O and an inhibitor to the water oxidation reaction in photosystem II. To test whether or not NH(3) is able to replace substrate water molecules on the oxygen-evolving complex in photosystem II, we studied the effects of NH(3) on the high-frequency region (3750-3550 cm(-1)) of the S(2)Q(A)(-)/S(1)Q(A) FTIR difference spectra (pH 7.5 at 250 K), where OH stretch modes of weak hydrogen-bonded active water molecules occur. Our results showed that NH(3) did not replace the active water molecule on the oxygen-evolving complex that gave rise to the S(1) mode at ~3586 cm(-1) and the S(2) mode at ~3613 cm(-1) in the S(2)Q(A)(-)/S(1)Q(A) FTIR difference spectrum of PSII. In addition, our mid-frequency FTIR results showed a clear difference between pH 6.5 and 7.5 on the concentration dependence of the NH(4)Cl-induced upshift of the S(2) state carboxylate mode at 1365 cm(-1) in the S(2)Q(A)(-)/S(1)Q(A) spectra of NH(4)Cl-treated PSII samples. Our results provided strong evidence that NH(3) induced this upshift in the spectra of NH(4)Cl-treated PSII samples at 250 K. Moreover, our low-frequency FTIR results showed that the Mn-O-Mn cluster vibrational mode at 606 cm(-1) in the S(2)Q(A)(-)/S(1)Q(A) spectrum of the NaCl control PSII sample was diminished in those samples treated with NH(4)Cl. Our results suggest that NH(3) induced a significant alteration on the core structure of the Mn(4)CaO(5) cluster in PSII. The implication of our findings on the structure of the NH(3)-binding site on the OEC in PSII will be discussed.

  5. An alternative method for calcium depletion of the oxygen evolving complex of photosystem II as revealed by the dark-stable multiline EPR signal.

    PubMed

    Haddy, Alice; Ore, Brandon M

    2010-05-11

    The dark-stable multiline EPR signal of photosystem II (PSII) is associated with a slow-decaying S(2) state that is due to Ca(2+) loss from the oxygen evolving complex. Formation of the signal was observed in intact PSII in the presence of 100-250 mM NaCl at pH 5.5. Both moderately high NaCl concentration and decreased pH were required for its appearance in intact PSII. It was estimated that only a portion of oxygen evolving complexes was responsible for the signal (about 20% in 250 mM NaCl), based on the loss of the normal S(2)-state multiline signal. The formation of the dark-stable multiline signal in intact PSII at pH 5.5 could be reversed by addition of 15 mM Ca(2+) in the presence of moderately high NaCl, confirming that it was the absence of Ca(2+) that led to its appearance. Formation of the dark-stable multiline signal in NaCl-washed PSII, which lacks the PsbP (23 kDa) and PsbQ (17 kDa) subunits, was observed in about 80% of the sample in the presence of 150 mM NaCl at pH 5.5, but some signal was also observed under normal buffer conditions. In both intact and NaCl-washed PSII, the S(2)Y(Z). signal, which is also characteristic of Ca(2+) depletion, appeared upon subsequent illumination. Formation of the dark-stable multiline signal took place in the absence of Ca(2+) chelator or polycarboxylic acids, indicating that the signal did not require their direct binding as has been proposed previously. The conditions used here were milder than those used to produce the signal in previous studies and included a preillumination protocol to maximize the dark-stable S(2) state. Based on these conditions, it is suggested that Ca(2+) release occurred through protonation of key residues that coordinate Ca(2+) at low pH, followed by displacement of Ca(2+) with Na(+) by mass action at the moderately high NaCl concentration.

  6. Regulation of ascorbate biosynthesis in green algae has evolved to enable rapid stress-induced response via the VTC2 gene encoding GDP-l-galactose phosphorylase.

    PubMed

    Vidal-Meireles, André; Neupert, Juliane; Zsigmond, Laura; Rosado-Souza, Laise; Kovács, László; Nagy, Valéria; Galambos, Anikó; Fernie, Alisdair R; Bock, Ralph; Tóth, Szilvia Z

    2017-04-01

    Ascorbate (vitamin C) plays essential roles in stress resistance, development, signaling, hormone biosynthesis and regulation of gene expression; however, little is known about its biosynthesis in algae. In order to provide experimental proof for the operation of the Smirnoff-Wheeler pathway described for higher plants and to gain more information on the regulation of ascorbate biosynthesis in Chlamydomonas reinhardtii, we targeted the VTC2 gene encoding GDP-l-galactose phosphorylase using artificial microRNAs. Ascorbate concentrations in VTC2 amiRNA lines were reduced to 10% showing that GDP-l-galactose phosphorylase plays a pivotal role in ascorbate biosynthesis. The VTC2 amiRNA lines also grow more slowly, have lower chlorophyll content, and are more susceptible to stress than the control strains. We also demonstrate that: expression of the VTC2 gene is rapidly induced by H2 O2 and (1) O2 resulting in a manifold increase in ascorbate content; in contrast to plants, there is no circadian regulation of ascorbate biosynthesis; photosynthesis is not required per se for ascorbate biosynthesis; and Chlamydomonas VTC2 lacks negative feedback regulation by ascorbate in the physiological concentration range. Our work demonstrates that ascorbate biosynthesis is also highly regulated in Chlamydomonas albeit via mechanisms distinct from those previously described in land plants.

  7. Orbital and physical parameters of eclipsing binaries from the All-Sky Automated Survey catalogue. III. Two new low-mass systems with rapidly evolving spots

    NASA Astrophysics Data System (ADS)

    Hełminiak, K. G.; Konacki, M.; Złoczewski, K.; Ratajczak, M.; Reichart, D. E.; Ivarsen, K. M.; Haislip, J. B.; Crain, J. A.; Foster, A. C.; Nysewander, M. C.; Lacluyze, A. P.

    2011-03-01

    Aims: We present the results of our spectroscopic and photometric analysis of two newly discovered low-mass detached eclipsing binaries found in the All-Sky Automated Survey (ASAS) catalogue: ASAS J093814-0104.4 and ASAS J212954-5620.1. Methods: Using the Grating Instrument for Radiation Analysis with a Fibre-Fed Echelle (GIRAFFE) on the 1.9-m Radcliffe telescope at the South African Astronomical Observatory (SAAO) and the University College London Echelle Spectrograph (UCLES) on the 3.9-m Anglo-Australian Telescope, we obtained high-resolution spectra of both objects and derived their radial velocities (RVs) at various orbital phases. The RVs of both objects were measured with the two-dimensional cross-correlation technique (TODCOR) using synthetic template spectra as references. We also obtained V and I band photometry using the 1.0-m Elizabeth telescope at SAAO and the 0.4-m Panchromatic Robotic Optical Monitoring and Polarimetry Telescopes (PROMPT) located at the Cerro Tololo Inter-American Observatory (CTIO). The orbital and physical parameters of the systems were derived with PHOEBE and JKTEBOP codes. We compared our results with several sets of widely-used isochrones. Results: Our multi-epoch photometric observations demonstrate that both objects show significant out-of-eclipse modulations, which vary in time. We believe that this effect is caused by stellar spots, which evolve on time scales of tens of days. For this reason, we constructed our models on the basis of photometric observations spanning short time scales (less than a month). Our modeling indicates that (1) ASAS J093814-0104.04 is a main sequence active system with nearly-twin components with masses of M1 = 0.771 ± 0.033 M⊙, M2 = 0.768 ± 0.021 M⊙ and radii of R1 = 0.772 ± 0.012 R⊙ and R2 = 0.769 ± 0.013 R⊙. (2) ASAS J212954-5620.1 is a main sequence active binary with component masses of M1 = 0.833 ± 0.017 M⊙, M2 = 0.703 ± 0.013 M⊙ and radii of R1 = 0.845 ± 0.012 R⊙ and R2

  8. Exome sequencing reveals RAG1 mutations in a child with autoimmunity and sterile chronic multifocal osteomyelitis evolving into disseminated granulomatous disease

    PubMed Central

    Reiff, Andreas; Bassuk, Alexander G; Church, Joseph A; Campbell, Elizabeth; Bing, Xinyu; Ferguson, Polly J

    2013-01-01

    We describe a boy who developed autoinflammatory (chronic sterile multifocal osteomyelitis) and autoimmune (autoimmune cytopenias; vitiligo) phenotypes who subsequently developed disseminated granulomatous disease. Whole exome sequencing revealed homozygous RAG1 mutations thus expanding the spectrum of combined immunodeficiency with autoimmunity and granuloma that can occur with RAG deficiency. PMID:24122031

  9. The evolutionary dynamics of highly pathogenic avian influenza H5N1 in south-central Vietnam reveals multiple clades evolving from Chinese and Cambodian viruses.

    PubMed

    Nguyen, Tinh Huu; Than, Van Thai; Thanh, Hien Dang; Nguyen, Van Quang; Nguyen, Kim Hue; Nguyen, Duc Tan; Park, Jong-Hwa; Chung, In Sik; Jeong, Dae Gwin; Chang, Kyu-Tae; Oh, Tae Kwang; Kim, Wonyong

    2015-10-01

    In Vietnam, highly pathogenic avian influenza (HPAI), such as that caused by H5N1 viruses, is the most highly contagious infectious disease that has been affecting domestic poultry in recent years. Vietnam might be an evolutionary hotspot and a potential source of globally pandemic strains. However, few studies have reported viruses circulating in the south-central region of Vietnam. In the present study, 47 H5N1-positive samples were collected from both vaccinated and unvaccinated poultry farms in the South Central Coast region of Vietnam during 2013-2014, and their genetic diversity was analyzed. A common sequence motif for HPAI virus was identified at HA-cleavage sites in all samples: either RERRRKR/G (clades 2.3.2.1c and 2.3.2.1a) or REGRRKKR/G (clade 1.1.2). Phylogenetic analysis of HA genes identified three clades of HPAI H5N1: 1.1.2 (n=1), 2.3.2.1a (n=1), and 2.3.2.1c (n=45). The phylogenetic analysis indicated that these Vietnamese clades may have evolved from Chinese and Cambodian virus clades isolated in 2012-2013 but are less closely related to the clades detected from the Tyva Republic, Bulgaria, Mongolia, Japan, and Korea in 2009-2011. Detection of the coexistence of virus clades 2.3.2.1 and the very virulent 1.1.2 in the south-central regions suggests their local importance and highlights concerns regarding their spread, both northwards and southwards, as well as the potential for reassortment. The obtained data highlight the importance of regular identification of viral evolution and the development and use of region-specific vaccines.

  10. Temporal changes in the outcomes of HIV-exposed infants in Kinshasa, Democratic Republic of Congo during a period of rapidly evolving guidelines for care (2007–2013)

    PubMed Central

    Feinstein, Lydia; Edmonds, Andrew; Chalachala, Jean Lambert; Okitolonda, Vitus; Lusiama, Jean; Van Rie, Annelies; Chi, Benjamin H.; Cole, Stephen R.; Behets, Frieda

    2015-01-01

    Objective Guidelines for prevention of mother-to-child transmission of HIV have developed rapidly, yet little is known about how outcomes of HIV-exposed infants have changed over time. We describe HIV-exposed infant outcomes in Kinshasa, Democratic Republic of Congo, between 2007 and 2013. Design Cohort study of mother–infant pairs enrolled in family-centered comprehensive HIV care. Methods Accounting for competing risks, we estimated the cumulative incidences of early infant diagnosis, HIV transmission, death, loss to follow-up, and combination antiretroviral therapy (cART) initiation for infants enrolled in three periods (2007–2008, 2009–2010, and 2011–2012). Results 1707 HIV-exposed infants enrolled at a median age of 2.6 weeks. Among infants whose mothers had recently enrolled into HIV care (N = 1411), access to EID by age two months increased from 28% (95% confidence limits [CL]: 24,34%) among infants enrolled in 2007-2008 to 63% (95% CL: 59,68%) among infants enrolled in 2011–2012 (Gray's p-value <0.01). The 18-month cumulative incidence of HIV declined from 16% (95% CL: 11,22%) for infants enrolled in 2007–2008 to 11% (95% CL: 8,16%) for infants enrolled in 2011–2012 (Gray's p-value = 0.19). The 18-month cumulative incidence of death also declined, from 8% (95% CL: 5,12%) to 3% (95% CL: 2,5%) (Gray's p-value = 0.02). LTFU did not improve, with 18-month cumulative incidences of 19% (95% CL: 15,23%) for infants enrolled in 2007-2008 and 22% (95% CL: 18,26%) for infants enrolled in 2011–2012 (Gray's p-value = 0.06). Among HIV-infected infants, the 24-month cumulative incidence of cART increased from 61% (95% CL: 43,75%) to 97% (95% CL: 82,100%) (Gray's p-value < 0.01); the median age at cART decreased from 17.9 to 9.3 months. Outcomes were better for infants whose mothers enrolled before pregnancy. Conclusions We observed encouraging improvements, but continued efforts are needed. PMID:24991903

  11. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

    SciTech Connect

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A.; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana M.; Bharti, Arvind K.; Donahoo, Ryan S.; Finely, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Sotrey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James R.; Affourtit, Jason P.; Han, Cliff S.; Chertkov, Olga; Lindquist, Erika A.; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

    2012-02-07

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

  12. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.

    PubMed

    Lamour, Kurt H; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A; Rice, Brandon J; Raffaele, Sylvain; Cano, Liliana M; Bharti, Arvind K; Donahoo, Ryan S; Finley, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Storey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J; Dinwiddie, Darrell L; Jenkins, Jerry; Knight, James R; Affourtit, Jason P; Han, Cliff S; Chertkov, Olga; Lindquist, Erika A; Detter, Chris; Grigoriev, Igor V; Kamoun, Sophien; Kingsmore, Stephen F

    2012-10-01

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

  13. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici

    PubMed Central

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A.; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana M.; Bharti, Arvind K.; Donahoo, Ryan S.; Finley, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Storey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James R.; Affourtit, Jason P.; Han, Cliff S.; Chertkov, Olga; Lindquist, Erika A.; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

    2013-01-01

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually-recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic/genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) and higher levels of SNVs than those reported for humans, plants, and P. infestans. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single nucleotide variant (SNV) sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici. PMID:22712506

  14. Impulsive energy release and non-thermal emission in a confined M4.0 flare triggered by rapidly evolving magnetic structures

    SciTech Connect

    Kushwaha, Upendra; Joshi, Bhuwan; Mathew, S. K.; Cho, Kyung-Suk; Veronig, Astrid

    2014-08-10

    We present observations of a confined M4.0 flare from NOAA 11302 on 2011 September 26. Observations at high temporal, spatial, and spectral resolution from the Solar Dynamics Observatory, Reuven Ramaty High Energy Solar Spectroscopic Imager, and Nobeyama Radioheliograph observations enabled us to explore the possible triggering and energy release processes of this flare despite its very impulsive behavior and compact morphology. The flare light curves exhibit an abrupt rise of non-thermal emission with co-temporal hard X-ray (HXR) and microwave (MW) bursts that peaked instantly without any precursor emission. This stage was associated with HXR emission up to 200 keV that followed a power law with photon spectral index (γ) ∼ 3. Another non-thermal peak, observed 32 s later, was more pronounced in the MW flux than the HXR profiles. Dual peaked structures in the MW and HXR light curves suggest a two-step magnetic reconnection process. Extreme ultraviolet (EUV) images exhibit a sequential evolution of the inner and outer core regions of magnetic loop systems while the overlying loop configuration remained unaltered. Combined observations in HXR, (E)UV, and Hα provide support for flare models involving the interaction of coronal loops. The magnetograms obtained by the Helioseismic and Magnetic Imager reveal emergence of magnetic flux that began ∼five hr before the flare. However, the more crucial changes in the photospheric magnetic flux occurred about one minute prior to the flare onset with opposite polarity magnetic transients appearing at the early flare location within the inner core region. The spectral, temporal, and spatial properties of magnetic transients suggest that the sudden changes in the small-scale magnetic field have likely triggered the flare by destabilizing the highly sheared pre-flare magnetic configuration.

  15. What spectroscopy reveals concerning the Mn oxidation levels in the oxygen evolving complex of photosystem II: X-ray to near infra-red.

    PubMed

    Pace, Ron J; Jin, Lu; Stranger, Rob

    2012-08-28

    Photosystem II (PS II), found in oxygenic photosynthetic organisms, catalyses the most energetically demanding reaction in nature, the oxidation of water to molecular oxygen and protons. The water oxidase in PS II contains a Mn(4)Ca cluster (oxygen evolving complex, OEC), whose catalytic mechanism has been extensively investigated but is still unresolved. In particular the precise Mn oxidation levels through which the cluster cycles during functional turnover are still contentious. In this, the first of several planned parts, we examine a broad range of published data relating to this question, while considering the recent atomic resolution PS II crystal structure of Umena et al. (Nature, 2011, 473, 55). Results from X-ray, UV-Vis and NIR spectroscopies are considered, using an approach that is mainly empirical, by comparison with published data from known model systems, but with some reliance on computational or other theoretical considerations. The intention is to survey the extent to which these data yield a consistent picture of the Mn oxidation states in functional PS II - in particular, to test their consistency with two current proposals for the mean redox levels of the OEC during turnover; the so called 'high' and 'low' oxidation state paradigms. These systematically differ by two oxidation equivalents throughout the redox accumulating catalytic S state cycle (states S(0)···S(3)). In summary, we find that the data, in total, substantially favor the low oxidation proposal, particularly as a result of the new analyses we present. The low oxidation state scheme is able to resolve a number of previously 'anomalous' results in the observed UV-Visible S state turnover spectral differences and in the resonant inelastic X-ray spectroscopy (RIXS) of the Mn pre-edge region of the S(1) and S(2) states. Further, the low oxidation paradigm is able to provide a 'natural' explanation for the known sensitivity of the OEC Mn cluster to cryogenic near infra-red (NIR

  16. Ammonia-induced structural changes of the oxygen-evolving complex in photosystem II as revealed by light-induced FTIR difference spectroscopy.

    PubMed

    Chu, Hsiu-An; Feng, Ya-Wen; Wang, Chiu-Ming; Chiang, Kuo-An; Ke, Shyue-Chu

    2004-08-31

    Light-induced Fourier transform infrared difference spectroscopy has been applied to studies of ammonia effects on the oxygen-evolving complex (OEC) of photosystem II (PSII). We found that NH(3) induced characteristic spectral changes in the region of the symmetric carboxylate stretching modes (1450-1300 cm(-1)) of the S(2)Q(A)(-)/S(1)Q(A) FTIR difference spectra of PSII. The S(2) state carboxylate mode at 1365 cm(-1) in the S(2)Q(A)(-)/S(1)Q(A) spectrum of the controlled samples was very likely upshifted to 1379 cm(-1) in that of NH(3)-treated samples; however, the frequency of the corresponding S(1) carboxylate mode at 1402 cm(-1) in the same spectrum was not significantly affected. These two carboxylate modes have been assigned to a Mn-ligating carboxylate whose coordination mode changes from bridging or chelating to unidentate ligation during the S(1) to S(2) transition [Noguchi, T., Ono, T., and Inoue, Y. (1995) Biochim. Biophys. Acta 1228, 189-200; Kimura, Y., and Ono, T.-A. (2001) Biochemistry 40, 14061-14068]. Therefore, our results show that NH(3) induced significant structural changes of the OEC in the S(2) state. In addition, our results also indicated that the NH(3)-induced spectral changes of the S(2)Q(A)(-)/S(1)Q(A) spectrum of PSII are dependent on the temperature of the FTIR measurement. Among the temperatures we measured, the strongest effect was seen at 250 K, a lesser effect was seen at 225 K, and little or no effect was seen at 200 K. Furthermore, our results also showed that the NH(3) effects on the S(2)Q(A)(-)/S(1)Q(A) spectrum of PSII are dependent on the concentrations of NH(4)Cl. The NH(3)-induced upshift of the 1365 cm(-1) mode is apparent at 5 mM NH(4)Cl and is completely saturated at 100 mM NH(4)Cl concentration. Finally, we found that CH(3)NH(2) has a small but clear effect on the spectral change of the S(2)Q(A)(-)/S(1)Q(A) FTIR difference spectrum of PSII. The effects of amines on the S(2)Q(A)(-)/S(1)Q(A) FTIR difference spectra (NH(3

  17. Splitting of a Prevalent Mycobacterium bovis Spoligotype by Variable-Number Tandem-Repeat Typing Reveals High Heterogeneity in an Evolving Clonal Group

    PubMed Central

    Rodriguez-Campos, Sabrina; Navarro, Yurena; Romero, Beatriz; de Juan, Lucía; Bezos, Javier; Mateos, Ana; Golby, Paul; Smith, Noel H.; Hewinson, Glyn R.; Domínguez, Lucas; García-de-Viedma, Darío

    2013-01-01

    Mycobacterium bovis populations in countries with persistent bovine tuberculosis usually show a prevalent spoligotype with a wide geographical distribution. This study applied mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing to a random panel of 115 M. bovis isolates that are representative of the most frequent spoligotype in the Iberian Peninsula, SB0121. VNTR typing targeted nine loci: ETR-A (alias VNTR2165), ETR-B (VNTR2461), ETR-D (MIRU4, VNTR580), ETR-E (MIRU31, VNTR3192), MIRU26 (VNTR2996), QUB11a (VNTR2163a), QUB11b (VNTR2163b), QUB26 (VNTR4052), and QUB3232 (VNTR3232). We found a high degree of diversity among the studied isolates (discriminatory index [D] = 0.9856), which were split into 65 different MIRU-VNTR types. An alternative short-format MIRU-VNTR typing targeting only the four loci with the highest variability values was found to offer an equivalent discriminatory index. Minimum spanning trees using the MIRU-VNTR data showed the hypothetical evolution of an apparent clonal group. MIRU-VNTR analysis was also applied to the isolates of 176 animals from 15 farms infected by M. bovis SB0121; in 10 farms, the analysis revealed the coexistence of two to five different MIRU types differing in one to six loci, which highlights the frequency of undetected heterogeneity. PMID:23985914

  18. Revealing the Evolving Accretion Disk Corona in AGNs with Multi-Epoch X-ray Spectroscopy: the case of Mrk 335

    NASA Astrophysics Data System (ADS)

    Ballantyne, David R.; Keek, Laurens

    2016-04-01

    Active galactic nuclei host an accretion disk with an X-ray producing corona around a supermassive black hole. In bright sources, such as the Seyfert 1 galaxy Mrk 335, reflection of the coronal emission off the accretion disk has been observed. Reflection produces numerous spectral features, such as the Fe Kα emission line and absorption edge, which allow various properties of the inner accretion disk and corona to be constrained. We perform a multi-epoch spectral analysis of a dozen XMM-Newton, Suzaku, and NuSTAR observations of Mrk 335, and optimize the fitting procedure to unveil correlations between the Eddington ratio and multiple spectral parameters. We find that the ionization parameter of the accretion disk correlates strongly with the Eddington ratio: the inner disk is more strongly ionized at higher flux. Interestingly, the slope of the correlation is less steep than previously predicted. Furthermore, the cut-off of the power-law spectrum increases in energy with the Eddington ratio, whereas the reflection fraction exhibits a decrease. We interpret this behaviour as geometrical changes of the corona as a function of the accretion rate. Below ~10% of the Eddington limit, the compact and optically thick corona is located close to the inner disk, whereas at higher accretion rates the corona is likely optically thin and extends vertically further away from the disk surface. Compared to previous work that considered individual spectra, we find that multi-epoch spectroscopy is essential for breaking degeneracies in the spectral fits and for obtaining accurate spectral parameters. Furthermore, we show that this method provides a powerful tool to study coronal evolution. The rich archives of XMM-Newton, Suzaku, and NuSTAR provide the opportunity to extend this investigation to include several other bright AGN, which will reveal whether the behaviour that we found is common or unique to Mrk 335.

  19. Electrochemical Sensing for a Rapidly Evolving World

    NASA Astrophysics Data System (ADS)

    Mullen, Max Robertson

    This dissertation focuses on three projects involving the development of harsh environment gas sensors. The first project discusses the development of a multipurpose oxygen sensor electrode for use in sealing with the common electrolyte yttria stabilized zirconia. The purpose of the sealing function is to produce an internal reference environment maintained by a metal/metal oxide mixture, a criteria for miniaturization of potentiometric oxygen sensing technology. This sensor measures a potential between the internal reference and a sensing environment. The second project discusses the miniaturization of an oxygen sensor and the fabrication of a more generalized electrochemical sensing platform. The third project discusses the discovery of a new mechanism in the electrochemical sensing of ammonia through molecular recognition and the utilization of a sensor taking advantage of the new mechanism. An initial study involving the development of a microwave synthesized La0.8Sr0.2Al0.9Mn0.1O3 sensor electrode material illustrates the ability of the material developed to meet ionic and electronic conducting requirements for effective and Nernstian oxygen sensing. In addition the material deforms plastically under hot isostatic pressing conditions in a similar temperature and pressure regime with yttria stabilized zirconia to produce a seal and survive temperatures up to 1350 °C. In the second project we show novel methods to seal an oxygen environment inside a device cavity to produce an electrochemical sensor body using room temperature plasma-activated bonding and low temperature and pressure assisted plasma-activated bonding with silicon bodies, both in a clean room environment. The evolution from isostatic hot pressing methods towards room temperature complementary metal oxide semiconductor (CMOS) compatible technologies using single crystal silicon substrates in the clean room allows the sealing of devices on a much larger scale. Through this evolution in bonding technology we move from performing non-scalable experiments to produce one sensor at a time to scalable experiments producing six. The bonding methods we use are compatible with wafer scale processing. Practically speaking this means that the oxygen sensor design is scalable to produce thousands of sensors from one single bond. Using this bonding technology we develop a generalized sensing platform that could be used for a variety of sensing applications, including oxygen sensing, but also potentially involving CO2 or NOx as well. Future efforts will involve completing of O2 sensor construction and adaption of the design for CO2 and NOx sensing. The final project focuses on a novel ammonia sensor and sensing mechanism in Ag loaded zeolite Y. The sensor resistance changes upon exposure to ammonia due to the molecular recognition of Ag+ and ammonia, producing Ag(NH3)x+ species. The sensing mechanism is a Grothuss like mechanism based on the hoping of Ag+ centers. The hopping frequency of Ag+ changes upon introduction of ammonia due to the reduced electrostatic interactions between Ag+ and the negatively charged zeolite framework upon formation of Ag(NH3) x+. The change in hopping frequency results in a measurable change in impedance.

  20. The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China.

    PubMed

    Li, Xiangdong; Zhu, Tiansheng; Yin, Xiao; Zhang, Chengling; Chen, Jia; Tian, Yanping; Liu, Jinliang

    2017-08-29

    Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis. To understand the genetic structure of TuMV from radish in China, the 3'-terminal genome of 90 TuMV isolates were determined and analyzed with other available Chinese isolates. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai'an, Weifang and Changchun was frequent. The genetic structure of Turnip mosaic virus population reveals the rapid expansion of a new emergent lineage in China.

  1. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous-Paleogene boundary.

    PubMed

    Feng, Yan-Jie; Blackburn, David C; Liang, Dan; Hillis, David M; Wake, David B; Cannatella, David C; Zhang, Peng

    2017-07-18

    Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

  2. Evolvable synthetic neural system

    NASA Technical Reports Server (NTRS)

    Curtis, Steven A. (Inventor)

    2009-01-01

    An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

  3. Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

    PubMed Central

    Feng, Yan-Jie; Liang, Dan; Hillis, David M.; Cannatella, David C.; Zhang, Peng

    2017-01-01

    Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. PMID:28673970

  4. Carbon and Nitrogen Isotopes from Top Predator Amino Acids Reveal Rapidly Shifting Ocean Biochemistry in the Outer California Current

    PubMed Central

    Ruiz-Cooley, Rocio I.; Koch, Paul L.; Fiedler, Paul C.; McCarthy, Matthew D.

    2014-01-01

    Climatic variation alters biochemical and ecological processes, but it is difficult both to quantify the magnitude of such changes, and to differentiate long-term shifts from inter-annual variability. Here, we simultaneously quantify decade-scale isotopic variability at the lowest and highest trophic positions in the offshore California Current System (CCS) by measuring δ15N and δ13C values of amino acids in a top predator, the sperm whale (Physeter macrocephalus). Using a time series of skin tissue samples as a biological archive, isotopic records from individual amino acids (AAs) can reveal the proximate factors driving a temporal decline we observed in bulk isotope values (a decline of ≥1 ‰) by decoupling changes in primary producer isotope values from those linked to the trophic position of this toothed whale. A continuous decline in baseline (i.e., primary producer) δ15N and δ13C values was observed from 1993 to 2005 (a decrease of ∼4‰ for δ15N source-AAs and 3‰ for δ13C essential-AAs), while the trophic position of whales was variable over time and it did not exhibit directional trends. The baseline δ15N and δ13C shifts suggest rapid ongoing changes in the carbon and nitrogen biogeochemical cycling in the offshore CCS, potentially occurring at faster rates than long-term shifts observed elsewhere in the Pacific. While the mechanisms forcing these biogeochemical shifts remain to be determined, our data suggest possible links to natural climate variability, and also corresponding shifts in surface nutrient availability. Our study demonstrates that isotopic analysis of individual amino acids from a top marine mammal predator can be a powerful new approach to reconstructing temporal variation in both biochemical cycling and trophic structure. PMID:25329915

  5. Carbon and nitrogen isotopes from top predator amino acids reveal rapidly shifting ocean biochemistry in the outer California Current.

    PubMed

    Ruiz-Cooley, Rocio I; Koch, Paul L; Fiedler, Paul C; McCarthy, Matthew D

    2014-01-01

    Climatic variation alters biochemical and ecological processes, but it is difficult both to quantify the magnitude of such changes, and to differentiate long-term shifts from inter-annual variability. Here, we simultaneously quantify decade-scale isotopic variability at the lowest and highest trophic positions in the offshore California Current System (CCS) by measuring δ15N and δ13C values of amino acids in a top predator, the sperm whale (Physeter macrocephalus). Using a time series of skin tissue samples as a biological archive, isotopic records from individual amino acids (AAs) can reveal the proximate factors driving a temporal decline we observed in bulk isotope values (a decline of ≥1 ‰) by decoupling changes in primary producer isotope values from those linked to the trophic position of this toothed whale. A continuous decline in baseline (i.e., primary producer) δ15N and δ13C values was observed from 1993 to 2005 (a decrease of ∼4‰ for δ15N source-AAs and 3‰ for δ13C essential-AAs), while the trophic position of whales was variable over time and it did not exhibit directional trends. The baseline δ15N and δ13C shifts suggest rapid ongoing changes in the carbon and nitrogen biogeochemical cycling in the offshore CCS, potentially occurring at faster rates than long-term shifts observed elsewhere in the Pacific. While the mechanisms forcing these biogeochemical shifts remain to be determined, our data suggest possible links to natural climate variability, and also corresponding shifts in surface nutrient availability. Our study demonstrates that isotopic analysis of individual amino acids from a top marine mammal predator can be a powerful new approach to reconstructing temporal variation in both biochemical cycling and trophic structure.

  6. Systems Biology Analysis of Brucella Infected Peyer's Patch Reveals Rapid Invasion with Modest Transient Perturbations of the Host Transcriptome

    PubMed Central

    Rossetti, Carlos A.; Drake, Kenneth L.; Siddavatam, Prasad; Lawhon, Sara D.; Nunes, Jairo E. S.; Gull, Tamara; Khare, Sangeeta; Everts, Robin E.; Lewin, Harris A.; Adams, Leslie Garry

    2013-01-01

    Brucella melitensis causes the most severe and acute symptoms of all Brucella species in human beings and infects hosts primarily through the oral route. The epithelium covering domed villi of jejunal-ileal Peyer's patches is an important site of entry for several pathogens, including Brucella. Here, we use the calf ligated ileal loop model to study temporal in vivo Brucella-infected host molecular and morphological responses. Our results document Brucella bacteremia occurring within 30 min after intraluminal inoculation of the ileum without histopathologic traces of lesions. Based on a system biology Dynamic Bayesian Network modeling approach (DBN) of microarray data, a very early transient perturbation of the host enteric transcriptome was associated with the initial host response to Brucella contact that is rapidly averted allowing invasion and dissemination. A detailed analysis revealed active expression of Syndecan 2, Integrin alpha L and Integrin beta 2 genes, which may favor initial Brucella adhesion. Also, two intestinal barrier-related pathways (Tight Junction and Trefoil Factors Initiated Mucosal Healing) were significantly repressed in the early stage of infection, suggesting subversion of mucosal epithelial barrier function to facilitate Brucella transepithelial migration. Simultaneously, the strong activation of the innate immune response pathways would suggest that the host mounts an appropriate protective immune response; however, the expression of the two key genes that encode innate immunity anti-Brucella cytokines such as TNF-α and IL12p40 were not significantly changed throughout the study. Furthermore, the defective expression of Toll-Like Receptor Signaling pathways may partially explain the lack of proinflammatory cytokine production and consequently the absence of morphologically detectable inflammation at the site of infection. Cumulatively, our results indicate that the in vivo pathogenesis of the early infectious process of Brucella is

  7. Systems biology analysis of Brucella infected Peyer's patch reveals rapid invasion with modest transient perturbations of the host transcriptome.

    PubMed

    Rossetti, Carlos A; Drake, Kenneth L; Siddavatam, Prasad; Lawhon, Sara D; Nunes, Jairo E S; Gull, Tamara; Khare, Sangeeta; Everts, Robin E; Lewin, Harris A; Adams, Leslie Garry

    2013-01-01

    Brucella melitensis causes the most severe and acute symptoms of all Brucella species in human beings and infects hosts primarily through the oral route. The epithelium covering domed villi of jejunal-ileal Peyer's patches is an important site of entry for several pathogens, including Brucella. Here, we use the calf ligated ileal loop model to study temporal in vivo Brucella-infected host molecular and morphological responses. Our results document Brucella bacteremia occurring within 30 min after intraluminal inoculation of the ileum without histopathologic traces of lesions. Based on a system biology Dynamic Bayesian Network modeling approach (DBN) of microarray data, a very early transient perturbation of the host enteric transcriptome was associated with the initial host response to Brucella contact that is rapidly averted allowing invasion and dissemination. A detailed analysis revealed active expression of Syndecan 2, Integrin alpha L and Integrin beta 2 genes, which may favor initial Brucella adhesion. Also, two intestinal barrier-related pathways (Tight Junction and Trefoil Factors Initiated Mucosal Healing) were significantly repressed in the early stage of infection, suggesting subversion of mucosal epithelial barrier function to facilitate Brucella transepithelial migration. Simultaneously, the strong activation of the innate immune response pathways would suggest that the host mounts an appropriate protective immune response; however, the expression of the two key genes that encode innate immunity anti-Brucella cytokines such as TNF-α and IL12p40 were not significantly changed throughout the study. Furthermore, the defective expression of Toll-Like Receptor Signaling pathways may partially explain the lack of proinflammatory cytokine production and consequently the absence of morphologically detectable inflammation at the site of infection. Cumulatively, our results indicate that the in vivo pathogenesis of the early infectious process of Brucella is

  8. Natural selection promotes antigenic evolvability.

    PubMed

    Graves, Christopher J; Ros, Vera I D; Stevenson, Brian; Sniegowski, Paul D; Brisson, Dustin

    2013-01-01

    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.

  9. Sequencing of the Chlamydophila psittaci ompA Gene Reveals a New Genotype, E/B, and the Need for a Rapid Discriminatory Genotyping Method

    PubMed Central

    Geens, Tom; Desplanques, Ann; Van Loock, Marnix; Bönner, Brigitte M.; Kaleta, Erhard F.; Magnino, Simone; Andersen, Arthur A.; Everett, Karin D. E.; Vanrompay, Daisy

    2005-01-01

    Twenty-one avian Chlamydophila psittaci isolates from different European countries were characterized using ompA restriction fragment length polymorphism, ompA sequencing, and major outer membrane protein serotyping. Results reveal the presence of a new genotype, E/B, in several European countries and stress the need for a discriminatory rapid genotyping method. PMID:15872282

  10. Languages evolve in punctuational bursts.

    PubMed

    Atkinson, Quentin D; Meade, Andrew; Venditti, Chris; Greenhill, Simon J; Pagel, Mark

    2008-02-01

    Linguists speculate that human languages often evolve in rapid or punctuational bursts, sometimes associated with their emergence from other languages, but this phenomenon has never been demonstrated. We used vocabulary data from three of the world's major language groups-Bantu, Indo-European, and Austronesian-to show that 10 to 33% of the overall vocabulary differences among these languages arose from rapid bursts of change associated with language-splitting events. Our findings identify a general tendency for increased rates of linguistic evolution in fledgling languages, perhaps arising from a linguistic founder effect or a desire to establish a distinct social identity.

  11. Nuclear transit studies of patients with intractable chronic constipation reveal a subgroup with rapid proximal colonic transit.

    PubMed

    Yik, Yee Ian; Cain, Timothy M; Tudball, Coral F; Cook, David J; Southwell, Bridget R; Hutson, John M

    2011-07-01

    Nuclear transit studies (NTS) allow us to follow transit through the stomach and the small and large intestines. We identified children with chronic constipation with rapid proximal colonic transit and characterized their clinical features. We reviewed NTS from 1998 to 2009 to identify patients with chronic constipation and rapid proximal colonic transit, defined as greater than 25% of tracer beyond hepatic flexure at 6 hour and/or greater than 25% of tracer beyond end of descending colon at 24 hour. This was correlated with clinical symptoms and outcome from patient records. Five hundred twenty children with chronic constipation underwent investigation by NTS, and 64 (12%) were identified with rapid proximal colonic transit. The clinical history, symptoms, and outcome in 55 of 64 available for analysis frequently showed family history of allergy (10.9%) and symptoms associated with food allergy/intolerance: abdominal pain (80%), anal fissure (27.3%), and other allergic symptoms (43.6%). Eighteen children were treated with dietary exclusion, with resolution of symptoms in 9 (50%). Some children with intractable chronic constipation have rapid proximal colonic transit, have symptoms consistent with possible food allergy/intolerance, and may respond to dietary exclusion. The NTS can identify these patients with rapid proximal transit that may be secondary to food intolerance. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes.

    Treesearch

    Richard C. Cronn; Randall L. Small; Tamara Hanselkorn; Jonathan F. Wendel

    2002-01-01

    Previous molecular phylogenetic studies have failed to resolve the branching order among the major cotton (Gossypium) lineages, and it has been unclear whether this reflects actual history (rapid radiation) or sampling properties of the genes evaluated. In this paper, we reconsider the phylogenetic relationships of diploid cotton genome groups using DNA sequences from...

  13. How evolvable are polarization machines?

    NASA Astrophysics Data System (ADS)

    Laan, Liedewij; Murray, Andrew

    2012-02-01

    In many different cell types proper polarization is essential for cell function. Polarization mechanisms however, differ between cell types and even closely related species use a variety of polarization machines. Budding yeast, for example, depends on several parallel mechanisms to establish polarity. One mechanism (i) depends on reaction and diffusion of proteins in the membrane. Another one (ii) depends on reorganization of the actin cytoskeleton. So why does yeast use several mechanisms simultaneously? Can yeast also polarize robustly in the absence of one of them? We addressed these questions by evolving budding yeast in the absence of mechanism (i) or (ii). We deleted a mechanism by deleting one or two genes that are essential for its function. After the deletion of either mechanism the growth rate of cells was highly decreased (2-5 fold) and their cell shape was highly perturbed. Subsequently, we evolved these cells for 10 days. Surprisingly, the evolved cells rapidly overcame most of their polarity defects. They grow at 0.9x wildtype growth rate and their cell shape is signifigantly less perturbed. Now we will study how these cells rescued polarization. Did they fix the deleted mechanism, strengthen other mechanisms or evolve a completely new one?

  14. Chess players' eye movements reveal rapid recognition of complex visual patterns: Evidence from a chess-related visual search task.

    PubMed

    Sheridan, Heather; Reingold, Eyal M

    2017-03-01

    To explore the perceptual component of chess expertise, we monitored the eye movements of expert and novice chess players during a chess-related visual search task that tested anecdotal reports that a key differentiator of chess skill is the ability to visualize the complex moves of the knight piece. Specifically, chess players viewed an array of four minimized chessboards, and they rapidly searched for the target board that allowed a knight piece to reach a target square in three moves. On each trial, there was only one target board (i.e., the "Yes" board), and for the remaining "lure" boards, the knight's path was blocked on either the first move (the "Easy No" board) or the second move (i.e., "the Difficult No" board). As evidence that chess experts can rapidly differentiate complex chess-related visual patterns, the experts (but not the novices) showed longer first-fixation durations on the "Yes" board relative to the "Difficult No" board. Moreover, as hypothesized, the task strongly differentiated chess skill: Reaction times were more than four times faster for the experts relative to novices, and reaction times were correlated with within-group measures of expertise (i.e., official chess ratings, number of hours of practice). These results indicate that a key component of chess expertise is the ability to rapidly recognize complex visual patterns.

  15. High-resolution lipidomics coupled with rapid fixation reveals novel ischemia-induced signaling in the rat neurolipidome.

    PubMed

    Trépanier, Marc-Olivier; Eiden, Michael; Morin-Rivron, Delphine; Bazinet, Richard P; Masoodi, Mojgan

    2017-03-01

    The field of lipidomics has evolved vastly since its creation 15 years ago. Advancements in mass spectrometry have allowed for the identification of hundreds of intact lipids and lipid mediators. However, because of the release of fatty acids from the phospholipid membrane in the brain caused by ischemia, identifying the neurolipidome has been challenging. Microwave fixation has been shown to reduce the ischemia-induced release of several lipid mediators. Therefore, this study aimed to develop a method combining high-resolution tandem mass spectrometry (MS/MS), high-energy head-focused microwave fixation and statistical modeling, allowing for the measurement of intact lipids and lipid mediators in order to eliminate the ischemia-induced release of fatty acids and identify the rat neurolipidome. In this study, we demonstrated the ischemia-induced production of bioactive lipid mediators, and the reduction in variability using microwave fixation in combination with liquid chromatography (LC)-MS/MS. We have also illustrated for the first time that microwave fixation eliminates the alterations in intact lipid species following ischemia. While many phospholipid species were unchanged by ischemia, other intact lipid classes, such as diacylglycerol, were lower in concentration following microwave fixation compared to ischemia. © 2016 International Society for Neurochemistry.

  16. Phosphoproteome Dynamics Upon Changes in Plant Water Status Reveal Early Events Associated With Rapid Growth Adjustment in Maize Leaves*

    PubMed Central

    Bonhomme, Ludovic; Valot, Benoît; Tardieu, François; Zivy, Michel

    2012-01-01

    Plant growth adjustment during water deficit is a crucial adaptive response. The rapid fine-tuned control achieved at the post-translational level is believed to be of considerable importance for regulating early changes in plant growth reprogramming. Aiming at a better understanding of early responses to contrasting plant water statuses, we carried out a survey of the protein phosphorylation events in the growing zone of maize leaves upon a range of water regimes. In this study, the impact of mild and severe water deficits were evaluated in comparison with constant optimal watering and with recovery periods lasting 5, 10, 20, 30, 45, and 60 min. Using four biological replicates per treatment and a robust quantitative phosphoproteomic methodology based on stable-isotope labeling, we identified 3664 unique phosphorylation sites on 2496 proteins. The abundance of nearly 1250 phosphorylated peptides was reproducibly quantified and profiled with high confidence among treatments. A total of 138 phosphopeptides displayed highly significant changes according to water regimes and enabled to identify specific patterns of response to changing plant water statuses. Further quantification of protein amounts emphasized that most phosphorylation changes did not reflect protein abundance variation. During water deficit and recovery, extensive changes in phosphorylation status occurred in critical regulators directly or indirectly involved in plant growth and development. These included proteins influencing epigenetic control, gene expression, cell cycle-dependent processes and phytohormone-mediated responses. Some of the changes depended on stress intensity whereas others depended on rehydration duration, including rapid recoveries that occurred as early as 5 or 10 mins after rewatering. By combining a physiological approach and a quantitative phosphoproteomic analysis, this work provides new insights into the in vivo early phosphorylation events triggered by rapid changes in

  17. Flexible, rapid and automatic neocortical word form acquisition mechanism in children as revealed by neuromagnetic brain response dynamics.

    PubMed

    Partanen, Eino; Leminen, Alina; de Paoli, Stine; Bundgaard, Anette; Skjold Kingo, Osman; Krøjgaard, Peter; Shtyrov, Yury

    2017-04-04

    Children learn new words and word forms with ease, often acquiring a new word after very few repetitions. Recent neurophysiological research on word form acquisition in adults indicates that novel words can be acquired within minutes of repetitive exposure to them, regardless of the individual's focused attention on the speech input. Although it is well-known that children surpass adults in language acquisition, the developmental aspects of such rapid and automatic neural acquisition mechanisms remain unexplored. To address this open question, we used magnetoencephalography (MEG) to scrutinise brain dynamics elicited by spoken words and word-like sounds in healthy monolingual (Danish) children throughout a 20-minute repetitive passive exposure session. We found rapid neural dynamics manifested as an enhancement of early (~100 ms) brain activity over the short exposure session, with distinct spatiotemporal patterns for different novel sounds. For novel Danish word forms, signs of such enhancement were seen in the left temporal regions only, suggesting reliance on pre-existing language circuits for acquisition of novel word forms with native phonology. In contrast, exposure both to novel word forms with non-native phonology and to novel non-speech sounds led to activity enhancement in both left and right hemispheres, suggesting that more wide-spread cortical networks contribute to the build-up of memory traces for non-native and non-speech sounds. Similar studies in adults have previously reported more sluggish (~15-25minutes, as opposed to 4minutes in the present study) or non-existent neural dynamics for non-native sound acquisition, which might be indicative of a higher degree of plasticity in the children's brain. Overall, the results indicate a rapid and highly plastic mechanism for a dynamic build-up of memory traces for novel acoustic information in the children's brain that operates automatically and recruits bilateral temporal cortical circuits.

  18. Phosphoproteome dynamics upon changes in plant water status reveal early events associated with rapid growth adjustment in maize leaves.

    PubMed

    Bonhomme, Ludovic; Valot, Benoît; Tardieu, François; Zivy, Michel

    2012-10-01

    Plant growth adjustment during water deficit is a crucial adaptive response. The rapid fine-tuned control achieved at the post-translational level is believed to be of considerable importance for regulating early changes in plant growth reprogramming. Aiming at a better understanding of early responses to contrasting plant water statuses, we carried out a survey of the protein phosphorylation events in the growing zone of maize leaves upon a range of water regimes. In this study, the impact of mild and severe water deficits were evaluated in comparison with constant optimal watering and with recovery periods lasting 5, 10, 20, 30, 45, and 60 min. Using four biological replicates per treatment and a robust quantitative phosphoproteomic methodology based on stable-isotope labeling, we identified 3664 unique phosphorylation sites on 2496 proteins. The abundance of nearly 1250 phosphorylated peptides was reproducibly quantified and profiled with high confidence among treatments. A total of 138 phosphopeptides displayed highly significant changes according to water regimes and enabled to identify specific patterns of response to changing plant water statuses. Further quantification of protein amounts emphasized that most phosphorylation changes did not reflect protein abundance variation. During water deficit and recovery, extensive changes in phosphorylation status occurred in critical regulators directly or indirectly involved in plant growth and development. These included proteins influencing epigenetic control, gene expression, cell cycle-dependent processes and phytohormone-mediated responses. Some of the changes depended on stress intensity whereas others depended on rehydration duration, including rapid recoveries that occurred as early as 5 or 10 mins after rewatering. By combining a physiological approach and a quantitative phosphoproteomic analysis, this work provides new insights into the in vivo early phosphorylation events triggered by rapid changes in

  19. Spatiotemporal characteristics of form analysis in the human visual cortex revealed by rapid event-related fMRI adaptation.

    PubMed

    Kourtzi, Zoe; Huberle, Elisabeth

    2005-11-01

    The integration of local elements to coherent forms is at the core of understanding visual perception. Accumulating evidence suggests that both early retinotopic and higher occipitotemporal areas contribute to the integration of local elements to global forms. However, the spatiotemporal characteristics of form analysis in the human visual cortex remain largely unknown. The aim of this study was to investigate form analysis at different spatial (global vs. local structure) and temporal (different stimulus presentation rates) scales across stages of visual analysis (from V1 to the lateral occipital complex-LOC) in the human brain. We used closed contours rendered by Gabor elements and manipulated either the global contour structure or the orientation of the local Gabor elements. Our rapid event-related fMRI adaptation studies suggest that contour integration and form processing in early visual areas is transient and limited within the local neighborhood of their cells' receptive field. In contrast, higher visual areas appear to process the perceived global form in a more sustained manner. Finally, we demonstrate that these spatiotemporal properties of form processing in the visual cortex are modulated by attention. Attention to the global form maintains sustained processing in occipitotemporal areas, whereas attention to local elements enhances their integration in early visual areas. These findings provide novel neuroimaging evidence for form analysis at different spatiotemporal scales across human visual areas and validate the use of rapid event-related fMRI adaptation for investigating processing across stages of visual analysis in the human brain.

  20. Fluorescence-Tracking of Activation Gating in Human ERG Channels Reveals Rapid S4 Movement and Slow Pore Opening

    PubMed Central

    Xiong, Ping Yu; Robertson, Gail A.; Fedida, David

    2010-01-01

    Background hERG channels are physiologically important ion channels which mediate cardiac repolarization as a result of their unusual gating properties. These are very slow activation compared with other mammalian voltage-gated potassium channels, and extremely rapid inactivation. The mechanism of slow activation is not well understood and is investigated here using fluorescence as a direct measure of S4 movement and pore opening. Methods and Findings Tetramethylrhodamine-5-maleimide (TMRM) fluorescence at E519 has been used to track S4 voltage sensor movement, and channel opening and closing in hERG channels. Endogenous cysteines (C445 and C449) in the S1–S2 linker bound TMRM, which caused a 10 mV hyperpolarization of the V½ of activation to −27.5±2.0 mV, and showed voltage-dependent fluorescence signals. Substitution of S1–S2 linker cysteines with valines allowed unobstructed recording of S3–S4 linker E519C and L520C emission signals. Depolarization of E519C channels caused rapid initial fluorescence quenching, fit with a double Boltzmann relationship, F-VON, with V½,1 = −37.8±1.7 mV, and V½,2 = 43.5±7.9 mV. The first phase, V½,1, was ∼20 mV negative to the conductance-voltage relationship measured from ionic tail currents (G-V½ = −18.3±1.2 mV), and relatively unchanged in a non-inactivating E519C:S620T mutant (V½ = −34.4±1.5 mV), suggesting the fast initial fluorescence quenching tracked S4 voltage sensor movement. The second phase of rapid quenching was absent in the S620T mutant. The E519C fluorescence upon repolarization (V½ = −20.6±1.2, k = 11.4 mV) and L520C quenching during depolarization (V½ = −26.8±1.0, k = 13.3 mV) matched the respective voltage dependencies of hERG ionic tails, and deactivation time constants from −40 to −110 mV, suggesting they detected pore-S4 rearrangements related to ionic current flow during pore opening and closing. Conclusion The data indicate: 1) that rapid

  1. Automated analysis of connected speech reveals early biomarkers of Parkinson's disease in patients with rapid eye movement sleep behaviour disorder.

    PubMed

    Hlavnička, Jan; Čmejla, Roman; Tykalová, Tereza; Šonka, Karel; Růžička, Evžen; Rusz, Jan

    2017-02-02

    For generations, the evaluation of speech abnormalities in neurodegenerative disorders such as Parkinson's disease (PD) has been limited to perceptual tests or user-controlled laboratory analysis based upon rather small samples of human vocalizations. Our study introduces a fully automated method that yields significant features related to respiratory deficits, dysphonia, imprecise articulation and dysrhythmia from acoustic microphone data of natural connected speech for predicting early and distinctive patterns of neurodegeneration. We compared speech recordings of 50 subjects with rapid eye movement sleep behaviour disorder (RBD), 30 newly diagnosed, untreated PD patients and 50 healthy controls, and showed that subliminal parkinsonian speech deficits can be reliably captured even in RBD patients, which are at high risk of developing PD or other synucleinopathies. Thus, automated vocal analysis should soon be able to contribute to screening and diagnostic procedures for prodromal parkinsonian neurodegeneration in natural environments.

  2. Rapid rotations about a vertical axis in a collisional setting revealed by the Palu Fault, Sulawesi, Indonesia

    NASA Astrophysics Data System (ADS)

    Stevens, C.; McCaffrey, R.; Bock, Y.; Genrich, J.; Endang, null; Subarya, C.; Puntodewo, S. S. O.; Fauzi, null; Vigny, C.

    Global Positioning System (GPS) measurements from 1992 to 1995 indicate that the left-lateral Palu fault in central Sulawesi slips at a rate of 38±8 mm/a with a locking depth between 2 and 8 km. From the measured slip rate and the historic seismicity of the fault, we estimate that the Palu fault currently has stored enough strain to produce a Mw>7 earthquake. The Palu and other nearby faults accommodate rapid clockwise rotation of nearly 4°/Ma of E Sulawesi relative to eastern Sunda. The rotation of east Sulawesi transfers E-W shortening between the Pacific and Eurasian plates to N-S subduction of the Celebes Basin beneath Sulawesi.

  3. Auditory evoked fields measured noninvasively with small-animal MEG reveal rapid repetition suppression in the guinea pig

    PubMed Central

    Christianson, G. Björn; Chait, Maria; de Cheveigné, Alain

    2014-01-01

    In animal models, single-neuron response properties such as stimulus-specific adaptation have been described as possible precursors to mismatch negativity, a human brain response to stimulus change. In the present study, we attempted to bridge the gap between human and animal studies by characterising responses to changes in the frequency of repeated tone series in the anesthetised guinea pig using small-animal magnetoencephalography (MEG). We showed that 1) auditory evoked fields (AEFs) qualitatively similar to those observed in human MEG studies can be detected noninvasively in rodents using small-animal MEG; 2) guinea pig AEF amplitudes reduce rapidly with tone repetition, and this AEF reduction is largely complete by the second tone in a repeated series; and 3) differences between responses to the first (deviant) and later (standard) tones after a frequency transition resemble those previously observed in awake humans using a similar stimulus paradigm. PMID:25231619

  4. Dissolved O2/Ar and other methods reveal rapid changes in productivity during a Lagrangian experiment in the Southern Ocean

    NASA Astrophysics Data System (ADS)

    Hamme, Roberta C.; Cassar, Nicolas; Lance, Veronica P.; Vaillancourt, Robert D.; Bender, Michael L.; Strutton, Peter G.; Moore, Tommy S.; Degrandpre, Michael D.; Sabine, Christopher L.; Ho, David T.; Hargreaves, Bruce R.

    2012-04-01

    We use continuous and discrete measurements of the dissolved O2/Ar ratio in the mixed layer to investigate the dynamics of biological productivity during the Southern Ocean Gas Exchange Experiment in March and April 2008. Injections of SF6 defined two water masses (patches) that were followed for up to 2 weeks. In the first patch, dissolved O2/Ar was supersaturated, indicating net biological production of organic carbon. In the second patch, rapidly decreasing O2/Ar could only be reasonably explained if the mixed layer was experiencing a period of net heterotrophy. The observations rule out dominant contributions from vertical mixing, lateral dilution, or respiration in the ship's underway seawater supply lines. We also compare nine different estimates of net community, new, primary, or gross production made during the experiment. Net community and new production estimates agreed well in the first patch but disagreed in the second patch, both during an initial net heterotrophic period but also during the apparently autotrophic period at the end of the observations. Rapidly changing productivity during the second patch complicated the comparison of methods that integrate over daily and several week timescales. Primary productivity values from on-deck 24 h 14C incubations and gross carbon production values from photosynthesis-irradiance experiments were nearly identical even during highly dynamic periods of net heterotrophy, while gross oxygen production measurements were 3.5-4.2 times higher but with uncertainties in that ratio near ±2. These comparisons show that the photosynthesis-irradiance experiments based on 1-2 h 14C incubations underestimated gross carbon production.

  5. Whole Exome Sequencing of Rapid Autopsy Tumors and Xenograft Models Reveals Possible Driver Mutations Underlying Tumor Progression

    PubMed Central

    Xie, Tao; Musteanu, Monica; Lopez-Casas, Pedro P.; Shields, David J.; Olson, Peter; Rejto, Paul A.; Hidalgo, Manuel

    2015-01-01

    Pancreatic Ductal Adenocarcinoma (PDAC) is a highly lethal malignancy due to its propensity to invade and rapidly metastasize and remains very difficult to manage clinically. One major hindrance towards a better understanding of PDAC is the lack of molecular data sets and models representative of end stage disease. Moreover, it remains unclear how molecularly similar patient-derived xenograft (PDX) models are to the primary tumor from which they were derived. To identify potential molecular drivers in metastatic pancreatic cancer progression, we obtained matched primary tumor, metastases and normal (peripheral blood) samples under a rapid autopsy program and performed whole exome sequencing (WES) on tumor as well as normal samples. PDX models were also generated, sequenced and compared to tumors. Across the matched data sets generated for three patients, there were on average approximately 160 single-nucleotide mutations in each sample. The majority of mutations in each patient were shared among the primary and metastatic samples and, importantly, were largely retained in the xenograft models. Based on the mutation prevalence in the primary and metastatic sites, we proposed possible clonal evolution patterns marked by functional mutations affecting cancer genes such as KRAS, TP53 and SMAD4 that may play an important role in tumor initiation, progression and metastasis. These results add to our understanding of pancreatic tumor biology, and demonstrate that PDX models derived from advanced or end-stage likely closely approximate the genetics of the disease in the clinic and thus represent a biologically and clinically relevant pre-clinical platform that may enable the development of effective targeted therapies for PDAC. PMID:26555578

  6. Rapid environmental change over the past decade revealed by isotopic analysis of the California mussel in the northeast Pacific.

    PubMed

    Pfister, Catherine A; McCoy, Sophie J; Wootton, J Timothy; Martin, Pamela A; Colman, Albert S; Archer, David

    2011-01-01

    The anthropogenic input of fossil fuel carbon into the atmosphere results in increased carbon dioxide (CO(2)) into the oceans, a process that lowers seawater pH, decreases alkalinity and can inhibit the production of shell material. Corrosive water has recently been documented in the northeast Pacific, along with a rapid decline in seawater pH over the past decade. A lack of instrumentation prior to the 1990s means that we have no indication whether these carbon cycle changes have precedence or are a response to recent anthropogenic CO(2) inputs. We analyzed stable carbon and oxygen isotopes (δ(13)C, δ(18)O) of decade-old California mussel shells (Mytilus californianus) in the context of an instrumental seawater record of the same length. We further compared modern shells to shells from 1000 to 1340 years BP and from the 1960s to the present and show declines in the δ(13)C of modern shells that have no historical precedent. Our finding of decline in another shelled mollusk (limpet) and our extensive environmental data show that these δ(13)C declines are unexplained by changes to the coastal food web, upwelling regime, or local circulation. Our observed decline in shell δ(13)C parallels other signs of rapid changes to the nearshore carbon cycle in the Pacific, including a decline in pH that is an order of magnitude greater than predicted by an equilibrium response to rising atmospheric CO(2), the presence of low pH water throughout the region, and a record of a similarly steep decline in δ(13)C in algae in the Gulf of Alaska. These unprecedented changes and the lack of a clear causal variable underscores the need for better quantifying carbon dynamics in nearshore environments.

  7. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders

    PubMed Central

    Fitzpatrick, Benjamin M; Johnson, Jarrett R; Kump, D Kevin; Shaffer, H Bradley; Smith, Jeramiah J; Voss, S Randal

    2009-01-01

    Background Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders. Results At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects. Conclusion While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain. PMID:19630983

  8. Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders.

    PubMed

    Fitzpatrick, Benjamin M; Johnson, Jarrett R; Kump, D Kevin; Shaffer, H Bradley; Smith, Jeramiah J; Voss, S Randal

    2009-07-24

    Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders. At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects. While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain.

  9. Traction force microscopy in rapidly moving cells reveals separate roles for ROCK and MLCK in the mechanics of retraction.

    PubMed

    Morin, Timothy R; Ghassem-Zadeh, Sean A; Lee, Juliet

    2014-08-15

    Retraction is a major rate-limiting step in cell motility, particularly in slow moving cell types that form large stable adhesions. Myosin II dependent contractile forces are thought to facilitate detachment by physically pulling up the rear edge. However, retraction can occur in the absence of myosin II activity in cell types that form small labile adhesions. To investigate the role of contractile force generation in retraction, we performed traction force microscopy during the movement of fish epithelial keratocytes. By correlating changes in local traction stress at the rear with the area retracted, we identified four distinct modes of retraction. "Recoil" retractions are preceded by a rise in local traction stress, while rear edge is temporarily stuck, followed by a sharp drop in traction stress upon detachment. This retraction type was most common in cells generating high average traction stress. In "pull" type retractions local traction stress and area retracted increase concomitantly. This was the predominant type of retraction in keratocytes and was observed mostly in cells generating low average traction stress. "Continuous" type retractions occur without any detectable change in traction stress, and are seen in cells generating low average traction stress. In contrast, to many other cell types, "release" type retractions occur in keratocytes following a decrease in local traction stress. Our identification of distinct modes of retraction suggests that contractile forces may play different roles in detachment that are related to rear adhesion strength. To determine how the regulation of contractility via MLCK or Rho kinase contributes to the mechanics of detachment, inhibitors were used to block or augment these pathways. Modulation of MLCK activity led to the most rapid change in local traction stress suggesting its importance in regulating attachment strength. Surprisingly, Rho kinase was not required for detachment, but was essential for localizing

  10. Cross-hole tracer experiment reveals rapid fluid flow and low effective porosity in the upper oceanic crust

    NASA Astrophysics Data System (ADS)

    Neira, N. M.; Clark, J. F.; Fisher, A. T.; Wheat, C. G.; Haymon, R. M.; Becker, K.

    2016-09-01

    Numerous field, laboratory, and modeling studies have explored the flows of fluid, heat, and solutes during seafloor hydrothermal circulation, but it has been challenging to determine transport rates and flow directions within natural systems. Here we present results from the first cross-hole tracer experiment in the upper oceanic crust, using four subseafloor borehole observatories equipped with autonomous samplers to track the transport of a dissolved tracer (sulfur hexafluoride, SF6) injected into a ridge-flank hydrothermal system. During the first three years after tracer injection, SF6 was transported both north and south through the basaltic aquifer. The observed tracer transport rate of ∼2-3 m/day is orders of magnitude greater than bulk rates of flow inferred from thermal and chemical observations and calculated with coupled fluid-heat flow simulations. Taken together, these results suggest that the effective porosity of the upper volcanic crust through which much tracer was transported is <1%, with fluid flowing rapidly along a few well-connected channels. This is consistent with the heterogeneous (layered, faulted, and/or fractured) nature of the volcanic upper oceanic crust.

  11. Depth investigation of rapid sand filters for drinking water production reveals strong stratification in nitrification biokinetic behavior.

    PubMed

    Tatari, K; Smets, B F; Albrechtsen, H-J

    2016-09-15

    The biokinetic behavior of NH4(+) removal was investigated at different depths of a rapid sand filter treating groundwater for drinking water preparation. Filter materials from the top, middle and bottom layers of a full-scale filter were exposed to various controlled NH4(+) loadings in a continuous-flow lab-scale assay. NH4(+) removal capacity, estimated from short term loading up-shifts, was at least 10 times higher in the top than in the middle and bottom filter layers, consistent with the stratification of Ammonium Oxidizing Bacteria (AOB). AOB density increased consistently with the NH4(+) removal rate, indicating their primarily role in nitrification under the imposed experimental conditions. The maximum AOB cell specific NH4(+) removal rate observed at the bottom was at least 3 times lower compared to the top and middle layers. Additionally, a significant up-shift capacity (4.6 and 3.5 times) was displayed from the top and middle layers, but not from the bottom layer at increased loading conditions. Hence, AOB with different physiological responses were active at the different depths. The biokinetic analysis predicted that despite the low NH4(+) removal capacity at the bottom layer, the entire filter is able to cope with a 4-fold instantaneous loading increase without compromising the effluent NH4(+). Ultimately, this filter up-shift capacity was limited by the density of AOB and their biokinetic behavior, both of which were strongly stratified. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Global field synchronization reveals rapid eye movement sleep as most synchronized brain state in the human EEG.

    PubMed

    Achermann, Peter; Rusterholz, Thomas; Dürr, Roland; König, Thomas; Tarokh, Leila

    2016-10-01

    Sleep is characterized by a loss of consciousness, which has been attributed to a breakdown of functional connectivity between brain regions. Global field synchronization (GFS) can estimate functional connectivity of brain processes. GFS is a frequency-dependent measure of global synchronicity of multi-channel EEG data. Our aim was to explore and extend the hypothesis of disconnection during sleep by comparing GFS spectra of different vigilance states. The analysis was performed on eight healthy adult male subjects. EEG was recorded during a baseline night, a recovery night after 40 h of sustained wakefulness and at 3 h intervals during the 40 h of wakefulness. Compared to non-rapid eye movement (NREM) sleep, REM sleep showed larger GFS values in all frequencies except in the spindle and theta bands, where NREM sleep showed a peak in GFS. Sleep deprivation did not affect GFS spectra in REM and NREM sleep. Waking GFS values were lower compared with REM and NREM sleep except for the alpha band. Waking alpha GFS decreased following sleep deprivation in the eyes closed condition only. Our surprising finding of higher synchrony during REM sleep challenges the view of REM sleep as a desynchronized brain state and may provide insight into the function of REM sleep.

  13. Counting on the motor system: rapid action planning reveals the format- and magnitude-dependent extraction of numerical quantity.

    PubMed

    Chapman, Craig S; Gallivan, Jason P; Wood, Daniel K; Milne, Jennifer L; Ansari, Daniel; Culham, Jody C; Goodale, Melvyn A

    2014-03-26

    Symbolic numbers (e.g., "2") acquire their meaning by becoming linked to the core nonsymbolic quantities they represent (e.g., two items). However, the extent to which symbolic and nonsymbolic information converges onto the same internal core representations of quantity remains a point of considerable debate. As nearly all previous work on this topic has employed perceptual tasks requiring the conscious reporting of numerical magnitudes, here we question the extent to which numerical processing via the visual-motor system might shed further light on the fundamental basis of how different number formats are encoded. We show, using a rapid reaching task and a detailed analysis of initial arm trajectories, that there are key differences in how the quantity information extracted from symbolic Arabic numerals and nonsymbolic collections of discrete items are used to guide action planning. In particular, we found that the magnitude derived from discrete dots resulted in movements being biased by an amount directly proportional to the actual quantities presented whereas the magnitude derived from numerals resulted in movements being biased only by the relative (e.g., larger than) quantities presented. In addition, we found that initial motor plans were more sensitive to changes in numerical quantity within small (1-3) than large (5-15) number ranges, irrespective of their format (dots or numerals). In light of previous work, our visual-motor results clearly show that the processing of numerical quantity information is both format and magnitude dependent.

  14. CRISPR-engineered mosaicism rapidly reveals that loss of Kcnj13 function in mice mimics human disease phenotypes

    PubMed Central

    Zhong, Hua; Chen, Yiyun; Li, Yumei; Chen, Rui; Mardon, Graeme

    2015-01-01

    The era of genomics has demanded the development of more efficient and timesaving approaches to validate gene function in disease. Here, we utilized the CRISPR-Cas9 system to generate Kcnj13 mutant mice by zygote injection to verify the pathogenic role of human KCNJ13, mutations of which are thought to cause Leber congenital amaurosis (LCA), an early-onset form of blindness. We found that complete loss of Kcnj13 is likely postnatal lethal. Among surviving F0-generation mice examined, 80% show mosaic KCNJ13 expression in the retinal pigment epithelium (RPE). Mosaic expression correlates with decreased response to light and photoreceptor degeneration, indicating that Kcnj13 mutant mice mimic human KCNJ13-related LCA disease. Importantly, mosaic animals enable us to directly compare Kcnj13 mutant and wild-type RPE cells in the same eye. We found that RPE cells lacking KCNJ13 protein still survive but overlying photoreceptors exhibit cell degeneration. At the same time, wild-type RPE cells can rescue neighboring photoreceptor cells that overlie mutant RPE cells. These results suggest that KCNJ13 expression is required for RPE cells to maintain photoreceptor survival. Moreover, we show that CRISPR-Cas9 engineered mosaicism can be used to rapidly test candidate gene function in vivo. PMID:25666713

  15. Rapid Categorization of Human and Ape Faces in 9-Month-Old Infants Revealed by Fast Periodic Visual Stimulation.

    PubMed

    Peykarjou, Stefanie; Hoehl, Stefanie; Pauen, Sabina; Rossion, Bruno

    2017-10-02

    This study investigates categorization of human and ape faces in 9-month-olds using a Fast Periodic Visual Stimulation (FPVS) paradigm while measuring EEG. Categorization responses are elicited only if infants discriminate between different categories and generalize across exemplars within each category. In study 1, human or ape faces were presented as standard and deviant stimuli in upright and inverted trials. Upright ape faces presented among humans elicited strong categorization responses, whereas responses for upright human faces and for inverted ape faces were smaller. Deviant inverted human faces did not elicit categorization. Data were best explained by a model with main effects of species and orientation. However, variance of low-level image characteristics was higher for the ape than the human category. Variance was matched to replicate this finding in an independent sample (study 2). Both human and ape faces elicited categorization in upright and inverted conditions, but upright ape faces elicited the strongest responses. Again, data were best explained by a model of two main effects. These experiments demonstrate that 9-month-olds rapidly categorize faces, and unfamiliar faces presented among human faces elicit increased categorization responses. This likely reflects habituation for the familiar standard category, and stronger release for the unfamiliar category deviants.

  16. Global field synchronization reveals rapid eye movement sleep as most synchronized brain state in the human EEG

    PubMed Central

    Achermann, Peter; Rusterholz, Thomas; Dürr, Roland; König, Thomas

    2016-01-01

    Sleep is characterized by a loss of consciousness, which has been attributed to a breakdown of functional connectivity between brain regions. Global field synchronization (GFS) can estimate functional connectivity of brain processes. GFS is a frequency-dependent measure of global synchronicity of multi-channel EEG data. Our aim was to explore and extend the hypothesis of disconnection during sleep by comparing GFS spectra of different vigilance states. The analysis was performed on eight healthy adult male subjects. EEG was recorded during a baseline night, a recovery night after 40 h of sustained wakefulness and at 3 h intervals during the 40 h of wakefulness. Compared to non-rapid eye movement (NREM) sleep, REM sleep showed larger GFS values in all frequencies except in the spindle and theta bands, where NREM sleep showed a peak in GFS. Sleep deprivation did not affect GFS spectra in REM and NREM sleep. Waking GFS values were lower compared with REM and NREM sleep except for the alpha band. Waking alpha GFS decreased following sleep deprivation in the eyes closed condition only. Our surprising finding of higher synchrony during REM sleep challenges the view of REM sleep as a desynchronized brain state and may provide insight into the function of REM sleep. PMID:27853537

  17. RAPID-COMMUNICATION Genetic diversity and differentiation in natural populations of Arapaima gigas from lower Amazon revealed by microsatellites.

    PubMed

    Fazzi-Gomes, P F; Melo, N; Palheta, G; Guerreiro, S; Amador, M; Ribeiro-Dos-Santos, A K; Santos, S; Hamoy, I

    2017-02-08

    Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A. gigas analyzed had high levels of genetic variability, which were similar to those described in previous studies. These two populations had a significant population differentiation supported by the estimates of FST and RST (0.06), by Bayesian analysis (K = 2), and by population assignment tests, which revealed a moderate genetic distance.

  18. Ranking in evolving complex networks

    NASA Astrophysics Data System (ADS)

    Liao, Hao; Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng; Zhou, Ming-Yang

    2017-05-01

    Complex networks have emerged as a simple yet powerful framework to represent and analyze a wide range of complex systems. The problem of ranking the nodes and the edges in complex networks is critical for a broad range of real-world problems because it affects how we access online information and products, how success and talent are evaluated in human activities, and how scarce resources are allocated by companies and policymakers, among others. This calls for a deep understanding of how existing ranking algorithms perform, and which are their possible biases that may impair their effectiveness. Many popular ranking algorithms (such as Google's PageRank) are static in nature and, as a consequence, they exhibit important shortcomings when applied to real networks that rapidly evolve in time. At the same time, recent advances in the understanding and modeling of evolving networks have enabled the development of a wide and diverse range of ranking algorithms that take the temporal dimension into account. The aim of this review is to survey the existing ranking algorithms, both static and time-aware, and their applications to evolving networks. We emphasize both the impact of network evolution on well-established static algorithms and the benefits from including the temporal dimension for tasks such as prediction of network traffic, prediction of future links, and identification of significant nodes.

  19. Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation

    PubMed Central

    2016-01-01

    Angraecum. The macroevolutionary model-based phylogeny failed to detect shifts in diversification that could be associated directly with morphological diversification. Diversification in Angraecum resulted from gradual species accumulation through time rather than from rapid radiation, a diversification pattern often encountered in tropical rain forests. PMID:27669569

  20. Diversification of Angraecum (Orchidaceae, Vandeae) in Madagascar: Revised Phylogeny Reveals Species Accumulation through Time Rather than Rapid Radiation.

    PubMed

    Andriananjamanantsoa, Herinandrianina N; Engberg, Shannon; Louis, Edward E; Brouillet, Luc

    Angraecum. The macroevolutionary model-based phylogeny failed to detect shifts in diversification that could be associated directly with morphological diversification. Diversification in Angraecum resulted from gradual species accumulation through time rather than from rapid radiation, a diversification pattern often encountered in tropical rain forests.

  1. Tomographic particle image velocimetry of desert locust wakes: instantaneous volumes combine to reveal hidden vortex elements and rapid wake deformation.

    PubMed

    Bomphrey, Richard J; Henningsson, Per; Michaelis, Dirk; Hollis, David

    2012-12-07

    Aerodynamic structures generated by animals in flight are unstable and complex. Recent progress in quantitative flow visualization has advanced our understanding of animal aerodynamics, but measurements have hitherto been limited to flow velocities at a plane through the wake. We applied an emergent, high-speed, volumetric fluid imaging technique (tomographic particle image velocimetry) to examine segments of the wake of desert locusts, capturing fully three-dimensional instantaneous flow fields. We used those flow fields to characterize the aerodynamic footprint in unprecedented detail and revealed previously unseen wake elements that would have gone undetected by two-dimensional or stereo-imaging technology. Vortex iso-surface topographies show the spatio-temporal signature of aerodynamic force generation manifest in the wake of locusts, and expose the extent to which animal wakes can deform, potentially leading to unreliable calculations of lift and thrust when using conventional diagnostic methods. We discuss implications for experimental design and analysis as volumetric flow imaging becomes more widespread.

  2. Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

    PubMed Central

    Zhang, Zhengjian; English, Brian P.; Grimm, Jonathan B.; Kazane, Stephanie A.; Hu, Wenxin; Tsai, Albert; Inouye, Carla; You, Changjiang; Piehler, Jacob; Schultz, Peter G.; Lavis, Luke D.; Revyakin, Andrey; Tjian, Robert

    2016-01-01

    Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II). A “step-wise” preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, we established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Here we performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB–promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II–TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions. PMID:27798851

  3. A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning

    PubMed Central

    Wang, Qixuan; Oh, Ji Won; Lee, Hye-Lim; Dhar, Anukriti; Peng, Tao; Ramos, Raul; Guerrero-Juarez, Christian Fernando; Wang, Xiaojie; Zhao, Ran; Cao, Xiaoling; Le, Jonathan; Fuentes, Melisa A; Jocoy, Shelby C; Rossi, Antoni R; Vu, Brian; Pham, Kim; Wang, Xiaoyang; Mali, Nanda Maya; Park, Jung Min; Choi, June-Hyug; Lee, Hyunsu; Legrand, Julien M D; Kandyba, Eve; Kim, Jung Chul; Kim, Moonkyu; Foley, John; Yu, Zhengquan; Kobielak, Krzysztof; Andersen, Bogi; Khosrotehrani, Kiarash; Nie, Qing; Plikus, Maksim V

    2017-01-01

    The control principles behind robust cyclic regeneration of hair follicles (HFs) remain unclear. Using multi-scale modeling, we show that coupling inhibitors and activators with physical growth of HFs is sufficient to drive periodicity and excitability of hair regeneration. Model simulations and experimental data reveal that mouse skin behaves as a heterogeneous regenerative field, composed of anatomical domains where HFs have distinct cycling dynamics. Interactions between fast-cycling chin and ventral HFs and slow-cycling dorsal HFs produce bilaterally symmetric patterns. Ear skin behaves as a hyper-refractory domain with HFs in extended rest phase. Such hyper-refractivity relates to high levels of BMP ligands and WNT antagonists, in part expressed by ear-specific cartilage and muscle. Hair growth stops at the boundaries with hyper-refractory ears and anatomically discontinuous eyelids, generating wave-breaking effects. We posit that similar mechanisms for coupled regeneration with dominant activator, hyper-refractory, and wave-breaker regions can operate in other actively renewing organs. DOI: http://dx.doi.org/10.7554/eLife.22772.001 PMID:28695824

  4. Tomographic particle image velocimetry of desert locust wakes: instantaneous volumes combine to reveal hidden vortex elements and rapid wake deformation

    PubMed Central

    Bomphrey, Richard J.; Henningsson, Per; Michaelis, Dirk; Hollis, David

    2012-01-01

    Aerodynamic structures generated by animals in flight are unstable and complex. Recent progress in quantitative flow visualization has advanced our understanding of animal aerodynamics, but measurements have hitherto been limited to flow velocities at a plane through the wake. We applied an emergent, high-speed, volumetric fluid imaging technique (tomographic particle image velocimetry) to examine segments of the wake of desert locusts, capturing fully three-dimensional instantaneous flow fields. We used those flow fields to characterize the aerodynamic footprint in unprecedented detail and revealed previously unseen wake elements that would have gone undetected by two-dimensional or stereo-imaging technology. Vortex iso-surface topographies show the spatio-temporal signature of aerodynamic force generation manifest in the wake of locusts, and expose the extent to which animal wakes can deform, potentially leading to unreliable calculations of lift and thrust when using conventional diagnostic methods. We discuss implications for experimental design and analysis as volumetric flow imaging becomes more widespread. PMID:22977102

  5. An Evolving Astrobiology Glossary

    NASA Astrophysics Data System (ADS)

    Meech, K. J.; Dolci, W. W.

    2009-12-01

    One of the resources that evolved from the Bioastronomy 2007 meeting was an online interdisciplinary glossary of terms that might not be universally familiar to researchers in all sub-disciplines feeding into astrobiology. In order to facilitate comprehension of the presentations during the meeting, a database driven web tool for online glossary definitions was developed and participants were invited to contribute prior to the meeting. The glossary was downloaded and included in the conference registration materials for use at the meeting. The glossary web tool is has now been delivered to the NASA Astrobiology Institute so that it can continue to grow as an evolving resource for the astrobiology community.

  6. High-Throughput Sequencing Reveals Hypothalamic MicroRNAs as Novel Partners Involved in Timing the Rapid Development of Chicken (Gallus gallus) Gonads.

    PubMed

    Han, Wei; Zou, Jianmin; Wang, Kehua; Su, Yijun; Zhu, Yunfen; Song, Chi; Li, Guohui; Qu, Liang; Zhang, Huiyong; Liu, Honglin

    2015-01-01

    Onset of the rapid gonad growth is a milestone in sexual development that comprises many genes and regulatory factors. The observations in model organisms and mammals including humans have shown a potential link between miRNAs and development timing. To determine whether miRNAs play roles in this process in the chicken (Gallus gallus), the Solexa deep sequencing was performed to analyze the profiles of miRNA expression in the hypothalamus of hens from two different pubertal stages, before onset of the rapid gonad development (BO) and after onset of the rapid gonad development (AO). 374 conserved and 46 novel miRNAs were identified as hypothalamus-expressed miRNAs in the chicken. 144 conserved miRNAs were showed to be differentially expressed (reads > 10, P < 0.05) during the transition from BO to AO. Five differentially expressed miRNAs were validated by real-time quantitative RT-PCR (qRT-PCR) method. 2013 putative genes were predicted as the targets of the 15 most differentially expressed miRNAs (fold-change > 4.0, P < 0.01). Of these genes, 7 putative circadian clock genes, Per2, Bmal1/2, Clock, Cry1/2, and Star were found to be targeted multiple times by the miRNAs. qRT-PCR revealed the basic transcription levels of these clock genes were much higher (P < 0.01) in AO than in BO. Further functional analysis suggested that these 15 miRNAs play important roles in transcriptional regulation and signal transduction pathways. The results provide new insights into miRNAs functions in timing the rapid development of chicken gonads. Considering the characteristics of miRNA functional conservation, the results will contribute to the research on puberty onset in humans.

  7. High-Throughput Sequencing Reveals Hypothalamic MicroRNAs as Novel Partners Involved in Timing the Rapid Development of Chicken (Gallus gallus) Gonads

    PubMed Central

    Han, Wei; Zou, Jianmin; Wang, Kehua; Su, Yijun; Zhu, Yunfen; Song, Chi; Li, Guohui; Qu, Liang; Zhang, Huiyong; Liu, Honglin

    2015-01-01

    Onset of the rapid gonad growth is a milestone in sexual development that comprises many genes and regulatory factors. The observations in model organisms and mammals including humans have shown a potential link between miRNAs and development timing. To determine whether miRNAs play roles in this process in the chicken (Gallus gallus), the Solexa deep sequencing was performed to analyze the profiles of miRNA expression in the hypothalamus of hens from two different pubertal stages, before onset of the rapid gonad development (BO) and after onset of the rapid gonad development (AO). 374 conserved and 46 novel miRNAs were identified as hypothalamus-expressed miRNAs in the chicken. 144 conserved miRNAs were showed to be differentially expressed (reads > 10, P < 0.05) during the transition from BO to AO. Five differentially expressed miRNAs were validated by real-time quantitative RT-PCR (qRT-PCR) method. 2013 putative genes were predicted as the targets of the 15 most differentially expressed miRNAs (fold-change > 4.0, P < 0.01). Of these genes, 7 putative circadian clock genes, Per2, Bmal1/2, Clock, Cry1/2, and Star were found to be targeted multiple times by the miRNAs. qRT-PCR revealed the basic transcription levels of these clock genes were much higher (P < 0.01) in AO than in BO. Further functional analysis suggested that these 15 miRNAs play important roles in transcriptional regulation and signal transduction pathways. The results provide new insights into miRNAs functions in timing the rapid development of chicken gonads. Considering the characteristics of miRNA functional conservation, the results will contribute to the research on puberty onset in humans. PMID:26061962

  8. Methods Evolved by Observation

    ERIC Educational Resources Information Center

    Montessori, Maria

    2016-01-01

    Montessori's idea of the child's nature and the teacher's perceptiveness begins with amazing simplicity, and when she speaks of "methods evolved," she is unveiling a methodological system for observation. She begins with the early childhood explosion into writing, which is a familiar child phenomenon that Montessori has written about…

  9. [The evolving of cardiac interventions].

    PubMed

    Billinger, Michael

    2014-12-01

    Treatment modalities for heart diseases have considerable evolved during the last 20 years. Coronary and valvular heart disease are treated increasingly by less invasive percutaneous catheter based procedures instead of open-heart surgery. In addition, new cutting-edge interventions allow to cure heart disease for which until recently only medical treatment options were available. Whilst many patients benefit from these innovative therapies, rapidly developing technologies potentially carry the risk of overtreatment. In order to select patients for the most appropriate treatment, an intensive interdisciplinary teamwork between cardiologists and cardiac surgeons is a mandatory requirement. Additionally, knowledge transfer between cardiologists, their growing subspecialties and practitioners should be encouraged. Finally, timely scientific evaluation of new therapies and subsequent incorporation in guidelines remains crucial.

  10. A screen for modulators reveals that orexin-A rapidly stimulates thyrotropin releasing hormone expression and release in hypothalamic cell culture.

    PubMed

    Cote-Vélez, Antonieta; Martínez Báez, Anabel; Lezama, Leticia; Uribe, Rosa María; Joseph-Bravo, Patricia; Charli, Jean-Louis

    2017-02-02

    In the paraventricular nucleus of the mammalian hypothalamus, hypophysiotropic thyrotropin releasing hormone (TRH) neurons integrate metabolic information and control the activity of the thyroid axis. Additional populations of TRH neurons reside in various hypothalamic areas, with poorly defined connections and functions, albeit there is evidence that some may be related to energy balance. To establish extracellular modulators of TRH hypothalamic neurons activity, we performed a screen of neurotransmitters effects in hypothalamic cultures. Cell culture conditions were chosen to facilitate the full differentiation of the TRH neurons; these conditions had permitted the characterization of the effects of known modulators of hypophysiotropic TRH neurons. The major end-point of the screen was Trh mRNA levels, since they are generally rapidly (0.5-3h) modified by synaptic inputs onto TRH neurons; in some experiments, TRH cell content or release was also analyzed. Various modulators, including histamine, serotonin, β-endorphin, met-enkephalin, and melanin concentrating hormone, had no effect. Glutamate, as well as ionotropic agonists (kainate and N-Methyl-d-aspartic acid), increased Trh mRNA levels. Baclofen, a GABAB receptor agonist, and dopamine enhanced Trh mRNA levels. An endocannabinoid receptor 1 inverse agonist promoted TRH release. Somatostatin increased Trh mRNA levels and TRH cell content. Orexin-A rapidly increased Trh mRNA levels, TRH cell content and release, while orexin-B decreased Trh mRNA levels. These data reveal unaccounted regulators, which exert potent effects on hypothalamic TRH neurons in vitro.

  11. Self Evolving Modular Network

    NASA Astrophysics Data System (ADS)

    Tokunaga, Kazuhiro; Kawabata, Nobuyuki; Furukawa, Tetsuo

    We propose a novel modular network called the Self-Evolving Modular Network (SEEM). The SEEM has a modular network architecture with a graph structure and these following advantages: (1) new modules are added incrementally to allow the network to adapt in a self-organizing manner, and (2) graph's paths are formed based on the relationships between the models represented by modules. The SEEM is expected to be applicable to evolving functions of an autonomous robot in a self-organizing manner through interaction with the robot's environment and categorizing large-scale information. This paper presents the architecture and an algorithm for the SEEM. Moreover, performance characteristic and effectiveness of the network are shown by simulations using cubic functions and a set of 3D-objects.

  12. Evolvable Neural Software System

    NASA Technical Reports Server (NTRS)

    Curtis, Steven A.

    2009-01-01

    The Evolvable Neural Software System (ENSS) is composed of sets of Neural Basis Functions (NBFs), which can be totally autonomously created and removed according to the changing needs and requirements of the software system. The resulting structure is both hierarchical and self-similar in that a given set of NBFs may have a ruler NBF, which in turn communicates with other sets of NBFs. These sets of NBFs may function as nodes to a ruler node, which are also NBF constructs. In this manner, the synthetic neural system can exhibit the complexity, three-dimensional connectivity, and adaptability of biological neural systems. An added advantage of ENSS over a natural neural system is its ability to modify its core genetic code in response to environmental changes as reflected in needs and requirements. The neural system is fully adaptive and evolvable and is trainable before release. It continues to rewire itself while on the job. The NBF is a unique, bilevel intelligence neural system composed of a higher-level heuristic neural system (HNS) and a lower-level, autonomic neural system (ANS). Taken together, the HNS and the ANS give each NBF the complete capabilities of a biological neural system to match sensory inputs to actions. Another feature of the NBF is the Evolvable Neural Interface (ENI), which links the HNS and ANS. The ENI solves the interface problem between these two systems by actively adapting and evolving from a primitive initial state (a Neural Thread) to a complicated, operational ENI and successfully adapting to a training sequence of sensory input. This simulates the adaptation of a biological neural system in a developmental phase. Within the greater multi-NBF and multi-node ENSS, self-similar ENI s provide the basis for inter-NBF and inter-node connectivity.

  13. Highly-evolved stars

    NASA Technical Reports Server (NTRS)

    Heap, S. R.

    1981-01-01

    The ways in which the IUE has proved useful in studying highly evolved stars are reviewed. The importance of high dispersion spectra for abundance analyses of the sd0 stars and for studies of the wind from the central star of NGC 6543 and the wind from the 0 type component of Vela X-1 is shown. Low dispersion spectra are used for absolute spectrophotometry of the dwarf nova, Ex Hya. Angular resolution is important for detecting and locating UV sources in globular clusters.

  14. Regolith Evolved Gas Analyzer

    NASA Technical Reports Server (NTRS)

    Hoffman, John H.; Hedgecock, Jud; Nienaber, Terry; Cooper, Bonnie; Allen, Carlton; Ming, Doug

    2000-01-01

    The Regolith Evolved Gas Analyzer (REGA) is a high-temperature furnace and mass spectrometer instrument for determining the mineralogical composition and reactivity of soil samples. REGA provides key mineralogical and reactivity data that is needed to understand the soil chemistry of an asteroid, which then aids in determining in-situ which materials should be selected for return to earth. REGA is capable of conducting a number of direct soil measurements that are unique to this instrument. These experimental measurements include: (1) Mass spectrum analysis of evolved gases from soil samples as they are heated from ambient temperature to 900 C; and (2) Identification of liberated chemicals, e.g., water, oxygen, sulfur, chlorine, and fluorine. REGA would be placed on the surface of a near earth asteroid. It is an autonomous instrument that is controlled from earth but does the analysis of regolith materials automatically. The REGA instrument consists of four primary components: (1) a flight-proven mass spectrometer, (2) a high-temperature furnace, (3) a soil handling system, and (4) a microcontroller. An external arm containing a scoop or drill gathers regolith samples. A sample is placed in the inlet orifice where the finest-grained particles are sifted into a metering volume and subsequently moved into a crucible. A movable arm then places the crucible in the furnace. The furnace is closed, thereby sealing the inner volume to collect the evolved gases for analysis. Owing to the very low g forces on an asteroid compared to Mars or the moon, the sample must be moved from inlet to crucible by mechanical means rather than by gravity. As the soil sample is heated through a programmed pattern, the gases evolved at each temperature are passed through a transfer tube to the mass spectrometer for analysis and identification. Return data from the instrument will lead to new insights and discoveries including: (1) Identification of the molecular masses of all of the gases

  15. Infrared video tracking of Anopheles gambiae at insecticide-treated bed nets reveals rapid decisive impact after brief localised net contact

    PubMed Central

    Parker, Josephine E.A.; Angarita-Jaimes, Natalia; Abe, Mayumi; Towers, Catherine E.; Towers, David; McCall, Philip J.

    2015-01-01

    Long-lasting insecticidal bed nets (LLINs) protect humans from malaria transmission and are fundamental to malaria control worldwide, but little is known of how mosquitoes interact with nets. Elucidating LLIN mode of action is essential to maintain or improve efficacy, an urgent need as emerging insecticide resistance threatens their future. Tracking multiple free-flying Anopheles gambiae responding to human-occupied bed nets in a novel large-scale system, we characterised key behaviours and events. Four behavioural modes with different levels of net contact were defined: swooping, visiting, bouncing and resting. Approximately 75% of all activity occurred at the bed net roof where multiple brief contacts were focussed above the occupant’s torso. Total flight and net contact times were lower at LLINs than untreated nets but the essential character of the response was unaltered. LLINs did not repel mosquitoes but impacted rapidly: LLIN contact of less than 1 minute per mosquito during the first ten minutes reduced subsequent activity; after thirty minutes, activity at LLINs was negligible. Velocity measurements showed that mosquitoes detected nets, including unbaited untreated nets, prior to contact. This is the most complete characterisation of mosquito-LLIN interactions to date, and reveals many aspects of LLIN mode of action, important for developing the next generation of LLINs. PMID:26323965

  16. Genomewide SNP data reveal cryptic phylogeographic structure and microallopatric divergence in a rapids-adapted clade of cichlids from the Congo River.

    PubMed

    Alter, S Elizabeth; Munshi-South, Jason; Stiassny, Melanie L J

    2017-03-01

    The lower Congo River is a freshwater biodiversity hot spot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome, we analysed double-digest restriction-associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD-Seq data in understanding diversification processes operating both below and above the species level.

  17. Infrared video tracking of Anopheles gambiae at insecticide-treated bed nets reveals rapid decisive impact after brief localised net contact.

    PubMed

    Parker, Josephine E A; Angarita-Jaimes, Natalia; Abe, Mayumi; Towers, Catherine E; Towers, David; McCall, Philip J

    2015-09-01

    Long-lasting insecticidal bed nets (LLINs) protect humans from malaria transmission and are fundamental to malaria control worldwide, but little is known of how mosquitoes interact with nets. Elucidating LLIN mode of action is essential to maintain or improve efficacy, an urgent need as emerging insecticide resistance threatens their future. Tracking multiple free-flying Anopheles gambiae responding to human-occupied bed nets in a novel large-scale system, we characterised key behaviours and events. Four behavioural modes with different levels of net contact were defined: swooping, visiting, bouncing and resting. Approximately 75% of all activity occurred at the bed net roof where multiple brief contacts were focussed above the occupant's torso. Total flight and net contact times were lower at LLINs than untreated nets but the essential character of the response was unaltered. LLINs did not repel mosquitoes but impacted rapidly: LLIN contact of less than 1 minute per mosquito during the first ten minutes reduced subsequent activity; after thirty minutes, activity at LLINs was negligible. Velocity measurements showed that mosquitoes detected nets, including unbaited untreated nets, prior to contact. This is the most complete characterisation of mosquito-LLIN interactions to date, and reveals many aspects of LLIN mode of action, important for developing the next generation of LLINs.

  18. Our evolving universe

    NASA Astrophysics Data System (ADS)

    Longair, Malcolm S.

    Our Evolving Universe is a lucid, non-technical and infectiously enthusiastic introduction to current astronomy and cosmology. Highly illustrated throughout with the latest colour images from the world's most advanced telescopes, it also provides a colourful view of our Universe. Malcolm Longair takes us on a breathtaking tour of the most dramatic recent results astronomers have on the birth of stars, the hunt for black holes and dark matter, on gravitational lensing and the latest tests of the Big Bang. He leads the reader right up to understand the key questions that future research in astronomy and cosmology must answer. A clear and comprehensive glossary of technical terms is also provided. For the general reader, student or professional wishing to understand the key questions today's astronomers and cosmologists are trying to answer, this is an invaluable and inspiring read.

  19. Evolution of evolvability and phenotypic plasticity in virtual cells.

    PubMed

    Cuypers, Thomas D; Rutten, Jacob P; Hogeweg, Paulien

    2017-02-28

    Changing environmental conditions pose a challenge for the survival of species. To meet this challenge organisms adapt their phenotype by physiological regulation (phenotypic plasticity) or by evolving. Regulatory mechanisms that ensure a constant internal environment in the face of continuous external fluctuations (homeostasis) are ubiquitous and essential for survival. However, more drastic and enduring environmental change, often requires lineages to adapt by mutating. In vitro evolutionary experiments with microbes show that adaptive, large phenotypic changes occur remarkably quickly, requiring only a few mutations. It has been proposed that the high evolvability demonstrated by these microbes, is an evolved property. If both regulation (phenotypic plasticity) and evolvability can evolve as strategies to adapt to change, what are the conditions that favour the emergence of either of these strategy? Does evolution of one strategy hinder or facilitate evolution of the other strategy? Here we investigate this with computational evolutionary modelling in populations of Virtual Cells. During a preparatory evolutionary phase, Virtual Cells evolved homeostasis regulation for internal metabolite concentrations in a fluctuating environment. The resulting wild-type Virtual Cell strains (WT-VCS) were then exposed to periodic, drastic environmental changes, while maintaining selection on homeostasis regulation. In different sets of simulations the nature and frequencies of environmental change were varied. Pre-evolved WT-VCS were highly evolvable, showing rapid evolutionary adaptation after novel environmental change. Moreover, continued low frequency changes resulted in evolutionary restructuring of the genome that enables even faster adaptation with very few mutations. In contrast, when change frequency is high, lineages evolve phenotypic plasticity that allows them to be fit in different environments without mutations. Yet, evolving phenotypic plasticity is a

  20. IR Spectroscopy of Gasses Evolved During Roasting Coffee Beans

    NASA Astrophysics Data System (ADS)

    Clain, Alexander; Capaldi, Xavier; Amanuel, Samuel

    2014-03-01

    We measured the IR spectra of the gasses that evolve during roasting of coffee beans. The spectra recorded at different temperature revealed that the intensity of certain IR bands increase as the temperature increases. For instance, the intensity of the CO2 band increased by a factor of four and reached a plateau as the roasting temperature approached 200°C. The intensity further increased as the temperature increased above 200°C, however, in two steps. Similarly the intensity of the OH bands monotonically increased until 200°C and then increased further in two rapid steps above 200°C. The temperature ranges where IR intensities change in two steps coincides with the temperature ranges where typically commercial roasting is done and where the first and second ``cracks'' are heard during roasting.

  1. Visible light induction of an electron paramagnetic resonance split signal in Photosystem II in the S(2) state reveals the importance of charges in the oxygen-evolving center during catalysis: a unifying model.

    PubMed

    Sjöholm, Johannes; Styring, Stenbjörn; Havelius, Kajsa G V; Ho, Felix M

    2012-03-13

    Cryogenic illumination of Photosystem II (PSII) can lead to the trapping of the metastable radical Y(Z)(•), the radical form of the redox-active tyrosine residue D1-Tyr161 (known as Y(Z)). Magnetic interaction between this radical and the CaMn(4) cluster of PSII gives rise to so-called split electron paramagnetic resonance (EPR) signals with characteristics that are dependent on the S state. We report here the observation and characterization of a split EPR signal that can be directly induced from PSII centers in the S(2) state through visible light illumination at 10 K. We further show that the induction of this split signal takes place via a Mn-centered mechanism, in the same way as when using near-infrared light illumination [Koulougliotis, D., et al. (2003) Biochemistry 42, 3045-3053]. On the basis of interpretations of these results, and in combination with literature data for other split signals induced under a variety of conditions (temperature and light quality), we propose a unified model for the mechanisms of split signal induction across the four S states (S(0), S(1), S(2), and S(3)). At the heart of this model is the stability or instability of the Y(Z)(•)(D1-His190)(+) pair that would be formed during cryogenic oxidation of Y(Z). Furthermore, the model is closely related to the sequence of transfers of protons and electrons from the CaMn(4) cluster during the S cycle and further demonstrates the utility of the split signals in probing the immediate environment of the oxygen-evolving center in PSII.

  2. Why did heterospory evolve?

    PubMed

    Petersen, Kurt B; Burd, Martin

    2016-10-11

    The primitive land plant life cycle featured the production of spores of unimodal size, a condition called homospory. The evolution of bimodal size distributions with small male spores and large female spores, known as heterospory, was an innovation that occurred repeatedly in the history of land plants. The importance of desiccation-resistant spores for colonization of the land is well known, but the adaptive value of heterospory has never been well established. It was an addition to a sexual life cycle that already involved male and female gametes. Its role as a precursor to the evolution of seeds has received much attention, but this is an evolutionary consequence of heterospory that cannot explain the transition from homospory to heterospory (and the lack of evolutionary reversal from heterospory to homospory). Enforced outcrossing of gametophytes has often been mentioned in connection to heterospory, but we review the shortcomings of this argument as an explanation of the selective advantage of heterospory. Few alternative arguments concerning the selective forces favouring heterospory have been proposed, a paucity of attention that is surprising given the importance of this innovation in land plant evolution. In this review we highlight two ideas that may lead us to a better understanding of why heterospory evolved. First, models of optimal resource allocation - an approach that has been used for decades in evolutionary ecology to help understand parental investment and other life-history patterns - suggest that an evolutionary increase in spore size could reach a threshold at which small spores yielding small, sperm-producing gametophytes would return greater fitness per unit of resource investment than would large spores and bisexual gametophytes. With the advent of such microspores, megaspores would evolve under frequency-dependent selection. This argument can account for the appearance of heterospory in the Devonian, when increasingly tall and complex

  3. Epitope-tagged dopamine transporter knock-in mice reveal rapid endocytic trafficking and filopodia targeting of the transporter in dopaminergic axons

    PubMed Central

    Rao, Anjali; Richards, Toni L.; Simmons, Diana; Zahniser, Nancy R.; Sorkin, Alexander

    2012-01-01

    The plasma membrane dopamine (DA) transporter (DAT) is essential for reuptake of extracellular DA. DAT function in heterologous cells is regulated by subcellular targeting, endocytosis, and intracellular trafficking, but the mechanisms regulating neuronal DAT remain poorly understood. Hence, we generated a knock-in mouse expressing a hemagglutinin (HA)-epitope-tagged DAT to study endogenous transporter trafficking. Introduction of the HA tag into the second extracellular loop of mouse DAT did not perturb its expression level, distribution pattern, or substrate uptake kinetics. Live-cell fluorescence microscopy imaging using fluorescently labeled HA-specific antibody and a quantitative HA-antibody endocytosis assay demonstrated that in axons HA-DAT was primarily located in the plasma membrane and internalized mostly in growth cones and varicosities, where synaptic vesicle markers were also concentrated. Formation of varicosities was frequently preceded or accompanied by highly dynamic filopodia-like membrane protrusions. Remarkably, HA-DAT often concentrated at the tips of these filopodia. This pool of HA-DATs exhibited low lateral membrane mobility. Thus, DAT-containing filopodia may be involved in synaptogenesis in developing DA neurons. Treatment of neurons with amphetamine increased mobility of filopodial HA-DAT and accelerated HA-DAT endocytosis in axons, suggesting that chronic amphetamine may interfere with DA synapse development. Interestingly, phorbol esters did not accelerate endocytosis of axonal DAT.—Rao, A., Richards, T. L., Simmons, D., Zahniser, N. R., Sorkin, A. Epitope-tagged dopamine transporter knock-in mice reveal rapid endocytic trafficking and filopodia targeting of the transporter in dopaminergic axons. PMID:22267337

  4. Assessing SfM-Photogrammetry potential at micro-scale on a rapidly evolving mud-bank: case study on a mesocosm study within pioneer mangroves in French Guiana (South America)

    NASA Astrophysics Data System (ADS)

    Fleury, Jules; Brunier, Guillaume; Michaud, Emma; Anthony, Edward; Dussouillez, Philippe; Morvan, Sylvain

    2016-04-01

    Mud banks are the loci of rich bio-geo-chemical processes occuring rapidly at infra-tide frequency. Their surface topography is commonly affected by many of these processes, including bioturbation, water drainage or dessication. Quantifying surface morphology and changes on a mud bank at the micro-scale is a challenging task due to a number of issues. First, the water-saturated nature of the soil makes it difficult to measure High Resolution Topography (HRT) with classical methods. Second, setting up an instrumented experiment without disrupting the signal being studied is hardly achieved at micro-scale. Finally, the highly mobile nature of this environment enhancing strong spatio-temporal heterogeneity is hard to capture. Terrestrial Laser Scanning (TLS) and SfM (Surface from Motion)-Photogrammetry are two techniques that enable mapping of micro-scale features, but the first technique is not suitable because of the poor quality of the backscattered laser signal on wet surfaces and the need to set up several measuring stations on a complex, unstable substrate. Thus, we set up an experiment to assess the feasibility and the accuracy of SfM in such a context. We took the opportunity of the installation of a pontoon dedicated to the study of bio-geochemical processes within benthic mesocosms installed on a mud bank inhabited by pioneer mangroves trees to develop an adapted photogrammetry protocol based on a full-frame remotely triggered camera sensor mounted on a pole. The incident light on the surface was also controlled with a light-diffusing device. We obtained sub-millimetric resolution 3D-topography and visible imagery. Surveys were carried out every 2 hours at low tide to detect surface changes due to water content variation as well as bioturbation mainly caused by crabs digging galleries and feeding on sediment surface. Both the qualitative and quantitative results seem very promising and lead us to expect new insights into heterogeneous surface processes on a

  5. Evolving a photosynthetic organelle.

    PubMed

    Nakayama, Takuro; Archibald, John M

    2012-04-24

    The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles.The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis--the conversion of solar energy into chemical energy--and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

  6. Communicability across evolving networks.

    PubMed

    Grindrod, Peter; Parsons, Mark C; Higham, Desmond J; Estrada, Ernesto

    2011-04-01

    Many natural and technological applications generate time-ordered sequences of networks, defined over a fixed set of nodes; for example, time-stamped information about "who phoned who" or "who came into contact with who" arise naturally in studies of communication and the spread of disease. Concepts and algorithms for static networks do not immediately carry through to this dynamic setting. For example, suppose A and B interact in the morning, and then B and C interact in the afternoon. Information, or disease, may then pass from A to C, but not vice versa. This subtlety is lost if we simply summarize using the daily aggregate network given by the chain A-B-C. However, using a natural definition of a walk on an evolving network, we show that classic centrality measures from the static setting can be extended in a computationally convenient manner. In particular, communicability indices can be computed to summarize the ability of each node to broadcast and receive information. The computations involve basic operations in linear algebra, and the asymmetry caused by time's arrow is captured naturally through the noncommutativity of matrix-matrix multiplication. Illustrative examples are given for both synthetic and real-world communication data sets. We also discuss the use of the new centrality measures for real-time monitoring and prediction.

  7. Evolving Concepts of Asthma

    PubMed Central

    Ray, Anuradha; Wenzel, Sally E.

    2015-01-01

    Our understanding of asthma has evolved over time from a singular disease to a complex of various phenotypes, with varied natural histories, physiologies, and responses to treatment. Early therapies treated most patients with asthma similarly, with bronchodilators and corticosteroids, but these therapies had varying degrees of success. Similarly, despite initial studies that identified an underlying type 2 inflammation in the airways of patients with asthma, biologic therapies targeted toward these type 2 pathways were unsuccessful in all patients. These observations led to increased interest in phenotyping asthma. Clinical approaches, both biased and later unbiased/statistical approaches to large asthma patient cohorts, identified a variety of patient characteristics, but they also consistently identified the importance of age of onset of disease and the presence of eosinophils in determining clinically relevant phenotypes. These paralleled molecular approaches to phenotyping that developed an understanding that not all patients share a type 2 inflammatory pattern. Using biomarkers to select patients with type 2 inflammation, repeated trials of biologics directed toward type 2 cytokine pathways saw newfound success, confirming the importance of phenotyping in asthma. Further research is needed to clarify additional clinical and molecular phenotypes, validate predictive biomarkers, and identify new areas for possible interventions. PMID:26161792

  8. Evolving synergetic interactions

    PubMed Central

    Wu, Bin; Arranz, Jordi; Du, Jinming; Zhou, Da; Traulsen, Arne

    2016-01-01

    Cooperators forgo their own interests to benefit others. This reduces their fitness and thus cooperators are not likely to spread based on natural selection. Nonetheless, cooperation is widespread on every level of biological organization ranging from bacterial communities to human society. Mathematical models can help to explain under which circumstances cooperation evolves. Evolutionary game theory is a powerful mathematical tool to depict the interactions between cooperators and defectors. Classical models typically involve either pairwise interactions between individuals or a linear superposition of these interactions. For interactions within groups, however, synergetic effects may arise: their outcome is not just the sum of its parts. This is because the payoffs via a single group interaction can be different from the sum of any collection of two-player interactions. Assuming that all interactions start from pairs, how can such synergetic multiplayer games emerge from simpler pairwise interactions? Here, we present a mathematical model that captures the transition from pairwise interactions to synergetic multiplayer ones. We assume that different social groups have different breaking rates. We show that non-uniform breaking rates do foster the emergence of synergy, even though individuals always interact in pairs. Our work sheds new light on the mechanisms underlying such synergetic interactions. PMID:27466437

  9. Disgust: Evolved Function and Structure

    ERIC Educational Resources Information Center

    Tybur, Joshua M.; Lieberman, Debra; Kurzban, Robert; DeScioli, Peter

    2013-01-01

    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and that of information processing. Although there is…

  10. Evolving virtual creatures and catapults.

    PubMed

    Chaumont, Nicolas; Egli, Richard; Adami, Christoph

    2007-01-01

    We present a system that can evolve the morphology and the controller of virtual walking and block-throwing creatures (catapults) using a genetic algorithm. The system is based on Sims' work, implemented as a flexible platform with an off-the-shelf dynamics engine. Experiments aimed at evolving Sims-type walkers resulted in the emergence of various realistic gaits while using fairly simple objective functions. Due to the flexibility of the system, drastically different morphologies and functions evolved with only minor modifications to the system and objective function. For example, various throwing techniques evolved when selecting for catapults that propel a block as far as possible. Among the strategies and morphologies evolved, we find the drop-kick strategy, as well as the systematic invention of the principle behind the wheel, when allowing mutations to the projectile.

  11. "Reinventing Life": Introductory Biology for a Rapidly Evolving World

    ERIC Educational Resources Information Center

    Coker, Jeffrey Scott

    2009-01-01

    Evolutionary concepts are essential for a scientific understanding of most issues surrounding modern medicine, agriculture, biotechnology, and the environment. If the mantra for biology education in the 20th century was, "Nothing in biology makes sense except in the light of evolution," the mantra for the 21st century must be, "Nothing in biology…

  12. Observational constraints on models of rapidly evolving luminous stars

    NASA Astrophysics Data System (ADS)

    Rosenfield, Philip A.

    Resolved stellar populations in galaxies are excellent laboratories for testing our understanding of galaxy formation, integrated colors and luminosities, supernova progenitor masses, and energy input from stellar feedback. However, the usefulness of resolved stellar populations rests on the ability to accurately model the evolution of the underlying stars. In this dissertation, I present three projects, the first uses stellar evolution models of hot post-horizontal branch stars to explain the some of the of excess ultra-violet (UV) flux emitted from the center of the Andromeda galaxy. This flux was imaged as part of the Panchromatic Hubble Andromeda Treasury HST multi-cycle program, and excess of UV light from the centers of large elliptical galaxies has been well documented. Therefore, the results of this project go beyond stellar evolution and understanding M31. I find that this population of stars are indeed failed AGB stars or left the AGB early. I also find the stars producing the excess UV light are strongly concentrated in the central regions of the M31 bulge, which must shed light on the progenitor stars. The subsequent two projects each constrain uncertain aspects of uncertain phases of stellar evolution using nearby dwarf galaxies from the HST ACS Nearby galaxy Survey Treasury and a follow-up HST/SNAP campaign which imaged a subset of ANGST galaxies in the near infrared. The two uncertain phases of stellar evolution studied are the luminous core Helium burning (HeB) phase and the thermally pulsating AGB phase. Dwarf galaxies from the ANGST are an ideal environment to test new models because they span ~2 dex in metallicity, more than 30 galaxies have significant HeB populations, and we have HST/NIR follow up data for 26 galaxies with a large AGB population. I find that the convection occurring the HeB stars must increase in strength with increasing mass, and I find constrains on the mass loss prescriptions for low metallicity TP-AGB stars from 0.8 -- ~4 stellar masses.

  13. Emerging Zika Virus Infection: A Rapidly Evolving Situation.

    PubMed

    Bordi, Licia; Avsic-Zupanc, Tatjana; Lalle, Eleonora; Vairo, Francesco; Rosaria Capobianchi, Maria; da Costa Vasconcelos, Pedro Fernando

    2016-12-29

    Zika virus is a mosquito-borne flavivirus, firstly identified in Uganda and responsible for sporadic human cases in Africa and Asia until recently, when large outbreak occurred in Pacific Ocean and the Americas. Since the main vectors during its spread outside of Africa have been Ae. albopictus and Ae. aegypti mosquitoes, which are widely distributed all over the world, there is urgent need for a coordinated response for prevention and spread of ZIKV epidemics.Despite clinical manifestation of Zika virus infection are usually mild and self limiting, there are reports suggesting, during the recent epidemic, an association of ZIKV infection with severe consequences, including fetal/newborn microcephaly, due to vertical in utero transmission, autoimmune-neurological presentations including cranial nerve dysfunction, and Guillain-Barré Syndrome in adults. The primary mode of transmission of Zika virus between humans is through the bite of an infected female mosquito of the Aedes genus, but also sexual and blood transfusion transmission may occur. Moreover, a case of non-sexual spread from one person to another has been described, indicating that we still have more to learn about Zika transmission.Biological basis for pathogenetic effects are under investigation. Laboratory diagnosis is challenging since, so far, there are no "gold standard" diagnostic tools, and the low and short viremia in the acute phase, and together with the high cross-reactivity among the members of flavivirus genus are the most challenging aspects to be overcome.

  14. "Reinventing Life": Introductory Biology for a Rapidly Evolving World

    ERIC Educational Resources Information Center

    Coker, Jeffrey Scott

    2009-01-01

    Evolutionary concepts are essential for a scientific understanding of most issues surrounding modern medicine, agriculture, biotechnology, and the environment. If the mantra for biology education in the 20th century was, "Nothing in biology makes sense except in the light of evolution," the mantra for the 21st century must be, "Nothing in biology…

  15. Treatment of severe, refractory and rapidly evolving thrombotic thrombocytopenic purpura.

    PubMed

    Acedillo, Rey R; Govind, Mayur; Kashgary, Abdullah; Clark, William F

    2016-06-09

    A 36-year-old man presented to hospital with gross haematuria and evidence of severe, refractory thrombotic thrombocytopenic purpura. Initial treatment with high-volume plasma exchange therapy and early administration of rituximab failed to achieve a sustained clinical response. His clinical course was complicated by left hemianopsia and despite an urgent splenectomy he developed a large right-sided stroke with malignant cerebral oedema that required an emergent decompressive craniotomy. He also had numerous infectious complications as a consequence of an aggressive immunosuppressive strategy. While the patient did not respond to cyclophosphamide, cyclosporine, N-acetylcysteine, and one course of bortezomib, he eventually responded to a second course of bortezomib. One year later, the patient remains in remission and maintains excellent cognitive function. However, he has not completely recovered from his stroke and continues to participate in rehabilitation for his residual physical deficits. 2016 BMJ Publishing Group Ltd.

  16. Collateral damage: rapid exposure-induced evolution of pesticide resistance leads to increased susceptibility to parasites.

    PubMed

    Jansen, Mieke; Stoks, Robby; Coors, Anja; van Doorslaer, Wendy; de Meester, Luc

    2011-09-01

    Although natural populations may evolve resistance to anthropogenic stressors such as pollutants, this evolved resistance may carry costs. Using an experimental evolution approach, we exposed different Daphnia magna populations in outdoor containers to the carbamate pesticide carbaryl and control conditions, and assessed the resulting populations for both their resistance to carbaryl as well as their susceptibility to infection by the widespread bacterial microparasite Pasteuria ramosa. Our results show that carbaryl selection led to rapid evolution of carbaryl resistance with seemingly no cost when assessed in a benign environment. However, carbaryl-resistant populations were more susceptible to parasite infection than control populations. Exposure to both stressors reveals a synergistic effect on sterilization rate by P. ramosa, but this synergism did not evolve under pesticide selection. Assessing costs of rapid adaptive evolution to anthropogenic stress in a semi-natural context may be crucial to avoid too optimistic predictions for the fitness of the evolving populations. © 2011 The Author(s).

  17. Rapid carbon-carbon bond formation and cleavage revealed by carbon isotope exchange between the carboxyl carbon and inorganic carbon in hydrothermal fluids

    NASA Astrophysics Data System (ADS)

    Glein, C. R.; Cody, G. D.

    2013-12-01

    The carbon isotopic composition of organic compounds in water-rock systems (e.g., hydrothermal vents, sedimentary basins, and carbonaceous meteorites) is generally interpreted in terms of the isotopic composition of the sources of such molecules, and the kinetic isotope effects of metabolic or abiotic reactions that generate or transform such molecules. This hinges on the expectation that the carbon isotopic composition of many organic compounds is conserved under geochemical conditions. This expectation is reasonable in light of the strength of carbon-carbon bonds (ca. 81 kcal/mol); in general, environmental conditions conducive to carbon-carbon bond cleavage typically lead to transformations of organic molecules (decarboxylation is a notable example). Geochemically relevant reactions that involve isotopic exchange between carbon atoms in organic molecules and inorganic forms of carbon with no change in molecular structure appear to be rare. Notwithstanding such rarity, there have been preliminary reports of relatively rapid carbon isotope exchange between the carboxyl group in carboxylic acids and carbon dioxide in hot water [1,2]. We have performed laboratory hydrothermal experiments to gain insights into the mechanism of this surprising reaction, using phenylacetate as a model structure. By mass spectrometry, we confirm that the carboxyl carbon undergoes facile isotopic exchange with 13C-labeled bicarbonate at moderate temperatures (i.e., 230 C). Detailed kinetic analysis reveals that the reaction rate is proportional to the concentrations of both reactants. Further experiments demonstrate that the exchange reaction only occurs if the carbon atom adjacent to the carboxyl carbon is bonded to a hydrogen atom. As an example, no carbon isotope exchange was observed for benzoate in experiments lasting up to one month. The requirement of an alpha C-H bond suggests that enolization (i.e., deprotonation of the H) is a critical step in the mechanism of the exchange

  18. Synchrotron-based P K-edge XANES spectroscopy reveals rapid changes of phosphorus speciation in the topsoil of two glacier foreland chronosequences

    NASA Astrophysics Data System (ADS)

    Prietzel, Jörg; Dümig, Alexander; Wu, Yanhong; Zhou, Jun; Klysubun, Wantana

    2013-05-01

    Phosphorus (P) is a crucial element for life on Earth, and the bioavailability of P in terrestrial ecosystems, which is dependent on the soil P stock and its speciation, may limit ecosystem productivity and succession. In our study, for the first time a direct speciation of soil P in two glacier foreland chronosequences has been conducted using synchrotron-based X-ray Absorption Near-Edge Structure (XANES) spectroscopy. The chronosequences are located in the forefields of Hailuogou Glacier (Gongga Shan, China) and Damma Glacier (Swiss Alps). The age since deglaciation of the investigated soils ranges from 0 to 120 years at Hailuogou, and from 15 to >700 years at Damma. Differences in climate conditions (cooler at Damma, in contrast to Hailuogou precluding the establishment of forest in advanced ecosystem succession stages) and in the chemical composition of the parent material result in different soil contents of total P and Fe/Al oxyhydroxides, which are much smaller at Damma than at Hailuogou. Nevertheless, both chronosequences show similar trends of their topsoil P status with increasing soil age. Our study reveals a rapid change of topsoil P speciation in glacier retreat areas already during initial stages of pedogenesis: Initially dominating bedrock-derived apatite-P and Al-bound P is depleted; Fe-bound P and particularly organically-bound P is accumulated. Organic P strongly dominates in the topsoil of the mature soils outside the proglacial area of Damma Glacier (age 700-3000 years), and already 50 years after deglacation in the topsoil of the retreat area of Hailuogou Glacier. A key factor for the change in topsoil P speciation is the establishment of vegetation, resulting in soil organic matter (SOM) accumulation as well as accelerated soil acidification and apatite dissolution by organic acids, which are produced by SOM-degrading micro-organisms, mykorrhiza fungi, and plant roots. Particularly the succession of grassland to forest seems to accelerate the

  19. Rapid increase in total torquetenovirus (TTV) plasma viremia load reveals an apparently transient superinfection by a TTV of a novel group 2 genotype.

    PubMed

    Maggi, Fabrizio; Andreoli, Elisabetta; Lanini, Letizia; Meschi, Silvia; Rocchi, Jara; Fornai, Claudia; Vatteroni, Maria Linda; Pistello, Mauro; Bendinelli, Mauro

    2006-07-01

    An apparently transient infection by a superimposed torquetenovirus (TTV) in a subject who already carried three different genotypes of the virus is described. The superinfection induced a rapid increase in the plasma TTV load and a decline in immunocomplexed virus. The superinfecting TTV was a novel group 2 genotype.

  20. Voyages Through Time: Everything Evolves

    NASA Astrophysics Data System (ADS)

    Pendleton, Y. J.; Tarter, J. C.; DeVore, E. K.; O'Sullivan, K. A.; Taylor, S. M.

    2001-12-01

    Evolutionary change is a powerful framework for studying our world and our place therein. It is a recurring theme in every realm of science: over time, the universe, the planet Earth, life, and human technologies all change, albeit on vastly different scales. Evolution offers scientific explanations for the age-old question, "Where did we come from?" In addition, historical perspectives of science show how our understanding has evolved over time. The complexities of all of these systems will never reveal a "finished" story. But it is a story of epic size, capable of inspiring awe and of expanding our sense of time and place, and eminently worthy of investigating. This story is the basis of Voyages Through Time. Voyages Through Time (VTT), provides teachers with not only background science content and pedagogy, but also with materials and resources for the teaching of evolution. The six modules, Cosmic Evolution, Planetary Evolution, Origin of Life, Evolution of Life, Hominid Evolution, and Evolution of Technology, emphasize student inquiry, and promote the nature of science, as recommended in the NSES and BSL. The modules are unified by the overarching theme of evolution and the meta questions: "What is changing?" "What is the rate of change?" and "What is the mechanism of change?" Determination of student outcomes for the project required effective collaboration of scientists, teachers, students and media specialists. The broadest curricula students outcomes are 1) an enjoyment of science, 2) an understanding of the nature of science, especially the understanding of evidence and re-evaluation, and 3) key science content. The curriculum is being developed by the SETI Institute, NASA Ames Research Center, California Academy of Sciences, and San Francisco State University, and is funded by the NSF (IMD 9730693), with support form Hewlett-Packard Company, The Foundation for Microbiology, Combined Federated Charities, NASA Astrobiology Institute, and NASA Fundamental

  1. How did the cilium evolve?

    PubMed

    Satir, Peter; Mitchell, David R; Jékely, Gáspár

    2008-01-01

    The cilium is a characteristic organelle of eukaryotes constructed from over 600 proteins. Bacterial flagella are entirely different. 9 + 2 motile cilia evolved before the divergence of the last eukaryotic common ancestor (LECA). This chapter explores, compares, and contrasts two potential pathways of evolution: (1) via invasion of a centriolar-like virus and (2) via autogenous formation from a pre-existing microtubule-organizing center (MTOC). In either case, the intraflagellar transport (IFT) machinery that is nearly universally required for the assembly and maintenance of cilia derived from the evolving intracellular vesicular transport system. The sensory function of cilia evolved first and the ciliary axoneme evolved gradually with ciliary motility, an important selection mechanism, as one of the driving forces.

  2. Continuous Evaluation of Evolving Behavioral Intervention Technologies

    PubMed Central

    Mohr, David C.; Cheung, Ken; Schueller, Stephen M.; Brown, C. Hendricks; Duan, Naihua

    2013-01-01

    Behavioral intervention technologies (BITs) are web-based and mobile interventions intended to support patients and consumers in changing behaviors related to health, mental health, and well-being. BITs are provided to patients and consumers in clinical care settings and commercial marketplaces, frequently with little or no evaluation. Current evaluation methods, including RCTs and implementation studies, can require years to validate an intervention. This timeline is fundamentally incompatible with the BIT environment, where technology advancement and changes in consumer expectations occur quickly, necessitating rapidly evolving interventions. However, BITs can routinely and iteratively collect data in a planned and strategic manner and generate evidence through systematic prospective analyses, thereby creating a system that can “learn.” A methodologic framework, Continuous Evaluation of Evolving Behavioral Intervention Technologies (CEEBIT), is proposed that can support the evaluation of multiple BITs or evolving versions, eliminating those that demonstrate poorer outcomes, while allowing new BITs to be entered at any time. CEEBIT could be used to ensure the effectiveness of BITs provided through deployment platforms in clinical care organizations or BIT marketplaces. The features of CEEBIT are described, including criteria for the determination of inferiority, determination of BIT inclusion, methods of assigning consumers to BITs, definition of outcomes, and evaluation of the usefulness of the system. CEEBIT offers the potential to collapse initial evaluation and postmarketing surveillance, providing ongoing assurance of safety and efficacy to patients and consumers, payers, and policymakers. PMID:24050429

  3. Transistor Level Circuit Experiments using Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    Stoica, A.; Zebulum, R. S.; Keymeulen, D.; Ferguson, M. I.; Daud, Taher; Thakoor, A.

    2005-01-01

    The Jet Propulsion Laboratory (JPL) performs research in fault tolerant, long life, and space survivable electronics for the National Aeronautics and Space Administration (NASA). With that focus, JPL has been involved in Evolvable Hardware (EHW) technology research for the past several years. We have advanced the technology not only by simulation and evolution experiments, but also by designing, fabricating, and evolving a variety of transistor-based analog and digital circuits at the chip level. EHW refers to self-configuration of electronic hardware by evolutionary/genetic search mechanisms, thereby maintaining existing functionality in the presence of degradations due to aging, temperature, and radiation. In addition, EHW has the capability to reconfigure itself for new functionality when required for mission changes or encountered opportunities. Evolution experiments are performed using a genetic algorithm running on a DSP as the reconfiguration mechanism and controlling the evolvable hardware mounted on a self-contained circuit board. Rapid reconfiguration allows convergence to circuit solutions in the order of seconds. The paper illustrates hardware evolution results of electronic circuits and their ability to perform under 230 C temperature as well as radiations of up to 250 kRad.

  4. Continuous evaluation of evolving behavioral intervention technologies.

    PubMed

    Mohr, David C; Cheung, Ken; Schueller, Stephen M; Hendricks Brown, C; Duan, Naihua

    2013-10-01

    Behavioral intervention technologies (BITs) are web-based and mobile interventions intended to support patients and consumers in changing behaviors related to health, mental health, and well-being. BITs are provided to patients and consumers in clinical care settings and commercial marketplaces, frequently with little or no evaluation. Current evaluation methods, including RCTs and implementation studies, can require years to validate an intervention. This timeline is fundamentally incompatible with the BIT environment, where technology advancement and changes in consumer expectations occur quickly, necessitating rapidly evolving interventions. However, BITs can routinely and iteratively collect data in a planned and strategic manner and generate evidence through systematic prospective analyses, thereby creating a system that can "learn." A methodologic framework, Continuous Evaluation of Evolving Behavioral Intervention Technologies (CEEBIT), is proposed that can support the evaluation of multiple BITs or evolving versions, eliminating those that demonstrate poorer outcomes, while allowing new BITs to be entered at any time. CEEBIT could be used to ensure the effectiveness of BITs provided through deployment platforms in clinical care organizations or BIT marketplaces. The features of CEEBIT are described, including criteria for the determination of inferiority, determination of BIT inclusion, methods of assigning consumers to BITs, definition of outcomes, and evaluation of the usefulness of the system. CEEBIT offers the potential to collapse initial evaluation and postmarketing surveillance, providing ongoing assurance of safety and efficacy to patients and consumers, payers, and policymakers.

  5. Spacetimes containing slowly evolving horizons

    SciTech Connect

    Kavanagh, William; Booth, Ivan

    2006-08-15

    Slowly evolving horizons are trapping horizons that are ''almost'' isolated horizons. This paper reviews their definition and discusses several spacetimes containing such structures. These include certain Vaidya and Tolman-Bondi solutions as well as (perturbatively) tidally distorted black holes. Taking into account the mass scales and orders of magnitude that arise in these calculations, we conjecture that slowly evolving horizons are the norm rather than the exception in astrophysical processes that involve stellar-scale black holes.

  6. Variation of Genetic Diversity in a Rapidly Expanding Population of the Greater Long-Tailed Hamster (Tscherskia triton) as Revealed by Microsatellites

    PubMed Central

    Xu, Laixiang; Xue, Huiliang; Song, Mingjing; Zhao, Qinghua; Dong, Jingping; Liu, Juan; Guo, Yu; Xu, Tongqin; Cao, Xiaoping; Wang, Fusheng; Wang, Shuqing; Hao, Shushen; Yang, Hefang; Zhang, Zhibin

    2013-01-01

    Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984–1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn. PMID:23349815

  7. Variation of genetic diversity in a rapidly expanding population of the greater long-tailed hamster (Tscherskia triton) as revealed by microsatellites.

    PubMed

    Xu, Laixiang; Xue, Huiliang; Song, Mingjing; Zhao, Qinghua; Dong, Jingping; Liu, Juan; Guo, Yu; Xu, Tongqin; Cao, Xiaoping; Wang, Fusheng; Wang, Shuqing; Hao, Shushen; Yang, Hefang; Zhang, Zhibin

    2013-01-01

    Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984-1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn.

  8. Transcriptome profiles of hybrid poplar (Populus trichocarpa × deltoides) reveal rapid changes in undamaged, systemic sink leaves after simulated feeding by forest tent caterpillar (Malacosoma disstria).

    PubMed

    Philippe, Ryan N; Ralph, Steven G; Mansfield, Shawn D; Bohlmann, Jörg

    2010-11-01

    • Poplar has been established as a model tree system for genomic research of the response to biotic stresses. This study describes a series of induced transcriptome changes and the associated physiological characterization of local and systemic responses in hybrid poplar (Populus trichocarpa × deltoides) after simulated herbivory. • Responses were measured in local source (LSo), systemic source (SSo), and systemic sink (SSi) leaves following application of forest tent caterpillar (Malacosoma disstria) oral secretions to mechanically wounded leaves. • Transcriptome analyses identified spatially and temporally dynamic, distinct patterns of local and systemic gene expression in LSo, SSo and SSi leaves. Galactinol synthase was strongly and rapidly upregulated in SSi leaves. Genome analyses and full-length cDNA cloning established an inventory of poplar galactinol synthases. Induced changes of galactinol and raffinose oligosaccharides were detected by anion-exchange high-pressure liquid chromatography. • The LSo leaves showed a rapid and strong transcriptome response compared with a weaker and slower response in adjacent SSo leaves. Surprisingly, the transcriptome response in distant, juvenile SSi leaves was faster and stronger than that observed in SSo leaves. Systemic transcriptome changes of SSi leaves have signatures of rapid change of metabolism and signaling, followed by later induction of defense genes.

  9. Revisiting human natural killer cell subset function revealed cytolytic CD56dimCD16+ NK cells as rapid producers of abundant IFN-γ on activation

    PubMed Central

    De Maria, Andrea; Bozzano, Federica; Cantoni, Claudia; Moretta, Lorenzo

    2011-01-01

    The two major functions of human natural killer (NK) cells are conventionally associated with distinct cell subsets. Thus, cytolytic activity is mostly confined to the CD56dimCD16+ subset, whereas cytokine production is generally assigned to CD56brightCD16+/− cells. In this study, we reevaluated the functional capabilities of these NK subsets with regard to the production of IFN-γ at different time points after cell triggering via NKp46 and NKp30 activating receptors. Different from previous studies, cytokine production was also assessed at early intervals. We show that CD56dim NK cells produce IFN-γ already at 2 to 4 h, whereas no cytokine production is detected beyond 16 h. In contrast, CD56bright cells release IFN-γ only at late time intervals (>16 h after stimulation). The rapid IFN-γ production by CD56dim NK cells is in line with the presence of IFN-γ mRNA in freshly isolated cells. Rapid IFN-γ production was also induced by combinations of IL-2, IL-12, and IL-15. Our data indicate that not only cytolytic activity but also early IFN-γ production is a functional property of CD56dim NK cells. Thus, this subset can assure a rapid and comprehensive NK cell intervention during the early phases of innate responses. PMID:21187373

  10. 18O/16O in CO2 evolved from goethite during some unusually rapid solid state α-FeOOH to α-Fe2O3 phase transitions: Test of an exchange model for possible use in oxygen isotope analyses of goethite

    NASA Astrophysics Data System (ADS)

    Yapp, Crayton J.

    2015-12-01

    The initial ∼60% of an isothermal vacuum dehydration of goethite can commonly be approximated by first order kinetics. Also, natural goethites contain small amounts of an Fe(CO3)OH component in apparent solid solution. The 18O/16O of CO2 evolved from the Fe(CO3)OH during isothermal vacuum dehydrations is related to the 18O/16O of the goethite by an apparent fractionation factor (αapp) that is, in turn, correlated with a first order rate constant, |m|. A kinetic exchange model predicts that αapp should decrease as |m| increases for a range of |m| that corresponds to relatively slow rates of dehydration. This pattern has been observed in published results. In contrast, for rapid rates of dehydration, αapp is predicted to increase with increasing |m|. Isothermal vacuum dehydrations of two natural goethites had unusually large values of |m| and provided serendipitous tests of this rapid-rate prediction. For these experiments, the measured values of αapp were consistent with patterns of variation predicted by the model. This allowed an estimate of the activation energy (E2) of a model parameter, K2, which is the rate constant for oxygen isotope exchange between CO2 and H2O during the solid-state goethite to hematite phase transition. The estimated value of E2 is only ∼9 kJ/mol. Heterogeneous catalysis tends to decrease the activation energies of gas reactions. Consequently, the inferred value of E2 suggests that goethite and/or hematite catalyze oxygen isotope exchange between CO2 and H2O during the solid-state phase change. Yield, δ13C, and δ18O values are routinely measured for increments of CO2 evolved from the Fe(CO3)OH component during isothermal vacuum dehydration of goethite. Model-predicted values of αapp can be combined with plateau δ18O values of the evolved CO2 to estimate the δ18O of the goethite with a less than optimal, but potentially useful, precision of about ±0.8‰. Therefore, a single analytical procedure (incremental dehydration

  11. Robustness to Faults Promotes Evolvability: Insights from Evolving Digital Circuits

    PubMed Central

    Nolfi, Stefano

    2016-01-01

    We demonstrate how the need to cope with operational faults enables evolving circuits to find more fit solutions. The analysis of the results obtained in different experimental conditions indicates that, in absence of faults, evolution tends to select circuits that are small and have low phenotypic variability and evolvability. The need to face operation faults, instead, drives evolution toward the selection of larger circuits that are truly robust with respect to genetic variations and that have a greater level of phenotypic variability and evolvability. Overall our results indicate that the need to cope with operation faults leads to the selection of circuits that have a greater probability to generate better circuits as a result of genetic variation with respect to a control condition in which circuits are not subjected to faults. PMID:27409589

  12. Robustness to Faults Promotes Evolvability: Insights from Evolving Digital Circuits.

    PubMed

    Milano, Nicola; Nolfi, Stefano

    2016-01-01

    We demonstrate how the need to cope with operational faults enables evolving circuits to find more fit solutions. The analysis of the results obtained in different experimental conditions indicates that, in absence of faults, evolution tends to select circuits that are small and have low phenotypic variability and evolvability. The need to face operation faults, instead, drives evolution toward the selection of larger circuits that are truly robust with respect to genetic variations and that have a greater level of phenotypic variability and evolvability. Overall our results indicate that the need to cope with operation faults leads to the selection of circuits that have a greater probability to generate better circuits as a result of genetic variation with respect to a control condition in which circuits are not subjected to faults.

  13. Measuring microscale strain fields in articular cartilage during rapid impact reveals thresholds for chondrocyte death and a protective role for the superficial layer

    PubMed Central

    Bartell, Lena R.; Fortier, Lisa A.; Bonassar, Lawrence J.; Cohen, Itai

    2015-01-01

    Articular cartilage is a heterogeneous soft tissue that dissipates and distributes loads in mammalian joints. Though robust, cartilage is susceptible to damage from loading at high rates or magnitudes. Such injurious loads have been implicated in degenerative changes, including chronic osteoarthritis (OA), which remains a leading cause of disability in developed nations. Despite decades of research, mechanisms of OA initiation after trauma remain poorly understood. Indeed, although bulk cartilage mechanics are measurable during impact, current techniques cannot access microscale mechanics at those rapid time scales. We aimed to address this knowledge gap by imaging the microscale mechanics and corresponding acute biological changes of cartilage in response to rapid loading. In this study, we utilized fast-camera and confocal microscopy to achieve roughly 85 μm spatial resolution of the cartilage deformation during a rapid (~3 ms), localized impact and the chondrocyte death following impact. Our results showed that, at these high rates, strain and chondrocyte death were highly correlated (p<0.001) with a threshold of 8% microscale strain norm before any cell death occurred. Additionally, chondrocyte death had developed by two hours after impact, suggesting a time frame for clinical therapeutics. Moreover, when the superficial layer was removed, strain – and subsequently chondrocyte death – penetrated deeper into the samples (p<0.001), suggesting a protective role for the superficial layer of articular cartilage. Combined, these results provide insight regarding the detailed biomechanics that drive early chondrocyte damage after trauma and emphasize the importance of understanding cartilage and its mechanics on the microscale. PMID:26150096

  14. Episodic rapid uplift in the Himalaya revealed by sup 40 Ar/ sup 39 Ar analysis of detrital K-feldspar and muscovite, Bengal fan

    SciTech Connect

    Harrison, T.M.; Copeland, P. )

    1990-04-01

    Detrital K-feldspar and muscovite samples from Ocean Drilling Program Leg 116 cores have been dated by the {sup 40}Ar/{sup 39}Ar technique and have depositional ages from 0 to 18 Ma. From 4 to 13 individual K-feldspars and 1 to 12 individual muscovites have been dated from 7 stratigraphic levels. In every level at least one K-feldspar and one muscovite yielded a minimum age identical, within uncertainty, to the age of deposition. These results indicate that a significant portion of the material in the Bengal fan is first-cycle detritus derived from the Himalaya. Therefore, the substantial amount of sediment deposited in the distal fan in early to middle Miocene time can be ascribed to a significant pulse of uplift and erosion in the collision zone at this time. Moreover, these data indicate that throughout the Neogene, some part of the Himalayan orogen was undergoing rapid erosion (1 to 10 mm/yr); this erosion must have been less than or equal to uplift relative to sea level. The lack of granulite facies rocks in the eastern Himalaya and Tibetan plateau suggests to us that very rapid uplift must have been distributed in brief pulses over different parts of the mountain belt. These data are incompatible with tectonic models in which the Himalaya and Tibetan plateau are uplifted either uniformly over the past 40 m.y. or mostly within the past 2 to 5 m.y.

  15. Scar State on Time-evolving Wavepacket

    NASA Astrophysics Data System (ADS)

    Tomiya, Mitsuyoshi; Tsuyuki, Hiroyoshi; Kawamura, Kentaro; Sakamoto, Shoichi; Heller, Eric J.

    2015-09-01

    The scar-like enhancement is found in the accumulation of the time-evolving wavepacket in stadium billiard. It appears close to unstable periodic orbits, when the wavepackets are launched along the orbits. The enhancement is essentially due to the same mechanism of the well-known scar states in stationary eigenstates. The weighted spectral function reveals that the enhancement is the pileup of contributions from scar states on the same periodic orbit. The availavility of the weighted spectrum to the semiclassical approximation is also disscussed.

  16. Challenge of Pigs with Classical Swine Fever Viruses after C-Strain Vaccination Reveals Remarkably Rapid Protection and Insights into Early Immunity

    PubMed Central

    Haines, Felicity J.; Johns, Helen L.; Sosan, Olubukola A.; Salguero, Francisco J.; Clifford, Derek J.; Steinbach, Falko; Drew, Trevor W.; Crooke, Helen R.

    2012-01-01

    Pre-emptive culling is becoming increasingly questioned as a means of controlling animal diseases, including classical swine fever (CSF). This has prompted discussions on the use of emergency vaccination to control future CSF outbreaks in domestic pigs. Despite a long history of safe use in endemic areas, there is a paucity of data on aspects important to emergency strategies, such as how rapidly CSFV vaccines would protect against transmission, and if this protection is equivalent for all viral genotypes, including highly divergent genotype 3 strains. To evaluate these questions, pigs were vaccinated with the Riemser® C-strain vaccine at 1, 3 and 5 days prior to challenge with genotype 2.1 and 3.3 challenge strains. The vaccine provided equivalent protection against clinical disease caused by for the two challenge strains and, as expected, protection was complete at 5 days post-vaccination. Substantial protection was achieved after 3 days, which was sufficient to prevent transmission of the 3.3 strain to animals in direct contact. Even by one day post-vaccination approximately half the animals were partially protected, and were able to control the infection, indicating that a reduction of the infectious potential is achieved very rapidly after vaccination. There was a close temporal correlation between T cell IFN-γ responses and protection. Interestingly, compared to responses of animals challenged 5 days after vaccination, challenge of animals 3 or 1 days post-vaccination resulted in impaired vaccine-induced T cell responses. This, together with the failure to detect a T cell IFN-γ response in unprotected and unvaccinated animals, indicates that virulent CSFV can inhibit the potent antiviral host defences primed by C-strain in the early period post vaccination. PMID:22235283

  17. Smooth and rapid slip near the Japan Trench during the 2011 Tohoku-oki earthquake revealed by a hybrid back-projection method

    NASA Astrophysics Data System (ADS)

    Yagi, Yuji; Nakao, Atsushi; Kasahara, Amato

    2012-11-01

    We developed a new back-projection method that uses teleseismic P-waveforms to integrate the direct P-phase with reflected phases from structural discontinuities near the source and used it to estimate the spatiotemporal distribution of the seismic energy release of the 2011 Tohoku-oki earthquake. We projected a normalized cross-correlation of observed waveforms with corresponding Green's functions onto the seismic source region to obtain a high-resolution image of the seismic energy release. Applying this method to teleseismic P-waveform data of the 2011 Tohoku-oki earthquake, we obtained spatiotemporal distributions of seismic energy release for two frequency bands, a low-frequency dataset and a high-frequency dataset. We showed that the energy radiated in the dip direction was strongly frequency dependent. The area of major high-frequency seismic radiation extended only downdip from the hypocenter, whereas the area of major low-frequency seismic radiation propagated both downdip and updip from the hypocenter. We detected a large release of seismic energy near the Japan Trench in the area of maximum slip, which was also the source area of the gigantic tsunami, when we used only the low-frequency dataset. The timing of this large seismic energy release corresponded to an episode of smooth and rapid slip near the Japan Trench, and reflects the strong dependence of the seismic energy distribution obtained on the frequency band of the input waveform dataset. The episode of smooth and rapid slip may have been the trigger for a release of roughly all of the accumulated elastic strain in the seismic source region of the 2011 Tohoku-oki earthquake.

  18. A novel cell lysis approach reveals that caspase-2 rapidly translocates from the nucleus to the cytoplasm in response to apoptotic stimuli.

    PubMed

    Tinnikov, Alexander A; Samuels, Herbert H

    2013-01-01

    Unlike other caspases, caspase-2 appears to be a nuclear protein although immunocytochemical studies have suggested that it may also be localized to the cytosol and golgi. Where and how caspase-2 is activated in response to apoptotic signals is not clear. Earlier immunocytochemistry studies suggest that caspase-2 is activated in the nucleus and through cleavage of BID leads to increased mitochondrial permeability. More recent studies using bimolecular fluorescence complementation found that caspase-2 oligomerization that leads to activation only occurs in the cytoplasm. Thus, apoptotic signals may lead to activation of caspase-2 which may already reside in the cytoplasm or lead to release of nuclear caspase-2 to the extra-nuclear cytoplasmic compartment. It has not been possible to study release of nuclear caspase-2 to the cytoplasm by cell fractionation studies since cell lysis is known to release nuclear caspase-2 to the extra-nuclear fraction. This is similar to what is known about unliganded nuclear estrogen receptor-α (ERα ) when cells are disrupted. In this study we found that pre-treatment of cells with N-ethylmaleimide (NEM), which alkylates cysteine thiol groups in proteins, completely prevents redistribution of caspase-2 and ERα from the nucleus to the extra-nuclear fraction when cells are lysed. Using this approach we provide evidence that apoptotic signals rapidly leads to a shift of caspase-2 from the nucleus to the extra-nuclear fraction, which precedes the detection of apoptosis. These findings are consistent with a model where apoptotic signals lead to a rapid shift of caspase-2 from the nucleus to the cytoplasm where activation occurs.

  19. Tuberculosis Case Finding in HIV-Infected Pregnant Women in Kenya Reveals Poor Performance of Symptom Screening and Rapid Diagnostic Tests.

    PubMed

    LaCourse, Sylvia M; Cranmer, Lisa M; Matemo, Daniel; Kinuthia, John; Richardson, Barbra A; John-Stewart, Grace; Horne, David J

    2016-02-01

    Tuberculosis (TB) during pregnancy in HIV-infected women is associated with poor maternal and infant outcomes. There are limited data on TB prevalence, optimal TB screening, and performance of rapid diagnostics in pregnant HIV-infected women. We conducted a cross-sectional study among HIV-infected pregnant women seeking antenatal care in western Kenya. After a standardized questionnaire, sputum smear microscopy for acid-fast bacilli, mycobacterial liquid culture, GeneXpert MTB/RIF (Xpert), urine lipoarabinomannan, and tuberculin skin testing were performed. We determined prevalence and correlates of culture-confirmed pulmonary TB, and compared diagnostic performance of World Health Organization (WHO) symptom screening and rapid diagnostic tests to sputum culture. Between July 2013 and July 2014, we enrolled 306 women. Among 288 women with a valid sputum culture result, 54% were on antiretroviral treatment, median CD4 cell count was 437 cell per cubic millimeter (IQR 342-565), and prevalence of culture-confirmed pulmonary TB was 2.4% (confidence interval: 1.0% to 4.9%). Cough >2 weeks (P = 0.04) and positive tuberculin skin testing (≥ 5 mm, P = 0.03) were associated with pulmonary TB. Women with TB were 23-fold (95% confidence interval: 4.4 to 116.6) more likely to report a household member with TB symptoms (P = 0.002). WHO symptom screen (43%), acid-fast bacilli smear (0%), Xpert (43%), and lipoarabinomannan (0%) had low sensitivity but high specificity (81%, 99%, 99%, and 95%, respectively) for pulmonary TB. HIV-infected pregnant women had appreciable prevalence of pulmonary TB despite modest immunosuppression. Current TB screening and diagnostic tools perform poorly in pregnant HIV-infected women. Adapted TB screening tools that include household member TB symptoms may be useful in this population.

  20. Medial prefrontal cortical estradiol rapidly alters memory system bias in female rats: ultrastructural analysis reveals membrane-associated estrogen receptors as potential mediators.

    PubMed

    Almey, Anne; Cannell, Elizabeth; Bertram, Kyla; Filardo, Edward; Milner, Teresa A; Brake, Wayne G

    2014-11-01

    High plasma levels of estradiol (E2) are associated with use of a place memory system over a response memory system. We examined whether infusing estradiol into the medial prefrontal cortex (mPFC) or anterior cingulate cortex (AC) could affect memory system bias in female rats. We also examined the ultrastructural distribution of estrogen receptor (ER)-α, ERβ, and G protein-coupled estrogen receptor 1 (GPER1) in the mPFC of female rats as a mechanism for the behavioral effects of E2 in the mPFC. Each rat was infused bilaterally with either E2 (0.13 μg) or vehicle into the mPFC or AC. The majority of E2 mPFC rats used place memory. In contrast, the majority of mPFC vehicle rats and AC E2 or vehicle rats used response memory. These data show that mPFC E2 rapidly biases females to use place memory. Electron microscopic analysis demonstrated that ERα, ERβ, and GPER1 are localized in the mPFC, almost exclusively at extranuclear sites. This is the first time that GPER1 has been localized to the mPFC of rats and the first time that ERα and ERβ have been described at extranuclear sites in the rat mPFC. The majority of receptors were observed on axons and axon terminals, suggesting that estrogens alter presynaptic transmission in the mPFC. This provides a mechanism via which ERs could rapidly alter transmission in the mPFC to alter PFC-dependent behaviors, such as memory system bias. The discrete nature of immunolabeling for these membrane-associated ERs may explain the discrepancy in previous light microscopy studies.

  1. Medial Prefrontal Cortical Estradiol Rapidly Alters Memory System Bias in Female Rats: Ultrastructural Analysis Reveals Membrane-Associated Estrogen Receptors as Potential Mediators

    PubMed Central

    Cannell, Elizabeth; Bertram, Kyla; Filardo, Edward; Milner, Teresa A.

    2014-01-01

    High plasma levels of estradiol (E2) are associated with use of a place memory system over a response memory system. We examined whether infusing estradiol into the medial prefrontal cortex (mPFC) or anterior cingulate cortex (AC) could affect memory system bias in female rats. We also examined the ultrastructural distribution of estrogen receptor (ER)-α, ERβ, and G protein-coupled estrogen receptor 1 (GPER1) in the mPFC of female rats as a mechanism for the behavioral effects of E2 in the mPFC. Each rat was infused bilaterally with either E2 (0.13 μg) or vehicle into the mPFC or AC. The majority of E2 mPFC rats used place memory. In contrast, the majority of mPFC vehicle rats and AC E2 or vehicle rats used response memory. These data show that mPFC E2 rapidly biases females to use place memory. Electron microscopic analysis demonstrated that ERα, ERβ, and GPER1 are localized in the mPFC, almost exclusively at extranuclear sites. This is the first time that GPER1 has been localized to the mPFC of rats and the first time that ERα and ERβ have been described at extranuclear sites in the rat mPFC. The majority of receptors were observed on axons and axon terminals, suggesting that estrogens alter presynaptic transmission in the mPFC. This provides a mechanism via which ERs could rapidly alter transmission in the mPFC to alter PFC-dependent behaviors, such as memory system bias. The discrete nature of immunolabeling for these membrane-associated ERs may explain the discrepancy in previous light microscopy studies. PMID:25211590

  2. Tuberculosis case finding in HIV-infected pregnant women in Kenya reveals poor performance of symptom screening and rapid diagnostic tests

    PubMed Central

    LaCourse, Sylvia M.; Cranmer, Lisa M.; Matemo, Daniel; Kinuthia, John; Richardson, Barbra A.; John-Stewart, Grace; Horne, David J.

    2015-01-01

    Background Tuberculosis (TB) during pregnancy in HIV-infected women is associated with poor maternal and infant outcomes. There are limited data on TB prevalence, optimal TB screening, and performance of rapid diagnostics in pregnant HIV-infected women. Methods We conducted a cross-sectional study among HIV-infected pregnant women seeking antenatal care in western Kenya. Following a standardized questionnaire, sputum smear microscopy for acid-fast bacilli (AFB), mycobacterial liquid culture, GeneXpert MTB/RIF (Xpert), urine lipoarabinomannan (LAM), and tuberculin skin testing (TST) were performed. We determined prevalence and correlates of culture-confirmed pulmonary TB, and compared diagnostic performance of World Health Organization (WHO) symptom screening and rapid diagnostic tests to sputum culture. Results Between July 2013 and July 2014, we enrolled 306 women. Among 288 women with a valid sputum culture result, 54% were on antiretroviral treatment, median CD4 cell count was 437 cell/mm3 (IQR 342–565), and prevalence of culture-confirmed pulmonary TB was 2.4% (CI 1.0–4.9%). Cough >2 weeks (p=0.04) and positive TST (≥5mm, p=0.03) were associated with pulmonary TB. Women with TB were 23-fold (95% CI 4.4–116.6) more likely to report a household member with TB symptoms (p=0.002). WHO symptom screen (43%), AFB smear (0%), Xpert (43%) and LAM (0%) had low sensitivity but high specificity (81%, 99%, 99% and 95%, respectively) for pulmonary TB. Conclusion HIV-infected pregnant women had appreciable prevalence of pulmonary TB despite modest immunosuppression. Current TB screening and diagnostic tools perform poorly in pregnant HIV-infected women. Adapted TB screening tools that include household member TB symptoms may be useful in this population. PMID:26334736

  3. The Evolving Status of Photojournalism Education. ERIC Digest.

    ERIC Educational Resources Information Center

    Cookman, Claude

    Noting that new technologies are resulting in extensive changes in the field of photojournalism, both as it is practiced and taught, this Digest reviews this rapidly evolving field of education and professional practice. It discusses what digital photography is; the history of digital photography; how digital photography has changed…

  4. Evolving Sensitivity Balances Boolean Networks

    PubMed Central

    Luo, Jamie X.; Turner, Matthew S.

    2012-01-01

    We investigate the sensitivity of Boolean Networks (BNs) to mutations. We are interested in Boolean Networks as a model of Gene Regulatory Networks (GRNs). We adopt Ribeiro and Kauffman’s Ergodic Set and use it to study the long term dynamics of a BN. We define the sensitivity of a BN to be the mean change in its Ergodic Set structure under all possible loss of interaction mutations. Insilico experiments were used to selectively evolve BNs for sensitivity to losing interactions. We find that maximum sensitivity was often achievable and resulted in the BNs becoming topologically balanced, i.e. they evolve towards network structures in which they have a similar number of inhibitory and excitatory interactions. In terms of the dynamics, the dominant sensitivity strategy that evolved was to build BNs with Ergodic Sets dominated by a single long limit cycle which is easily destabilised by mutations. We discuss the relevance of our findings in the context of Stem Cell Differentiation and propose a relationship between pluripotent stem cells and our evolved sensitive networks. PMID:22586459

  5. Slippery Texts and Evolving Literacies

    ERIC Educational Resources Information Center

    Mackey, Margaret

    2007-01-01

    The idea of "slippery texts" provides a useful descriptor for materials that mutate and evolve across different media. Eight adult gamers, encountering the slippery text "American McGee's Alice," demonstrate a variety of ways in which players attempt to manage their attention as they encounter a new text with many resonances. The range of their…

  6. Thermal and evolved gas analyzer

    NASA Technical Reports Server (NTRS)

    Williams, M. S.; Boynton, W. V.; James, R. L.; Verts, W. T.; Bailey, S. H.; Hamara, D. K.

    1998-01-01

    The Thermal and Evolved Gas Analyzer (TEGA) instrument will perform calorimetry and evolved gas analysis on soil samples collected from the Martian surface. TEGA is one of three instruments, along with a robotic arm, that form the Mars Volatile and Climate Survey (MVACS) payload. The other instruments are a stereo surface imager, built by Peter Smith of the University of Arizona and a meteorological station, built by JPL. The MVACS lander will investigate a Martian landing site at approximately 70 deg south latitude. Launch will take place from Kennedy Space Center in January, 1999. The TEGA project started in February, 1996. In the intervening 24 months, a flight instrument concept has been designed, prototyped, built as an engineering model and flight model, and tested. The instrument performs laboratory-quality differential-scanning calorimetry (DSC) over the temperature range of Mars ambient to 1400K. Low-temperature volatiles (water and carbon dioxide ices) and the carbonates will be analyzed in this temperature range. Carbonates melt and evolve carbon dioxide at temperatures above 600 C. Evolved oxygen (down to a concentration of 1 ppm) is detected, and C02 and water vapor and the isotopic variations of C02 and water vapor are detected and their concentrations measured. The isotopic composition provides important tests of the theory of solar system formation.

  7. The Evolving Demand for Skills.

    ERIC Educational Resources Information Center

    Greenspan, Alan

    From a macroeconomic perspective, the evolving demand for skills in the United States has been triggered by the accelerated expansion of computer and information technology, which has, in turn, brought significant changes to the workplace. Technological advances have made some wholly manual jobs obsolete. But even for many other workers, a rapidly…

  8. Signing Apes and Evolving Linguistics.

    ERIC Educational Resources Information Center

    Stokoe, William C.

    Linguistics retains from its antecedents, philology and the study of sacred writings, some of their apologetic and theological bias. Thus it has not been able to face squarely the question how linguistic function may have evolved from animal communication. Chimpanzees' use of signs from American Sign Language forces re-examination of language…

  9. Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance.

    PubMed

    Alexander, Michelle; Ho, Simon Y W; Molak, Martyna; Barnett, Ross; Carlborg, Örjan; Dorshorst, Ben; Honaker, Christa; Besnier, Francois; Wahlberg, Per; Dobney, Keith; Siegel, Paul; Andersson, Leif; Larson, Greger

    2015-10-01

    Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10(-7) mutations/site/year (95% confidence interval 3.75 × 10(-8)-1.12 × 10(-6)). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.

  10. Metabolomic analysis reveals key metabolites related to the rapid adaptation of Saccharomyce cerevisiae to multiple inhibitors of furfural, acetic acid, and phenol.

    PubMed

    Wang, Xin; Li, Bing-Zhi; Ding, Ming-Zhu; Zhang, Wei-Wen; Yuan, Ying-Jin

    2013-03-01

    During hydrolysis of lignocellulosic biomass, a broad range of inhibitors are generated, which interfere with yeast growth and bioethanol production. In order to improve the strain tolerance to multiple inhibitors--acetic acid, furfural, and phenol (three representative lignocellulose-derived inhibitors) and uncover the underlying tolerant mechanism, an adaptation experiment was performed in which the industrial Saccharomyces cerevisiae was cultivated repeatedly in a medium containing multiple inhibitors. The adaptation occurred quickly, accompanied with distinct increase in growth rate, glucose utilization rate, furfural metabolism rate, and ethanol yield, only after the first transfer. A similar rapid adaptation was also observed for the lab strains of BY4742 and BY4743. The metabolomic analysis was employed to investigate the responses of the industrial S. cereviaise to three inhibitors during the adaptation. The results showed that higher levels of 2-furoic acid, 2, 3-butanediol, intermediates in glycolytic pathway, and amino acids derived from glycolysis, were discovered in the adapted strains, suggesting that enhanced metabolic activity in these pathways may relate to resistance against inhibitors. Additionally, through single-gene knockouts, several genes related to alanine metabolism, GABA shunt, and glycerol metabolism were verified to be crucial for the resistance to multiple inhibitors. This study provides new insights into the tolerance mechanism against multiple inhibitors, and guides for the improvement of tolerant ethanologenic yeast strains for lignocellulose-bioethanol fermentation.

  11. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data.

    PubMed

    Tao, Yong; Ruan, Jue; Yeh, Shiou-Hwei; Lu, Xuemei; Wang, Yu; Zhai, Weiwei; Cai, Jun; Ling, Shaoping; Gong, Qiang; Chong, Zecheng; Qu, Zhengzhong; Li, Qianqian; Liu, Jiang; Yang, Jin; Zheng, Caihong; Zeng, Changqing; Wang, Hurng-Yi; Zhang, Jing; Wang, Sheng-Han; Hao, Lingtong; Dong, Lili; Li, Wenjie; Sun, Min; Zou, Wei; Yu, Caixia; Li, Chaohua; Liu, Guojing; Jiang, Lan; Xu, Jin; Huang, Huanwei; Li, Chunyan; Mi, Shuangli; Zhang, Bing; Chen, Baoxian; Zhao, Wenming; Hu, Songnian; Zhuang, Shi-Mei; Shen, Yang; Shi, Suhua; Brown, Christopher; White, Kevin P; Chen, Ding-Shinn; Chen, Pei-Jer; Wu, Chung-I

    2011-07-19

    We present the analysis of the evolution of tumors in a case of hepatocellular carcinoma. This case is particularly informative about cancer growth dynamics and the underlying driving mutations. We sampled nine different sections from three tumors and seven more sections from the adjacent nontumor tissues. Selected sections were subjected to exon as well as whole-genome sequencing. Putative somatic mutations were then individually validated across all 9 tumor and 7 nontumor sections. Among the mutations validated, 24 were amino acid changes; in addition, 22 large indels/copy number variants (>1 Mb) were detected. These somatic mutations define four evolutionary lineages among tumor cells. Separate evolution and expansion of these lineages were recent and rapid, each apparently having only one lineage-specific protein-coding mutation. Hence, by using a cell-population genetic definition, this approach identified three coding changes (CCNG1, P62, and an indel/fusion gene) as tumor driver mutations. These three mutations, affecting cell cycle control and apoptosis, are functionally distinct from mutations that accumulated earlier, many of which are involved in inflammation/immunity or cell anchoring. These distinct functions of mutations at different stages may reflect the genetic interactions underlying tumor growth.

  12. Non-uniform Evolving Hypergraphs and Weighted Evolving Hypergraphs

    PubMed Central

    Guo, Jin-Li; Zhu, Xin-Yun; Suo, Qi; Forrest, Jeffrey

    2016-01-01

    Firstly, this paper proposes a non-uniform evolving hypergraph model with nonlinear preferential attachment and an attractiveness. This model allows nodes to arrive in batches according to a Poisson process and to form hyperedges with existing batches of nodes. Both the number of arriving nodes and that of chosen existing nodes are random variables so that the size of each hyperedge is non-uniform. This paper establishes the characteristic equation of hyperdegrees, calculates changes in the hyperdegree of each node, and obtains the stationary average hyperdegree distribution of the model by employing the Poisson process theory and the characteristic equation. Secondly, this paper constructs a model for weighted evolving hypergraphs that couples the establishment of new hyperedges, nodes and the dynamical evolution of the weights. Furthermore, what is obtained are respectively the stationary average hyperdegree and hyperstrength distributions by using the hyperdegree distribution of the established unweighted model above so that the weighted evolving hypergraph exhibits a scale-free behavior for both hyperdegree and hyperstrength distributions. PMID:27845334

  13. Molecular 14-C analyses on lipid biomarkers in the water column and surface sediments reveal rapid aging of remobilized terrestrial organic carbon in a sub-Arctic basin

    NASA Astrophysics Data System (ADS)

    Vonk, J.; Gustafsson, Ö.; van Dongen, B.

    2009-04-01

    Riverine export of terrestrial organic carbon (terrOC) plays an important role in the global carbon cycle. Molecular composition, phase associations, transport and remineralization processes determine the fate of terrOC in the world's shelf areas, thereby potentially influencing climate through various carbon-climate feedback links. The vast sub-Arctic and Arctic terrestrial carbon pools, freeze-locked in northern peatlands, could be of particular interest in a warming climate scenario. The Kalix River, flowing into the Bothnian Bay in the northernmost Baltic Sea is one of Europe's largest unregulated rivers, draining sub-Arctic peatland prone to climate-warming effects. The Kalix is believed to resemble the great western Siberian-Arctic rivers that are far less accessible but draining similar, still partly frozen, high carbon content areas. Here we present compound-specific radiocarbon analysis (CSRA) on terrestrial lipid biomarkers in surface water particulate OC (POC) from the Kalix - Bothnian Bay system. In combination with bulk 14-C and CSRA on surface sediments from the same off-river transect this shows (1) a rapid apparent aging of long-chain n-alkanoic acids from water column to surface sediments and (2) long-chain n-alkane 14-C ages in surface sediments that are similar and even older than catchment peat basal ages. This combines with mass balance modelling results for this system to suggest a higher reactivity of remobilized recalcitrant terrOC than previously thought. We hypothesize that the terrOC is released from two different pools. Soil surface layers release humic-rich, easily degrading OC that mostly stays in suspension whereas OC that is coated to heavier mineral particles from deeper soil layers degrades slower and settles faster. Fraction modern 14-C signals in the range 0.18 - 0.47 of presumably mineral-bound terrestrial OC in surface sediments may indicate ongoing remobilization of ancient carbon reservoirs.

  14. In vitro degradation and cytocompatibility of dicalcium phosphate dihydrate cements prepared using the monocalcium phosphate monohydrate/hydroxyapatite system reveals rapid conversion to HA as a key mechanism.

    PubMed

    Alge, Daniel L; Goebel, W Scott; Chu, Tien-Min Gabriel

    2012-04-01

    We previously showed that dicalcium phosphate dihydrate (DCPD) cements can be prepared using monocalcium phosphate monohydrate (MCPM) and hydroxyapatite (HA). In this study, we have characterized the degradation properties and biocompatibility of these novel cements. To study the degradation properties, cements were prepared using MCPM:HA molar ratios of 4:1, 2:1, 2:3, and 2:5. Degradation was evaluated in vitro by static soaking in PBS, and changes in pH, mass, compressive strength, and composition were monitored. Conversion of DCPD to HA was noted in the 4:1 group, which initially consisted of pure DCPD. However, the 2:1 group, which initially consisted of DCPD and an intermediate amount of unreacted HA, underwent rapid conversion to HA associated with significantly greater pH drop and mass loss as well as a complete loss of mechanical integrity. On the basis of these results, we directly compared the cytocompatibility of 2:1 MCPM:HA cements to DCPD cements prepared with an equivalent percent molar excess of β-tricalcium phosphate (β-TCP) using an in vitro cell viability assay. Viability of cells co-cultured with 2:1 MCPM:HA cements was significantly reduced after just 48 h, while viability of cells cultured with the β-TCP-based cements was no different from control cells. In conclusion, this study demonstrates that conversion to HA plays an important role in the degradation of DCPD cements prepared with the MCPM/HA system, affecting both physical properties and cytocompatibility. These results could have important clinical implications for MCPM/HA cements.

  15. Renal cell carcinoma: Evolving and emerging subtypes

    PubMed Central

    Crumley, Suzanne M; Divatia, Mukul; Truong, Luan; Shen, Steven; Ayala, Alberto G; Ro, Jae Y

    2013-01-01

    Our knowledge of renal cell carcinoma (RCC) is rapidly expanding. For those who diagnose and treat RCC, it is important to understand the new developments. In recent years, many new renal tumors have been described and defined, and our understanding of the biology and clinical correlates of these tumors is changing. Evolving concepts in Xp11 translocation carcinoma, mucinous tubular and spindle cell carcinoma, multilocular cystic clear cell RCC, and carcinoma associated with neuroblastoma are addressed within this review. Tubulocystic carcinoma, thyroid-like follicular carcinoma of kidney, acquired cystic disease-associated RCC, and clear cell papillary RCC are also described. Finally, candidate entities, including RCC with t(6;11) translocation, hybrid oncocytoma/chromophobe RCC, hereditary leiomyomatosis and RCC syndrome, and renal angiomyoadenomatous tumor are reviewed. Knowledge of these new entities is important for diagnosis, treatment and subsequent prognosis. This review provides a targeted summary of new developments in RCC. PMID:24364021

  16. No surviving evolved companions of the progenitor of SN 1006.

    PubMed

    González Hernández, Jonay I; Ruiz-Lapuente, Pilar; Tabernero, Hugo M; Montes, David; Canal, Ramon; Méndez, Javier; Bedin, Luigi R

    2012-09-27

    Type Ia supernovae are thought to occur when a white dwarf made of carbon and oxygen accretes sufficient mass to trigger a thermonuclear explosion. The accretion could be slow, from an unevolved (main-sequence) or evolved (subgiant or giant) star (the single-degenerate channel), or rapid, as the primary star breaks up a smaller orbiting white dwarf (the double-degenerate channel). A companion star will survive the explosion only in the single-degenerate channel. Both channels might contribute to the production of type Ia supernovae, but the relative proportions of their contributions remain a fundamental puzzle in astronomy. Previous searches for remnant companions have revealed one possible case for SN 1572 (refs 8, 9), although that has been questioned. More recently, observations have restricted surviving companions to be small, main-sequence stars, ruling out giant companions but still allowing the single-degenerate channel. Here we report the results of a search for surviving companions of the progenitor of SN 1006 (ref. 14). None of the stars within 4 arc minutes of the apparent site of the explosion is associated with the supernova remnant, and we can firmly exclude all giant and subgiant stars from being companions of the progenitor. In combination with previous results, our findings indicate that fewer than 20 per cent of type Ia supernovae occur through the single-degenerate channel.

  17. Evolving vendor market for HITECH-certified ambulatory EHR products.

    PubMed

    Gold, Marsha; Hossain, Mynti; Charles, Dustin R; Furukawa, Michael F

    2013-11-01

    The ambitious goals of the Health Information Technology for Economic and Clinical Health (HITECH) Act require rapid development and certification of new ambulatory electronic health record (EHR) products. To examine where the vendor market for EHR products stands now and the policy issues emerging from the market's evolution. Descriptive study with policy analysis. We had 3 main sources of information: (1) documents describing this evolving market, which is not well represented in peer-reviewed literature; (2) operational data on certified ambulatory EHR products and their use by Medicareeligible professionals attesting for meaningful use payments from January 2011 to October 2012; and (3) telephone interviews with 10 vendors that account for 57% of the market. Those attesting for Medicare meaningful use payments used ambulatory EHRs from 353 different vendors, although 16 firms accounted for 75% of the market. The Herfindahl-Hirschman Index showed the ambulatory EHR market to be highly competitive, particularly for practices of 50 or fewer professionals. The interviewed vendors and the external analysts agreed that stage 1 requirements set a relatively low bar for market entry, but that likely will change as requirements get more demanding. The HITECH Act met its initial goals to motivate growth of diverse ambulatory EHR products. A market shakeout may emerge, though current data reveal no signs of it. Policy makers can influence the shape and value of such a shakeout, and the extent of disruption, through their approach to certification and "usability" and "interoperability" strategies and requirements.

  18. Chemically induced conditional rescue of the reduced epidermal fluorescence8 mutant of Arabidopsis reveals rapid restoration of growth and selective turnover of secondary metabolite pools.

    PubMed

    Kim, Jeong Im; Ciesielski, Peter N; Donohoe, Bryon S; Chapple, Clint; Li, Xu

    2014-02-01

    The phenylpropanoid pathway is responsible for the biosynthesis of diverse and important secondary metabolites including lignin and flavonoids. The reduced epidermal fluorescence8 (ref8) mutant of Arabidopsis (Arabidopsis thaliana), which is defective in a lignin biosynthetic enzyme p-coumaroyl shikimate 3'-hydroxylase (C3'H), exhibits severe dwarfism and sterility. To better understand the impact of perturbation of phenylpropanoid metabolism on plant growth, we generated a chemically inducible C3'H expression construct and transformed it into the ref8 mutant. Application of dexamethasone to these plants greatly alleviates the dwarfism and sterility and substantially reverses the biochemical phenotypes of ref8 plants, including the reduction of lignin content and hyperaccumulation of flavonoids and p-coumarate esters. Induction of C3'H expression at different developmental stages has distinct impacts on plant growth. Although early induction effectively restored the elongation of primary inflorescence stem, application to 7-week-old plants enabled them to produce new rosette inflorescence stems. Examination of hypocotyls of these plants revealed normal vasculature in the newly formed secondary xylem, presumably restoring water transport in the mutant. The ref8 mutant accumulates higher levels of salicylic acid than the wild type, but depletion of this compound in ref8 did not relieve the mutant's growth defects, suggesting that the hyperaccumulation of salicylic acid is unlikely to be responsible for dwarfism in this mutant.

  19. Coupled oscillators on evolving networks

    NASA Astrophysics Data System (ADS)

    Singh, R. K.; Bagarti, Trilochan

    2016-12-01

    In this work we study coupled oscillators on evolving networks. We find that the steady state behavior of the system is governed by the relative values of the spread in natural frequencies and the global coupling strength. For coupling strong in comparison to the spread in frequencies, the system of oscillators synchronize and when coupling strength and spread in frequencies are large, a phenomenon similar to amplitude death is observed. The network evolution provides a mechanism to build inter-oscillator connections and once a dynamic equilibrium is achieved, oscillators evolve according to their local interactions. We also find that the steady state properties change by the presence of additional time scales. We demonstrate these results based on numerical calculations studying dynamical evolution of limit-cycle and van der Pol oscillators.

  20. Evolvable Hardware for Space Applications

    NASA Technical Reports Server (NTRS)

    Lohn, Jason; Globus, Al; Hornby, Gregory; Larchev, Gregory; Kraus, William

    2004-01-01

    This article surveys the research of the Evolvable Systems Group at NASA Ames Research Center. Over the past few years, our group has developed the ability to use evolutionary algorithms in a variety of NASA applications ranging from spacecraft antenna design, fault tolerance for programmable logic chips, atomic force field parameter fitting, analog circuit design, and earth observing satellite scheduling. In some of these applications, evolutionary algorithms match or improve on human performance.

  1. 210Pb-226Ra chronology reveals rapid growth rate of Madrepora oculata and Lophelia pertusa on world's largest cold-water coral reef

    NASA Astrophysics Data System (ADS)

    Sabatier, P.; Reyss, J.-L.; Hall-Spencer, J. M.; Colin, C.; Frank, N.; Tisnérat-Laborde, N.; Bordier, L.; Douville, E.

    2011-12-01

    Here we show the use of the 210Pb-226Ra excess method to determine the growth rate of corals from one of the world's largest known cold-water coral reef, the Røst Reef off Norway. Two large branching framework-forming cold-water coral specimens, one Lophelia pertusa and one Madrepora oculata were collected alive at 350 m water depth from the Røst Reef at ~67° N and ~9° E. Pb and Ra isotopes were measured along the major growth axis of both specimens using low level alpha and gamma spectrometry and the corals trace element compositions were studied using ICP-QMS. Due to the different chemical behaviors of Pb and Ra in the marine environment, 210Pb and 226Ra were not incorporated the same way into the aragonite skeleton of those two cold-water corals. Thus to assess of the growth rates of both specimens we have here taken in consideration the exponential decrease of initially incorporated 210Pb as well as the ingrowth of 210Pb from the decay of 226Ra. Moreover a~post-depositional 210Pb incorporation is found in relation to the Mn-Fe coatings that could not be entirely removed from the oldest parts of the skeletons. The 226Ra activities in both corals were fairly constant, then assuming constant uptake of 210Pb through time the 210Pb-226Ra chronology can be applied to calculate linear growth rate. The 45.5 cm long branch of M. oculata reveals an age of 31 yr and a~linear growth rate of 14.4 ± 1.1 mm yr-1, i.e. 2.6 polyps per year. However, a correction regarding a remaining post-depositional Mn-Fe oxide coating is needed for the base of the specimen. The corrected age tend to confirm the radiocarbon derived basal age of 40 yr (using 14C bomb peak) with a mean growth rate of 2 polyps yr-1. This rate is similar to the one obtained in Aquaria experiments under optimal growth conditions. For the 80 cm-long specimen of L. pertusa a remaining contamination of metal-oxides is observed for the middle and basal part of the coral skeleton, inhibiting similar accurate age

  2. A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

    PubMed Central

    Halley, Yvette A.; Dowd, Scot E.; Decker, Jared E.; Seabury, Paul M.; Bhattarai, Eric; Johnson, Charles D.; Rollins, Dale; Tizard, Ian R.; Brightsmith, Donald J.; Peterson, Markus J.; Taylor, Jeremy F.; Seabury, Christopher M.

    2014-01-01

    Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts. PMID:24621616

  3. Differences in d-[3H]lysergic acid diethylamide binding in mouse cortex and hippocampus in vivo and in vitro revealed by radioautography and rapid filtration studies.

    PubMed

    Ebersole, B J; Weinstein, H; Maayani, S

    1984-06-01

    The localization of d-[3H]lysergic acid diethylamide ([3H]LSD) binding sites in mouse brain was compared in vivo and in vitro. Radioautography of brain sections incubated with 6 nM [3H]LSD in vitro revealed substantial specific binding in cortex (CTX), especially in layers III to IV and anterior cingulate gyrus, and in areas CA1 and dentate gyrus of hippocampus (HIP). In sections of brains from mice that received 100 nmol of [3H]LSD per kg and were killed 10, 15 or 30 min later, specific [3H]LSD binding in CTX had a pattern of distribution similar to that observed in vitro. In contrast, the pattern of specific [3H]LSD binding in HIP in vivo differed from the results obtained in vitro, in that it was sparse and lacked differential subregional distribution. The low specific [3H]LSD binding in vivo in HIP but not in CTX was confirmed by homogenate filtration studies of brain areas from mice that received 100 nmol of [3H]LSD per kg. The levels of free [3H]LSD, obtained after correction for time-dependent metabolism of [3H]LSD, did not vary among regions, but [3H]LSD specifically bound in HIP was 30 to 50% of that in CTX. In contrast, steady-state binding studies in vitro in membrane preparations from CTX and HIP demonstrated a similar density and affinity of [3H]LSD binding sites in the two regions. Comparison of [3H]LSD binding characteristics in vivo and in vitro suggests possible mechanisms causing the lower specific binding in HIP in vivo, including modulation of the binding sites that differ in CTX and HIP.

  4. Evolving Systems and Adaptive Key Component Control

    NASA Technical Reports Server (NTRS)

    Frost, Susan A.; Balas, Mark J.

    2009-01-01

    We propose a new framework called Evolving Systems to describe the self-assembly, or autonomous assembly, of actively controlled dynamical subsystems into an Evolved System with a higher purpose. An introduction to Evolving Systems and exploration of the essential topics of the control and stability properties of Evolving Systems is provided. This chapter defines a framework for Evolving Systems, develops theory and control solutions for fundamental characteristics of Evolving Systems, and provides illustrative examples of Evolving Systems and their control with adaptive key component controllers.

  5. Inheritance of evolved resistance to a novel herbicide (pyroxasulfone).

    PubMed

    Busi, Roberto; Gaines, Todd A; Vila-Aiub, Martin M; Powles, Stephen B

    2014-03-01

    Agricultural weeds have rapidly adapted to intensive herbicide selection and resistance to herbicides has evolved within ecological timescales. Yet, the genetic basis of broad-spectrum generalist herbicide resistance is largely unknown. This study aims to determine the genetic control of non-target-site herbicide resistance trait(s) that rapidly evolved under recurrent selection of the novel lipid biosynthesis inhibitor pyroxasulfone in Lolium rigidum. The phenotypic segregation of pyroxasulfone resistance in parental, F1 and back-cross (BC) families was assessed in plants exposed to a gradient of pyroxasulfone doses. The inheritance of resistance to chemically dissimilar herbicides (cross-resistance) was also evaluated. Evolved resistance to the novel selective agent (pyroxasulfone) is explained by Mendelian segregation of one semi-dominant allele incrementally herbicide-selected at higher frequency in the progeny. In BC families, cross-resistance is conferred by an incompletely dominant single major locus. This study confirms that herbicide resistance can rapidly evolve to any novel selective herbicide agents by continuous and repeated herbicide use. The results imply that the combination of herbicide options (rotation, mixtures or combinations) to exploit incomplete dominance can provide acceptable control of broad-spectrum generalist resistance-endowing monogenic traits. Herbicide diversity within a set of integrated management tactics can be one important component to reduce the herbicide selection intensity. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  6. The tortoise and the hare: slowly evolving T-cell responses take hastily evolving KIR

    PubMed Central

    van Bergen, Jeroen; Koning, Frits

    2010-01-01

    The killer cell immunoglobulin-like receptor (KIR) locus comprises a variable and rapidly evolving set of genes encoding multiple inhibitory and activating receptors. The activating receptors recently evolved from the inhibitory receptors and both bind HLA class I and probably also class I-like structures induced by viral infection. Although generally considered natural killer (NK) cell receptors, KIR are also expressed by a large fraction of effector memory T cells, which slowly accumulate during human life. These effector memory cells are functionally similar to NK cells, as they are immediate effector cells that are cytotoxic and produce IFN-γ. However, different rules apply to NK and T cells with respect to KIR expression and function. For example, KIR tend to modulate signals driven by the T-cell receptor (TCR) rather than to act independently, and use different signal transduction pathways to modulate only a subset of effector functions. The most important difference may lie in the rules governing tolerance: while NK cells with activating KIR binding self-HLA are hyporesponsive, the same is unlikely to apply to T cells. We argue that the expression of activating KIR on virus-specific T cells carrying TCR that weakly cross-react with autoantigens can unleash the autoreactive potential of these cells. This may be the case in rheumatoid arthritis, where cytomegalovirus-specific KIR2DS2+ T cells might cause vasculitis. Thus, the rapid evolution of activating KIR may have allowed for efficient NK-cell control of viruses, but may also have increased the risk that slowly evolving T-cell responses to persistent pathogens derail into autoimmunity. PMID:20722764

  7. The evolvability of programmable hardware

    PubMed Central

    Raman, Karthik; Wagner, Andreas

    2011-01-01

    In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected ‘neutral networks’ in genotype space. The size of such neutral networks endows biological systems not only with robustness to genetic change, but also with the ability to evolve a vast number of novel phenotypes that occur near any one neutral network. Whether technological systems can be designed to have similar properties is poorly understood. Here we ask this question for a class of programmable electronic circuits that compute digital logic functions. The functional flexibility of such circuits is important in many applications, including applications of evolutionary principles to circuit design. The functions they compute are at the heart of all digital computation. We explore a vast space of 1045 logic circuits (‘genotypes’) and 1019 logic functions (‘phenotypes’). We demonstrate that circuits that compute the same logic function are connected in large neutral networks that span circuit space. Their robustness or fault-tolerance varies very widely. The vicinity of each neutral network contains circuits with a broad range of novel functions. Two circuits computing different functions can usually be converted into one another via few changes in their architecture. These observations show that properties important for the evolvability of biological systems exist in a commercially important class of electronic circuitry. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry. PMID:20534598

  8. Evolvability of an Optimal Recombination Rate

    PubMed Central

    Lobkovsky, Alexander E.; Wolf, Yuri I.; Koonin, Eugene V.

    2016-01-01

    Evolution and maintenance of genetic recombination and its relation to the mutational process is a long-standing, fundamental problem in evolutionary biology that is linked to the general problem of evolution of evolvability. We explored a stochastic model of the evolution of recombination using additive fitness and infinite allele assumptions but no assumptions on the sign or magnitude of the epistasis and the distribution of mutation effects. In this model, fluctuating negative epistasis and predominantly deleterious mutations arise naturally as a consequence of the additive fitness and a reservoir from which new alleles arrive with a fixed distribution of fitness effects. Analysis of the model revealed a nonmonotonic effect of recombination intensity on fitness, with an optimal recombination rate value which maximized fitness in steady state. The optimal recombination rate depended on the mutation rate and was evolvable, that is, subject to selection. The predictions of the model were compatible with the observations on the dependence between genome rearrangement rate and gene flux in microbial genomes. PMID:26660159

  9. Evolvability of an Optimal Recombination Rate.

    PubMed

    Lobkovsky, Alexander E; Wolf, Yuri I; Koonin, Eugene V

    2015-12-10

    Evolution and maintenance of genetic recombination and its relation to the mutational process is a long-standing, fundamental problem in evolutionary biology that is linked to the general problem of evolution of evolvability. We explored a stochastic model of the evolution of recombination using additive fitness and infinite allele assumptions but no assumptions on the sign or magnitude of the epistasis and the distribution of mutation effects. In this model, fluctuating negative epistasis and predominantly deleterious mutations arise naturally as a consequence of the additive fitness and a reservoir from which new alleles arrive with a fixed distribution of fitness effects. Analysis of the model revealed a nonmonotonic effect of recombination intensity on fitness, with an optimal recombination rate value which maximized fitness in steady state. The optimal recombination rate depended on the mutation rate and was evolvable, that is, subject to selection. The predictions of the model were compatible with the observations on the dependence between genome rearrangement rate and gene flux in microbial genomes.

  10. Regolith Evolved Gas Analyzer (REGA)

    NASA Technical Reports Server (NTRS)

    Allen, Carlton C.; McKay, David S.

    1997-01-01

    The instrument consists of five subsystems: (1) a programmable furnace which can be loaded with samples of regolith, (2) a mass spectrometer which detects and measures atmospheric gases or gases evolved during heating, (3) a tank of pressurized gas which can be introduced to the regolith material while detecting and measuring volatile reaction products, (4) a mechanism for dumping the regolith sample and repeating the experiment on a fresh sample, and (5) a data system which controls and monitors the furnace, gas system, and mass spectrometer.

  11. The 'E' factor -- evolving endodontics.

    PubMed

    Hunter, M J

    2013-03-01

    Endodontics is a constantly developing field, with new instruments, preparation techniques and sealants competing with trusted and traditional approaches to tooth restoration. Thus general dental practitioners must question and understand the significance of these developments before adopting new practices. In view of this, the aim of this article, and the associated presentation at the 2013 British Dental Conference & Exhibition, is to provide an overview of endodontic methods and constantly evolving best practice. The presentation will review current preparation techniques, comparing rotary versus reciprocation, and question current trends in restoration of the endodontically treated tooth.

  12. Regolith Evolved Gas Analyzer (REGA)

    NASA Technical Reports Server (NTRS)

    Allen, Carlton C.; McKay, David S.

    1997-01-01

    The instrument consists of five subsystems: (1) a programmable furnace which can be loaded with samples of regolith, (2) a mass spectrometer which detects and measures atmospheric gases or gases evolved during heating, (3) a tank of pressurized gas which can be introduced to the regolith material while detecting and measuring volatile reaction products, (4) a mechanism for dumping the regolith sample and repeating the experiment on a fresh sample, and (5) a data system which controls and monitors the furnace, gas system, and mass spectrometer.

  13. Improving Evolvability through Generative Representations

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.

    2004-01-01

    One of the main limitations of computer automated design systems is the representation used for encoding designs. Using computer programs as an analogy, representations can be thought of as having the properties of combination, control-flow and abstraction. Generative representations are those which have the ability to reuse elements in an encoding through either iteration, a form of control-flow, or abstraction. Here we argue that generative representations improve the evolvability of designs by capturing design dependencies in a way that makes them easier to change, and we support this with examples from two design substrates.

  14. Transport on randomly evolving trees

    NASA Astrophysics Data System (ADS)

    Pál, L.

    2005-11-01

    The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes, a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to nodes. It is assumed that at t=0 the tree consists of a single living node (root), from which the evolution may begin. At a certain time instant τ⩾0 , the root produces ν⩾0 living nodes connected by lines to the root which becomes dead at the moment of the offspring production. In the evolution process each of the new living nodes evolves further like a root independently of the others. By using the methods of the age-dependent branching processes we derive the joint distribution function of the numbers of living and dead nodes, and determine the correlation between these node numbers as a function of time. It is proved that the correlation function converges to 3/2 independently of the distributions of ν and τ when q1→1 and t→∞ . Also analyzed are the stochastic properties of the end nodes; and the correlation between the numbers of living and dead end nodes is shown to change its character suddenly at the very beginning of the evolution process. The survival probability of random trees is investigated and expressions are derived for this probability.

  15. Transport on randomly evolving trees.

    PubMed

    Pál, L

    2005-11-01

    The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes, a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to nodes. It is assumed that at t=0 the tree consists of a single living node (root), from which the evolution may begin. At a certain time instant tau> or =0, the root produces v> or =0 living nodes connected by lines to the root which becomes dead at the moment of the offspring production. In the evolution process each of the new living nodes evolves further like a root independently of the others. By using the methods of the age-dependent branching processes we derive the joint distribution function of the numbers of living and dead nodes, and determine the correlation between these node numbers as a function of time. It is proved that the correlation function converges to square root of 3/2 independently of the distributions of v and tau when q1-->1 and t-->infinity. Also analyzed are the stochastic properties of the end nodes; and the correlation between the numbers of living and dead end nodes is shown to change its character suddenly at the very beginning of the evolution process. The survival probability of random trees is investigated and expressions are derived for this probability.

  16. Stability of Evolving Multiagent Systems.

    PubMed

    De Wilde, P; Briscoe, G

    2011-08-01

    A multiagent system is a distributed system where the agents or nodes perform complex functions that cannot be written down in analytic form. Multiagent systems are highly connected, and the information they contain is mostly stored in the connections. When agents update their state, they take into account the state of the other agents, and they have access to those states via the connections. There is also external user-generated input into the multiagent system. As so much information is stored in the connections, agents are often memory less. This memory-less property, together with the randomness of the external input, has allowed us to model multiagent systems using Markov chains. In this paper, we look at multiagent systems that evolve, i.e., the number of agents varies according to the fitness of the individual agents. We extend our Markov chain model and define stability. This is the start of a methodology to control multiagent systems. We then build upon this to construct an entropy-based definition for the degree of instability (entropy of the limit probabilities), which we used to perform a stability analysis. We then investigated the stability of evolving agent populations through simulation and show that the results are consistent with the original definition of stability in nonevolving multiagent systems, proposed by Chli and De Wilde. This paper forms the theoretical basis for the construction of digital business ecosystems, and applications have been reported elsewhere.

  17. Evolving Robust Gene Regulatory Networks

    PubMed Central

    Noman, Nasimul; Monjo, Taku; Moscato, Pablo; Iba, Hitoshi

    2015-01-01

    Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of ‘parts’ and ‘devices’. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in synthetic biology. A recent study shows that Darwinian evolution can gradually develop higher topological robustness. Subsequently, this work presents an evolutionary algorithm that simulates natural evolution in silico, for identifying network topologies that are robust to perturbations. We present a Monte Carlo based method for quantifying topological robustness and designed a fitness approximation approach for efficient calculation of topological robustness which is computationally very intensive. The proposed framework was verified using two classic GRN behaviors: oscillation and bistability, although the framework is generalized for evolving other types of responses. The algorithm identified robust GRN architectures which were verified using different analysis and comparison. Analysis of the results also shed light on the relationship among robustness, cooperativity and complexity. This study also shows that nature has already evolved very robust architectures for its crucial systems; hence simulation of this natural process can be very valuable for designing robust biological systems. PMID:25616055

  18. Digalactosyldiacylglycerol is required for stabilization of the oxygen-evolving complex in photosystem II.

    PubMed

    Sakurai, Isamu; Mizusawa, Naoki; Wada, Hajime; Sato, Naoki

    2007-12-01

    The galactolipid digalactosyldiacylglycerol (DGDG) is present in the thylakoid membranes of oxygenic photosynthetic organisms such as higher plants and cyanobacteria. Recent x-ray crystallographic analysis of protein-cofactor supercomplexes in thylakoid membranes revealed that DGDG molecules are present in the photosystem II (PSII) complex (four molecules per monomer), suggesting that DGDG molecules play important roles in folding and assembly of subunits in the PSII complex. However, the specific role of DGDG in PSII has not been fully clarified. In this study, we identified the dgdA gene (slr1508, a ycf82 homolog) of Synechocystis sp. PCC6803 that presumably encodes a DGDG synthase involved in the biosynthesis of DGDG by comparison of genomic sequence data. Disruption of the dgdA gene resulted in a mutant defective in DGDG synthesis. Despite the lack of DGDG, the mutant cells grew as rapidly as the wild-type cells, indicating that DGDG is not essential for growth in Synechocystis. However, we found that oxygen-evolving activity of PSII was significantly decreased in the mutant. Analyses of the PSII complex purified from the mutant cells indicated that the extrinsic proteins PsbU, PsbV, and PsbO, which stabilize the oxygen-evolving complex, were substantially dissociated from the PSII complex. In addition, we found that heat susceptibility but not dark-induced inactivation of oxygen-evolving activity was notably increased in the mutant cells in comparison to the wild-type cells, suggesting that the PsbU subunit is dissociated from the PSII complex even in vivo. These results demonstrate that DGDG plays important roles in PSII through the binding of extrinsic proteins required for stabilization of the oxygen-evolving complex.

  19. Do Infants Possess an Evolved Spider-Detection Mechanism?

    ERIC Educational Resources Information Center

    Rakison, David H.; Derringer, Jaime

    2008-01-01

    Previous studies with various non-human animals have revealed that they possess an evolved predator recognition mechanism that specifies the appearance of recurring threats. We used the preferential looking and habituation paradigms in three experiments to investigate whether 5-month-old human infants have a perceptual template for spiders that…

  20. Do Infants Possess an Evolved Spider-Detection Mechanism?

    ERIC Educational Resources Information Center

    Rakison, David H.; Derringer, Jaime

    2008-01-01

    Previous studies with various non-human animals have revealed that they possess an evolved predator recognition mechanism that specifies the appearance of recurring threats. We used the preferential looking and habituation paradigms in three experiments to investigate whether 5-month-old human infants have a perceptual template for spiders that…

  1. Programmed life span in the context of evolvability.

    PubMed

    Mitteldorf, Joshua; Martins, André C R

    2014-09-01

    Population turnover is necessary for progressive evolution. In the context of a niche with fixed carrying capacity, aging contributes to the rate of population turnover. Theoretically, a population in which death is programmed on a fixed schedule can evolve more rapidly than one in which population turnover is left to a random death rate. Could aging evolve on this basis? Quantitative realization of this idea is problematic, since the short-term individual fitness cost is likely to eliminate any hypothetical gene for programmed death before the long-term benefit can be realized. In 2011, one of us proposed the first quantitative model based on this mechanism that robustly evolves a finite, programmed life span. That model was based on a viscous population in a rapidly changing environment. Here, we strip this model to its essence and eliminate the assumption of environmental change. We conclude that there is no obvious way in which this model is unrealistic, and that it may indeed capture an important principle of nature's workings. We suggest aging may be understood within the context of the emerging science of evolvability.

  2. Primordial evolvability: Impasses and challenges.

    PubMed

    Vasas, Vera; Fernando, Chrisantha; Szilágyi, András; Zachár, István; Santos, Mauro; Szathmáry, Eörs

    2015-09-21

    While it is generally agreed that some kind of replicating non-living compounds were the precursors of life, there is much debate over their possible chemical nature. Metabolism-first approaches propose that mutually catalytic sets of simple organic molecules could be capable of self-replication and rudimentary chemical evolution. In particular, the graded autocatalysis replication domain (GARD) model, depicting assemblies of amphiphilic molecules, has received considerable interest. The system propagates compositional information across generations and is suggested to be a target of natural selection. However, evolutionary simulations indicate that the system lacks selectability (i.e. selection has negligible effect on the equilibrium concentrations). We elaborate on the lessons learnt from the example of the GARD model and, more widely, on the issue of evolvability, and discuss the implications for similar metabolism-first scenarios. We found that simple incorporation-type chemistry based on non-covalent bonds, as assumed in GARD, is unlikely to result in alternative autocatalytic cycles when catalytic interactions are randomly distributed. An even more serious problem stems from the lognormal distribution of catalytic factors, causing inherent kinetic instability of such loops, due to the dominance of efficiently catalyzed components that fail to return catalytic aid. Accordingly, the dynamics of the GARD model is dominated by strongly catalytic, but not auto-catalytic, molecules. Without effective autocatalysis, stable hereditary propagation is not possible. Many repetitions and different scaling of the model come to no rescue. Despite all attempts to show the contrary, the GARD model is not evolvable, in contrast to reflexively autocatalytic networks, complemented by rare uncatalyzed reactions and compartmentation. The latter networks, resting on the creation and breakage of chemical bonds, can generate novel ('mutant') autocatalytic loops from a given set of

  3. Evolving sequence-stratigraphic concepts: Emphasis on siliciclastic systems tracts

    SciTech Connect

    Brown, L.F. Jr.

    1994-11-01

    During the past five years, rapidly evolving new sequence-stratigraphic concepts have begun to impose significant changes in the application of stratigraphy in petroleum exploration and reservoir development. The growing number and variety of oral and published papers on sequence stratigraphy clearly document this stratigraphic revolution. Not since depositional systems concepts evolved in the 1960s to give rise to seismic stratigraphy in the 1970s has the field of stratigraphy changed so rapidly and so fundamentally. Within the next few years, sequence stratigraphy is destined to play an increasingly important role in the way basins are analyzed, hydrocarbon-play potential is assessed, and prospect and production strategies are devised. Geoscientists worldwide are struggling to keep up with the significance of all of these new ideas and techniques.

  4. Evolving phenotype of Marfan's syndrome

    PubMed Central

    Lipscomb, K.; Clayton-Smith, J.; Harris, R.

    1997-01-01

    Accepted 20 August 1996
 AIM—To examine evolution of the physical characteristics of Marfan's syndrome throughout childhood.
METHODS—40 children were ascertained during the development of a regional register for Marfan's syndrome. Evolution of the clinical characteristics was determined by repeat evaluation of 10 patients with sporadic Marfan's syndrome and 30 with a family history of the condition. DNA marker studies were used to facilitate diagnosis in those with the familial condition.
RESULTS—Musculoskeletal features predominated and evolved throughout childhood. Gene tracking enabled early diagnosis in children with familial Marfan's syndrome.
CONCLUSIONS—These observations may aid the clinical diagnosis of Marfan's syndrome in childhood, especially in those with the sporadic condition. Gene tracking has a role in the early diagnosis of familial Marfan's syndrome, allowing appropriate follow up and preventive care.

 PMID:9059160

  5. Isotopic Analysis and Evolved Gases

    NASA Technical Reports Server (NTRS)

    Swindle, Timothy D.; Boynton, William V.; Chutjian, Ara; Hoffman, John H.; Jordan, Jim L.; Kargel, Jeffrey S.; McEntire, Richard W.; Nyquist, Larry

    1996-01-01

    Precise measurements of the chemical, elemental, and isotopic composition of planetary surface material and gases, and observed variations in these compositions, can contribute significantly to our knowledge of the source(s), ages, and evolution of solar system materials. The analyses discussed in this paper are mostly made by mass spectrometers or some other type of mass analyzer, and address three broad areas of interest: (1) atmospheric composition - isotopic, elemental, and molecular, (2) gases evolved from solids, and (3) solids. Current isotopic data on nine elements, mostly from in situ analysis, but also from meteorites and telescopic observations are summarized. Potential instruments for isotopic analysis of lunar, Martian, Venusian, Mercury, and Pluto surfaces, along with asteroid, cometary and icy satellites, surfaces are discussed.

  6. The evolving Gleason grading system.

    PubMed

    Chen, Ni; Zhou, Qiao

    2016-02-01

    The Gleason grading system for prostate adenocarcinoma has evolved from its original scheme established in the 1960s-1970s, to a significantly modified system after two major consensus meetings conducted by the International Society of Urologic Pathology (ISUP) in 2005 and 2014, respectively. The Gleason grading system has been incorporated into the WHO classification of prostate cancer, the AJCC/UICC staging system, and the NCCN guidelines as one of the key factors in treatment decision. Both pathologists and clinicians need to fully understand the principles and practice of this grading system. We here briefly review the historical aspects of the original scheme and the recent developments of Gleason grading system, focusing on major changes over the years that resulted in the modern Gleason grading system, which has led to a new "Grade Group" system proposed by the 2014 ISUP consensus, and adopted by the 2016 WHO classification of tumours of the prostate.

  7. The evolving Gleason grading system

    PubMed Central

    Chen, Ni

    2016-01-01

    The Gleason grading system for prostate adenocarcinoma has evolved from its original scheme established in the 1960s–1970s, to a significantly modified system after two major consensus meetings conducted by the International Society of Urologic Pathology (ISUP) in 2005 and 2014, respectively. The Gleason grading system has been incorporated into the WHO classification of prostate cancer, the AJCC/UICC staging system, and the NCCN guidelines as one of the key factors in treatment decision. Both pathologists and clinicians need to fully understand the principles and practice of this grading system. We here briefly review the historical aspects of the original scheme and the recent developments of Gleason grading system, focusing on major changes over the years that resulted in the modern Gleason grading system, which has led to a new “Grade Group” system proposed by the 2014 ISUP consensus, and adopted by the 2016 WHO classification of tumours of the prostate. PMID:27041927

  8. Evolving networks by merging cliques

    NASA Astrophysics Data System (ADS)

    Takemoto, Kazuhiro; Oosawa, Chikoo

    2005-10-01

    We propose a model for evolving networks by merging building blocks represented as complete graphs, reminiscent of modules in biological system or communities in sociology. The model shows power-law degree distributions, power-law clustering spectra, and high average clustering coefficients independent of network size. The analytical solutions indicate that a degree exponent is determined by the ratio of the number of merging nodes to that of all nodes in the blocks, demonstrating that the exponent is tunable, and are also applicable when the blocks are classical networks such as Erdös-Rényi or regular graphs. Our model becomes the same model as the Barabási-Albert model under a specific condition.

  9. Behavioural plasticity in evolving robots.

    PubMed

    Carvalho, Jônata Tyska; Nolfi, Stefano

    2016-12-01

    In this paper, we show how the development of plastic behaviours, i.e., behaviour displaying a modular organisation characterised by behavioural subunits that are alternated in a context-dependent manner, can enable evolving robots to solve their adaptive task more efficiently also when it does not require the accomplishment of multiple conflicting functions. The comparison of the results obtained in different experimental conditions indicates that the most important prerequisites for the evolution of behavioural plasticity are: the possibility to generate and perceive affordances (i.e., opportunities for behaviour execution), the possibility to rely on flexible regulatory processes that exploit both external and internal cues, and the possibility to realise smooth and effective transitions between behaviours.

  10. Speech processing: An evolving technology

    SciTech Connect

    Crochiere, R.E.; Flanagan, J.L.

    1986-09-01

    As we enter the information age, speech processing is emerging as an important technology for making machines easier and more convenient for humans to use. It is both an old and a new technology - dating back to the invention of the telephone and forward, at least in aspirations, to the capabilities of HAL in 2001. Explosive advances in microelectronics now make it possible to implement economical real-time hardware for sophisticated speech processing - processing that formerly could be demonstrated only in simulations on main-frame computers. As a result, fundamentally new product concepts - as well as new features and functions in existing products - are becoming possible and are being explored in the marketplace. As the introductory piece to this issue, the authors draw a brief perspective on the evolving field of speech processing and assess the technology in the the three constituent sectors: speech coding, synthesis, and recognition.

  11. An invasive species induces rapid adaptive change in a native predator: cane toads and black snakes in Australia.

    PubMed

    Phillips, Ben L; Shine, Richard

    2006-06-22

    Rapid environmental change due to human activities has increased rates of extinction, but some species may be able to adapt rapidly enough to deal with such changes. Our studies of feeding behaviour and physiological resistance to toxins reveal surprisingly rapid adaptive responses in Australian black snakes (Pseudechis porphyriacus) following the invasion of a lethally toxic prey item, the cane toad (Bufo marinus). Snakes from toad-exposed localities showed increased resistance to toad toxin and a decreased preference for toads as prey. Separate laboratory experiments suggest that these changes are not attributable to learning (we were unable to teach naive snakes to avoid toxic prey) or to acquired resistance (repeated sub-lethal doses did not enhance resistance). These results strongly suggest that black snake behaviour and physiology have evolved in response to the presence of toads, and have done so rapidly. Toads were brought to Australia in 1935, so these evolved responses have occurred in fewer than 23 snake generations.

  12. An invasive species induces rapid adaptive change in a native predator: cane toads and black snakes in Australia

    PubMed Central

    Phillips, Ben L; Shine, Richard

    2006-01-01

    Rapid environmental change due to human activities has increased rates of extinction, but some species may be able to adapt rapidly enough to deal with such changes. Our studies of feeding behaviour and physiological resistance to toxins reveal surprisingly rapid adaptive responses in Australian black snakes (Pseudechis porphyriacus) following the invasion of a lethally toxic prey item, the cane toad (Bufo marinus). Snakes from toad-exposed localities showed increased resistance to toad toxin and a decreased preference for toads as prey. Separate laboratory experiments suggest that these changes are not attributable to learning (we were unable to teach naive snakes to avoid toxic prey) or to acquired resistance (repeated sub-lethal doses did not enhance resistance). These results strongly suggest that black snake behaviour and physiology have evolved in response to the presence of toads, and have done so rapidly. Toads were brought to Australia in 1935, so these evolved responses have occurred in fewer than 23 snake generations. PMID:16777750

  13. Seyfert's Sextet (HGC 79): An Evolved Stephan's Quintet?

    NASA Astrophysics Data System (ADS)

    Durbala, A.; Sulentic, J.; Rosado, M.; Del Olmo, A.; Perea, J.; Plana, H.

    Scanning Fabry-Perot interferometers MOS/SIS (3.6m CFHT)+PUMA (2.1m OAN-SPM, México) and the long-slit spectrograph ALFOSC (2.5m NOT, La Palma) were used to measure the kinematics of gas and stars in Seyfert's Sextet (HCG79). We interpret it as a highly evolved group that formed from sequential acquistion of mostly late-type galaxies that are now slowly coalescing and undergoing strong secular evolution. We find evidence for possible feedback as revealed by accretion and minor merger events in two of the most evolved members.

  14. Ultra-high-performance liquid chromatography-quadrupole/time of flight mass spectrometry based chemical profiling approach to rapidly reveal chemical transformation of sulfur-fumigated medicinal herbs, a case study on white ginseng.

    PubMed

    Li, Song-Lin; Shen, Hong; Zhu, Ling-Ying; Xu, Jun; Jia, Xiao-Bin; Zhang, Hong-Mei; Lin, Ge; Cai, Hao; Cai, Bao-Chang; Chen, Shi-Lin; Xu, Hong-Xi

    2012-03-30

    Sulfur-fumigation may induce chemical transformation of medicinal herbs. Development of rapid method to reveal potential sulfur-fumigation induced chemical transformation of herbs is a very important issue for efficacy and safety of herb application. In present study, a new strategy was proposed to rapidly reveal chemical transformation of sulfur-fumigated herbs by ultra-high-performance liquid chromatography-quadrupole/time of flight mass spectrometry (UHPLC-QTOF-MS/MS) based chemical profiling approach. The non-fumigated herb was water-wetted and further treated with burning sulfur to get sulfur-fumigated herb. Then the chemical fingerprints of both non-fumigated and sulfur-fumigated samples were compared by UHPLC-QTOF-MS/MS analysis. The identities of all detected peaks, in particular those newly generated in sulfur-fumigated samples were confirmed by comparing the mass spectra and retention times of peaks with that of reference compounds, and/or tentatively assigned by matching empirical molecular formula with that of published compounds, and/or elucidating quasi-molecular ions and fragment ions referring to available literature information. The identification could be rationalized through deducing possible reactions involved in the generation of these newly detected compounds. The proposed strategy was extensively investigated in the case of white ginseng. Total 82 components were detected in non-fumigated and sulfur-fumigated white ginseng samples, among them 35 sulfur-containing compounds detected only in sulfur-fumigated white ginseng and its decoction were assigned to be sulfate or sulfite derivatives of original ginsenosides, and were deduced to be generated via reactions of esterification, addition, hydrolysis and dehydration during sulfur-fumigation and decocting of white ginseng. The established approach was applied to discriminate sulfur-fumigated white ginseng among commercial samples from America, Canada, and Hong Kong SAR, Macau SAR and Mainland of

  15. A Quantitative Approach to Assessing System Evolvability

    NASA Technical Reports Server (NTRS)

    Christian, John A., III

    2004-01-01

    When selecting a system from multiple candidates, the customer seeks the one that best meets his or her needs. Recently the desire for evolvable systems has become more important and engineers are striving to develop systems that accommodate this need. In response to this search for evolvability, we present a historical perspective on evolvability, propose a refined definition of evolvability, and develop a quantitative method for measuring this property. We address this quantitative methodology from both a theoretical and practical perspective. This quantitative model is then applied to the problem of evolving a lunar mission to a Mars mission as a case study.

  16. Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata.

    PubMed

    Yao, Qiu-Yang; Xia, En-Hua; Liu, Fei-Hu; Gao, Li-Zhi

    2015-02-15

    WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes.

  17. Studying evolved stars with Herschel observations

    NASA Astrophysics Data System (ADS)

    da Silva Santos, João Manuel

    2016-07-01

    A systematic inspection of the far-infrared (FIR) properties of evolved stars allows not only to constrain physical models, but also to understand the chemical evolution that takes place in the end of their lives. In this work we intend to study the circumstellar envelopes (CSE) on a sample of stars in the THROES catalogue from AGB/post-AGB stars to planetary nebulae using photometry and spectroscopy provided by the PACS instrument on-board Herschel telescope. In the first part we are interested in obtaining an estimate of the size of FIR emitting region and to sort our targets in two classes: point-like and extended. Secondly, we focus on the molecular component of the envelope traced by carbon monoxide (CO) rotational lines. We conduct a line survey on a sample of evolved stars by identifying and measuring flux of both 12CO and 13CO isotopologues in the PACS range, while looking at the overall properties of the sample. Lastly, we will be interested in obtaining physical parameters of the CSE, namely gas temperature, mass and mass-loss rate on a sample of carbon stars. For that, we make use of PACS large wavelength coverage, which enables the simultaneous study of a large number of CO transitions, to perform the rotational diagram analysis. We report the detection of CO emission in a high number of stars from the catalogue, which were mostly classified as point-like targets with a few exceptions of planetary nebulae. High J rotational number transitions were detected in a number of targets, revealing the presence of a significant amount of hot gas (T ˜ 400-900 K) and high mass-loss rates. We conclude that Herschel/PACS is in a privileged position to detect a new population of warmer gas, typically missed in sub-mm/mm observations.

  18. Evolving role of MRI in Crohn's disease.

    PubMed

    Yacoub, Joseph H; Obara, Piotr; Oto, Aytekin

    2013-06-01

    MR enterography is playing an evolving role in the evaluation of small bowel Crohn's disease (CD). Standard MR enterography includes a combination of rapidly acquired T2 sequence, balanced steady-state acquisition, and contrast enhanced T1-weighted gradient echo sequence. The diagnostic performance of these sequences has been shown to be comparable, and in some respects superior, to other small bowel imaging modalities. The findings of CD on MR enterography have been well described in the literature. New and emerging techniques such as diffusion-weighted imaging (DWI), dynamic contrast enhanced MRI (DCE-MRI), cinematography, and magnetization transfer, may lead to improved accuracy in characterizing the disease. These advanced techniques can provide quantitative parameters that may prove to be useful in assessing disease activity, severity, and response to treatment. In the future, MR enterography may play an increasing role in management decisions for patients with small bowel CD; however, larger studies are needed to validate these emerging MRI parameters as imaging biomarkers.

  19. Increased longevity evolves from grandmothering.

    PubMed

    Kim, Peter S; Coxworth, James E; Hawkes, Kristen

    2012-12-22

    Postmenopausal longevity may have evolved in our lineage when ancestral grandmothers subsidized their daughters' fertility by provisioning grandchildren, but the verbal hypothesis has lacked mathematical support until now. Here, we present a formal simulation in which life spans similar to those of modern chimpanzees lengthen into the modern human range as a consequence of grandmother effects. Greater longevity raises the chance of living through the fertile years but is opposed by costs that differ for the sexes. Our grandmother assumptions are restrictive. Only females who are no longer fertile themselves are eligible, and female fertility extends to age 45 years. Initially, there are very few eligible grandmothers and effects are small. Grandmothers can support only one dependent at a time and do not care selectively for their daughters' offspring. They must take the oldest juveniles still relying on mothers; and infants under the age of 2 years are never eligible for subsidy. Our model includes no assumptions about brains, learning or pair bonds. Grandmother effects alone are sufficient to propel the doubling of life spans in less than sixty thousand years.

  20. Circumstellar Crystalline Silicates: Evolved Stars

    NASA Astrophysics Data System (ADS)

    Tartar, Josh; Speck, A. K.

    2008-05-01

    One of the most exciting developments in astronomy in the last 15 years was the discovery of crystalline silicate stardust by the Short Wavelength Spectrometer (SWS) on board of ISO; discovery of the crystalline grains was indeed one of the biggest surprises of the ISO mission. Initially discovered around AGB stars (evolved stars in the range of 0.8 > M/M¤>8) at far-infrared (IR) wavelengths, crystalline silicates have since been seen in many astrophysical environments including young stellar objects (T Tauri and Herbig Ae/Be), comets and Ultra Luminous Infrared Galaxies. Low and intermediate mass stars (LIMS) comprise 95% of the contributors to the ISM, so study of the formation of crystalline silicates is critical to our understanding of the ISM, which is thought to be primarily amorphous (one would expect an almost exact match between the composition of AGB dust shells and the dust in the ISM). Whether the crystalline dust is merely undetectable or amorphized remains a mystery. The FORCAST instrument on SOFIA as well as the PACS instrument on Herschel will provide exciting observing opportunities for the further study of crystalline silicates.

  1. Multicopy Suppression Underpins Metabolic Evolvability

    PubMed Central

    Patrick, Wayne M.; Quandt, Erik M.; Swartzlander, Dan B.; Matsumura, Ichiro

    2009-01-01

    Our understanding of the origins of new metabolic functions is based upon anecdotal genetic and biochemical evidence. Some auxotrophies can be suppressed by overexpressing substrate-ambiguous enzymes (i.e., those that catalyze the same chemical transformation on different substrates). Other enzymes exhibit weak but detectable catalytic promiscuity in vitro (i.e., they catalyze different transformations on similar substrates). Cells adapt to novel environments through the evolution of these secondary activities, but neither their chemical natures nor their frequencies of occurrence have been characterized en bloc. Here, we systematically identified multifunctional genes within the Escherichia coli genome. We screened 104 single-gene knockout strains and discovered that many (20%) of these auxotrophs were rescued by the overexpression of at least one noncognate E. coli gene. The deleted gene and its suppressor were generally unrelated, suggesting that promiscuity is a product of contingency. This genome-wide survey demonstrates that multifunctional genes are common and illustrates the mechanistic diversity by which their products enhance metabolic robustness and evolvability. PMID:17884825

  2. Magnetic fields around evolved stars

    NASA Astrophysics Data System (ADS)

    Leal-Ferreira, M.; Vlemmings, W.; Kemball, A.; Amiri, N.; Maercker, M.; Ramstedt, S.; Olofsson, G.

    2014-04-01

    A number of mechanisms, such as magnetic fields, (binary) companions and circumstellar disks have been suggested to be the cause of non-spherical PNe and in particular collimated outflows. This work investigates one of these mechanisms: the magnetic fields. While MHD simulations show that the fields can indeed be important, few observations of magnetic fields have been done so far. We used the VLBA to observe five evolved stars, with the goal of detecting the magnetic field by means of water maser polarization. The sample consists in four AGB stars (IK Tau, RT Vir, IRC+60370 and AP Lyn) and one pPN (OH231.8+4.2). In four of the five sources, several strong maser features were detected allowing us to measure the linear and/or circular polarization. Based on the circular polarization detections, we infer the strength of the component of the field along the line of sight to be between ~30 mG and ~330 mG in the water maser regions of these four sources. When extrapolated to the surface of the stars, the magnetic field strength would be between a few hundred mG and a few Gauss when assuming a toroidal field geometry and higher when assuming more complex magnetic fields. We conclude that the magnetic energy we derived in the water maser regions is higher than the thermal and kinetic energy, leading to the conclusion that, indeed, magnetic fields probably play an important role in shaping Planetary Nebulae.

  3. How do drumlin patterns evolve?

    NASA Astrophysics Data System (ADS)

    Ely, Jeremy; Clark, Chris; Spagnolo, Matteo; Hughes, Anna

    2016-04-01

    The flow of a geomorphic agent over a sediment bed creates patterns in the substrate composed of bedforms. Ice is no exception to this, organising soft sedimentary substrates into subglacial bedforms. As we are yet to fully observe their initiation and evolution beneath a contemporary ice mass, little is known about how patterns in subglacial bedforms develop. Here we study 36,222 drumlins, divided into 72 flowsets, left behind by the former British-Irish Ice sheet. These flowsets provide us with 'snapshots' of drumlin pattern development. The probability distribution functions of the size and shape metrics of drumlins within these flowsets were analysed to determine whether behaviour that is common of other patterned phenomena has occurred. Specifically, we ask whether drumlins i) are printed at a specific scale; ii) grow or shrink after they initiate; iii) stabilise at a specific size and shape; and iv) migrate. Our results indicate that drumlins initiate at a minimum size and spacing. After initiation, the log-normal distribution of drumlin size and shape metrics suggests that drumlins grow, or possibly shrink, as they develop. We find no evidence for stabilisation in drumlin length, supporting the idea of a subglacial bedform continuum. Drumlin migration is difficult to determine from the palaeo-record. However, there are some indications that a mixture of static and mobile drumlins occurs, which could potentially lead to collisions, cannibalisation and coarsening. Further images of modern drumlin fields evolving beneath ice are required to capture stages of drumlin pattern evolution.

  4. Increased longevity evolves from grandmothering

    PubMed Central

    Kim, Peter S.; Coxworth, James E.; Hawkes, Kristen

    2012-01-01

    Postmenopausal longevity may have evolved in our lineage when ancestral grandmothers subsidized their daughters' fertility by provisioning grandchildren, but the verbal hypothesis has lacked mathematical support until now. Here, we present a formal simulation in which life spans similar to those of modern chimpanzees lengthen into the modern human range as a consequence of grandmother effects. Greater longevity raises the chance of living through the fertile years but is opposed by costs that differ for the sexes. Our grandmother assumptions are restrictive. Only females who are no longer fertile themselves are eligible, and female fertility extends to age 45 years. Initially, there are very few eligible grandmothers and effects are small. Grandmothers can support only one dependent at a time and do not care selectively for their daughters' offspring. They must take the oldest juveniles still relying on mothers; and infants under the age of 2 years are never eligible for subsidy. Our model includes no assumptions about brains, learning or pair bonds. Grandmother effects alone are sufficient to propel the doubling of life spans in less than sixty thousand years. PMID:23097518

  5. Recommendation in evolving online networks

    NASA Astrophysics Data System (ADS)

    Hu, Xiao; Zeng, An; Shang, Ming-Sheng

    2016-02-01

    Recommender system is an effective tool to find the most relevant information for online users. By analyzing the historical selection records of users, recommender system predicts the most likely future links in the user-item network and accordingly constructs a personalized recommendation list for each user. So far, the recommendation process is mostly investigated in static user-item networks. In this paper, we propose a model which allows us to examine the performance of the state-of-the-art recommendation algorithms in evolving networks. We find that the recommendation accuracy in general decreases with time if the evolution of the online network fully depends on the recommendation. Interestingly, some randomness in users' choice can significantly improve the long-term accuracy of the recommendation algorithm. When a hybrid recommendation algorithm is applied, we find that the optimal parameter gradually shifts towards the diversity-favoring recommendation algorithm, indicating that recommendation diversity is essential to keep a high long-term recommendation accuracy. Finally, we confirm our conclusions by studying the recommendation on networks with the real evolution data.

  6. The evolving defense communications system

    NASA Astrophysics Data System (ADS)

    Testa, Ann M.; Jones, Walter I.

    1992-05-01

    Command, control, and communications (C3) systems 'help lift the fog of war that adds uncertainty to any military operation.' They multiply the effectiveness of weapon systems and are critical components of our nation's warfighting capability. One of these critical systems is the Defense Communications System (DCS) which evolved over the past 30 years. Several factors drove this evolution, including constrained budgets, the need to improve the effectiveness and efficiency of the service provided, compatibility and interoperability, and technological advances. Based on lessons learned from Desert Shield/Desert Storm and the changing environment, force structure, and strategy, it is time to advance the DCS to its next stage. The future DCS must be flexible enough to adapt to any situation anywhere in the world. Mobile, modular building block packages of communications equipment must be available to provide effective communications capability to deployed units immediately upon arrival. Total integration and interoperability among military, commercial, and other government agencies' communication systems is a must if survivable, robust connectivity is going to be available when needed. Integration planning must begin now.

  7. Multiscale modelling of evolving foams

    NASA Astrophysics Data System (ADS)

    Saye, R. I.; Sethian, J. A.

    2016-06-01

    We present a set of multi-scale interlinked algorithms to model the dynamics of evolving foams. These algorithms couple the key effects of macroscopic bubble rearrangement, thin film drainage, and membrane rupture. For each of the mechanisms, we construct consistent and accurate algorithms, and couple them together to work across the wide range of space and time scales that occur in foam dynamics. These algorithms include second order finite difference projection methods for computing incompressible fluid flow on the macroscale, second order finite element methods to solve thin film drainage equations in the lamellae and Plateau borders, multiphase Voronoi Implicit Interface Methods to track interconnected membrane boundaries and capture topological changes, and Lagrangian particle methods for conservative liquid redistribution during rearrangement and rupture. We derive a full set of numerical approximations that are coupled via interface jump conditions and flux boundary conditions, and show convergence for the individual mechanisms. We demonstrate our approach by computing a variety of foam dynamics, including coupled evolution of three-dimensional bubble clusters attached to an anchored membrane and collapse of a foam cluster.

  8. The Evolving Defense Industrial Base

    DTIC Science & Technology

    2007-05-16

    Base May 16, 2007 9 • Industry Is Focused on the Long Term – Earn a profit that exceeds the cost of capital – Corporate Value is Created through...VFW Fokker Dornier AISA Racal MBB …And the Same Industrial Consolidation has Taken Place in Europe 5 Rapid consolidation of core US sectors continues...Acquisition Landscape Year # Targets Acquired $ Value 2003 21 $2.7B 2004 19 $3.0B 2005 31 $7.4B Total 71 $13.2B Net Effect: Increased Global Teaming on

  9. Submillimeter observations of evolved stars

    SciTech Connect

    Sopka, R.J.; Hildebrand, R.; Jaffe, D.T.; Gatley, I.; Roellig, T.; Werner, M.; Jura, M.; Zuckerman, B.

    1985-07-01

    Broad-band submillimeter observations of the thermal emission from evolved stars have been obtained with the United Kingdom Infrared Telescope on Mauna Kea, Hawaii. These observations, at an effective wavelength of 400 ..mu..m, provide the most direct method for estimating the mass loss rate in dust from these stars and also help to define the long-wavelength thermal spectrum of the dust envelopes. The mass loss rates in dust that we derive range from 10/sup -9/ to 10/sup -6/ M/sub sun/ yr/sup -1/ and are compared with mass loss rates derived from molecular line observations to estimate gas-to-dust ratios in outflowing envelopes. These values are found to be generally compatible with the interstellar gas-to-dust ratio of approx.100 if submillimeter emissivities appropriate to amorphous grain structures are assumed. Our analysis of the spectrum of IRC+10216 confirms previous suggestions that the grain emissivity varies as lambda/sup -1.2/ rather than as lambda/sup -2/ for 10

  10. Idiopathic pulmonary fibrosis: evolving concepts.

    PubMed

    Ryu, Jay H; Moua, Teng; Daniels, Craig E; Hartman, Thomas E; Yi, Eunhee S; Utz, James P; Limper, Andrew H

    2014-08-01

    Idiopathic pulmonary fibrosis (IPF) occurs predominantly in middle-aged and older adults and accounts for 20% to 30% of interstitial lung diseases. It is usually progressive, resulting in respiratory failure and death. Diagnostic criteria for IPF have evolved over the years, and IPF is currently defined as a disease characterized by the histopathologic pattern of usual interstitial pneumonia occurring in the absence of an identifiable cause of lung injury. Understanding of the pathogenesis of IPF has shifted away from chronic inflammation and toward dysregulated fibroproliferative repair in response to alveolar epithelial injury. Idiopathic pulmonary fibrosis is likely a heterogeneous disorder caused by various interactions between genetic components and environmental exposures. High-resolution computed tomography can be diagnostic in the presence of typical findings such as bilateral reticular opacities associated with traction bronchiectasis/bronchiolectasis in a predominantly basal and subpleural distribution, along with subpleural honeycombing. In other circumstances, a surgical lung biopsy may be needed. The clinical course of IPF can be unpredictable and may be punctuated by acute deteriorations (acute exacerbation). Although progress continues in unraveling the mechanisms of IPF, effective therapy has remained elusive. Thus, clinicians and patients need to reach informed decisions regarding management options including lung transplant. The findings in this review were based on a literature search of PubMed using the search terms idiopathic pulmonary fibrosis and usual interstitial pneumonia, limited to human studies in the English language published from January 1, 2000, through December 31, 2013, and supplemented by key references published before the year 2000. Copyright © 2014 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

  11. Time-dependent effects of the flame retardant tris(1,3-dichloro-2-propyl) phosphate (TDCPP) on mRNA expression, in vitro and in ovo, reveal optimal sampling times for rapidly metabolized compounds.

    PubMed

    Farhat, Amani; Crump, Doug; Porter, Emily; Chiu, Suzanne; Letcher, Robert J; Su, Guanyong; Kennedy, Sean W

    2014-12-01

    The flame retardant, tris(1,3-dichloro-2-propyl) phosphate (TDCPP), was previously shown to affect chicken embryo growth, gallbladder size, and lipid homeostasis. A microarray study, however, revealed only modest transcriptional alterations in liver tissue of pipping embryos (days 20-21), which was attributed to the rapid metabolism of TDCPP throughout incubation. To identify the most appropriate sampling time for rapidly metabolized compounds, the present study assessed the time-dependent effects of TDCPP on 27 genes, in ovo (50 µg [116 nmol] TDCPP/g egg) and in vitro (10 µM), using a chicken ToxChip polymerase chain reaction array. The greatest magnitude in dysregulation (up to 362-fold) occurred on day 8 of incubation (in ovo) with alterations of genes involved in phase I, II, and III metabolism, among others. Gallbladder hypotrophy was observed by embryonic day 12, corroborating the finding in pipping embryos from our previous study. From days 12 to 19, genes involved in lipid homeostasis, steroid hormone metabolism, and oxidative stress were affected. In chicken embryonic hepatoctyes (CEHs), TDCPP was completely metabolized to bis(1,3-dichloro-2-propyl) phosphate (BDCPP) within 36 h, but transcriptional changes remained significant up to 36 h. These changes were not attributed to BDCPP exposure as it only altered 1 gene (CYP1A4). An 18-h exposure in CEHs altered the greatest number of genes, making it an appropriate time point for high-throughput chemical screening; however, depending on the biological pathways of interest, shorter or longer incubation times may be more informative. Overall, TDCPP elicits the transcriptional and phenotypic alterations observed in vitro and in ovo, whereas its major metabolite, BDCPP, is far less biologically active. © 2014 SETAC.

  12. The evolving energy budget of accretionary wedges

    NASA Astrophysics Data System (ADS)

    McBeck, Jessica; Cooke, Michele; Maillot, Bertrand; Souloumiac, Pauline

    2017-04-01

    The energy budget of evolving accretionary systems reveals how deformational processes partition energy as faults slip, topography uplifts, and layer-parallel shortening produces distributed off-fault deformation. The energy budget provides a quantitative framework for evaluating the energetic contribution or consumption of diverse deformation mechanisms. We investigate energy partitioning in evolving accretionary prisms by synthesizing data from physical sand accretion experiments and numerical accretion simulations. We incorporate incremental strain fields and cumulative force measurements from two suites of experiments to design numerical simulations that represent accretionary wedges with stronger and weaker detachment faults. One suite of the physical experiments includes a basal glass bead layer and the other does not. Two physical experiments within each suite implement different boundary conditions (stable base versus moving base configuration). Synthesizing observations from the differing base configurations reduces the influence of sidewall friction because the force vector produced by sidewall friction points in opposite directions depending on whether the base is fixed or moving. With the numerical simulations, we calculate the energy budget at two stages of accretion: at the maximum force preceding the development of the first thrust pair, and at the minimum force following the development of the pair. To identify the appropriate combination of material and fault properties to apply in the simulations, we systematically vary the Young's modulus and the fault static and dynamic friction coefficients in numerical accretion simulations, and identify the set of parameters that minimizes the misfit between the normal force measured on the physical backwall and the numerically simulated force. Following this derivation of the appropriate material and fault properties, we calculate the components of the work budget in the numerical simulations and in the

  13. Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.

    PubMed

    Glazer, Andrew M; Killingbeck, Emily E; Mitros, Therese; Rokhsar, Daniel S; Miller, Craig T

    2015-06-03

    Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis. Copyright © 2015 Glazer et al.

  14. Evolving evolutionary algorithms using linear genetic programming.

    PubMed

    Oltean, Mihai

    2005-01-01

    A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.

  15. Acquiring Evolving Technologies: Web Services Standards

    DTIC Science & Technology

    2016-06-30

    2006 Carnegie Mellon University Acquiring Evolving Technologies : Web Services Standards Harry L. Levinson Software Engineering Institute Carnegie...Acquiring Evolving Technologies : Web Services Standards 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 2 Acquiring Evolving Technologies : Web Services Standards © 2006 Carnegie Mellon University Acquiring

  16. Evolving fuzzy rules for relaxed-criteria negotiation.

    PubMed

    Sim, Kwang Mong

    2008-12-01

    In the literature on automated negotiation, very few negotiation agents are designed with the flexibility to slightly relax their negotiation criteria to reach a consensus more rapidly and with more certainty. Furthermore, these relaxed-criteria negotiation agents were not equipped with the ability to enhance their performance by learning and evolving their relaxed-criteria negotiation rules. The impetus of this work is designing market-driven negotiation agents (MDAs) that not only have the flexibility of relaxing bargaining criteria using fuzzy rules, but can also evolve their structures by learning new relaxed-criteria fuzzy rules to improve their negotiation outcomes as they participate in negotiations in more e-markets. To this end, an evolutionary algorithm for adapting and evolving relaxed-criteria fuzzy rules was developed. Implementing the idea in a testbed, two kinds of experiments for evaluating and comparing EvEMDAs (MDAs with relaxed-criteria rules that are evolved using the evolutionary algorithm) and EMDAs (MDAs with relaxed-criteria rules that are manually constructed) were carried out through stochastic simulations. Empirical results show that: 1) EvEMDAs generally outperformed EMDAs in different types of e-markets and 2) the negotiation outcomes of EvEMDAs generally improved as they negotiated in more e-markets.

  17. Water in evolved lunar rocks

    NASA Astrophysics Data System (ADS)

    Robinson, Katharine Lynn

    The Moon was thought to be completely anhydrous until indigenous water was found in lunar samples in 2008. This discovery raised two fundamental questions about the Moon: how much water is present in the bulk Moon and is water uniformly distributed in the lunar interior? To address these questions, I studied a suite of lunar samples rich in a chemical component called KREEP (K, Rare Earth Elements, P), all of which are incompatible elements. Water behaves as an incompatible element in magmas, so KREEP-rich lunar samples are potentially water rich. In this dissertation, I present the results of a petrologic study of KREEP-rich lunar rocks, measurements of their water contents and deuterium (D) to hydrogen (H) ratios (D/H), and examined where these rocks fit into our understanding of water in the Moon as a whole. We performed a study of highly evolved, KREEP-rich lunar rocks called felsites and determined that they contain quartz. Using cooling rates derived from quartz-Ti thermometry, we show the felsites originated at a minimum pressure of ˜1 kbar, corresponding to a minimum depth of 20-25 km in the lunar crust. We calculate that at that pressure water would have been soluble in the melt, indicating that degassing of H2O from the felsite parental melts was likely minimal and hydrogen isotopes in intrusive rocks are likely unfractionated. We then measured D/H in apatite in KREEP-rich intrusive rocks to clarify the solar system source of the Moon's water. When viewed in the context of other lunar D/H studies, our results indicate there are at least three distinctive reservoirs in the lunar interior, including an ultra-low D reservoir that could represent a primitive component in the Moon's interior. Furthermore, our measurements of residual glass in a KREEP basalt show that the KREEP basaltic magmas contained 10 times less water than the source of the Apollo 17 pyroclastic glass beads, indicating that, though wetter than previously thought, the concentration of

  18. The continually evolving Clostridium difficile species.

    PubMed

    Cairns, Michelle D; Stabler, Richard A; Shetty, Nandini; Wren, Brendan W

    2012-08-01

    Clostridium difficile is a spore-forming Gram-positive bacterium that causes chronic diarrhea and sometimes life-threatening disease mainly in elderly and hospitalized patients. The reported incidence of C. difficile infection has changed dramatically over the last decade and has been related to the emergence of distinct clonal lineages that appear more transmissible and cause more severe infection. These include PCR ribotypes 027, 017 and more recently 078. Population biology studies using multilocus sequence typing and whole-genome comparisons has helped to define the C. difficile species into four clonal complexes that include PCR ribotypes 027, 017, 078 and 023, as well as a general grouping of most other PCR ribotypes. Further analysis of strains from diverse sources and geographical origins reveal significant microdiversity of clonal complexes and confirms that C. difficile is continuing to evolve. The study of C. difficile represents a real-time global evolutionary experiment where the pathogen is responding to a range of selective pressures created by human activity and practices in healthcare settings. The advent of whole-genome sequencing coupled with phylogeny (phylogeography and phylohistory) will provide unprecedented detail on the local and global emergence and disappearance of C. difficile clones, and facilitate more rational approaches to disease control. This review will highlight the emergence of virulent C. difficile clones and our current understanding of molecular epidemiology of the species.

  19. Origins and evolvability of the PAX family.

    PubMed

    Paixão-Côrtes, Vanessa R; Salzano, Francisco M; Bortolini, Maria Cátira

    2015-08-01

    The paired box (PAX) family of transcription/developmental genes plays a key role in numerous stages of embryonic development, as well as in adult organogenesis. There is evidence linking the acquisition of a paired-like DNA binding domain (PD) to domestication of a Tc1/mariner transposon. Further duplication/deletion processes led to at least five paralogous metazoan protein groups, which can be classified into two supergroups, PAXB-like or PAXD-like, using ancestral defining structures; the PD plus an octapeptide motif (OP) and a paired-type homeobox DNA binding domain (PTHD), producing the PD-OP-PTHD structure characteristic of the PAXB-like group, whereas an additional domain, the paired-type homeodomain tail (PHT), is present in the PAXD-like group, producing a PD-OP-PTHD-PHT structure. We examined their patterns of distribution in various species, using both available data and new bioinformatic analyses, including vertebrate PAX genes and their shared and specific functions, as well as inter- and intraspecific variability of PAX in primates. These analyses revealed a relatively conserved PAX network, accompanied by specific changes that led to adaptive novelties. Therefore, both stability and evolvability shaped the molecular evolution of this key transcriptional network. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Evolving Approaches to Patients with Advanced Differentiated Thyroid Cancer

    PubMed Central

    Sherman, Steven I.

    2013-01-01

    Advanced differentiated thyroid cancer (DTC), defined by clinical characteristics including gross extrathyroidal invasion, distant metastases, radioiodine (RAI) resistance, and avidity for 18-fluorodeoxyglucose (positron emission tomography-positive), is found in approximately 10–20% of patients with DTC. Standard therapy (surgery, RAI, TSH suppression with levothyroxine) is ineffective for many of these patients, as is standard chemotherapy. Our understanding of the molecular mechanisms leading to DTC and the transformation to advanced DTC has rapidly evolved over the past 15–20 years. Newer targeted therapy, specifically inhibitors of intracellular kinase signaling pathways, and cooperative multicenter clinical trials have dramatically changed the therapeutic landscape for patients with advanced DTC. In this review focusing on morbidities, molecules, and medicinals, we present a patient with advanced DTC, explore the genetics and molecular biology of advanced DTC, and review evolving therapies for these patients including multikinase inhibitors, selective kinase inhibitors, and combination therapies. PMID:23575762

  1. The Problem of Evolving a Genetic Code

    ERIC Educational Resources Information Center

    Woese, Carl R.

    1970-01-01

    Proposes models for the evolution of the genetic code and translation mechanisms. Suggests that the translation process is so complex and precise that it must have evolved in many stages, and that the evolution of the code was influenced by the constraints imposed by the evolving translation mechanism. (EB)

  2. Evolving Technologies: A View to Tomorrow

    ERIC Educational Resources Information Center

    Tamarkin, Molly; Rodrigo, Shelley

    2011-01-01

    Technology leaders must participate in strategy creation as well as operational delivery within higher education institutions. The future of higher education--the view to tomorrow--is irrevocably integrated and intertwined with evolving technologies. This article focuses on two specific evolving technologies: (1) alternative IT sourcing; and (2)…

  3. Evolving Technologies: A View to Tomorrow

    ERIC Educational Resources Information Center

    Tamarkin, Molly; Rodrigo, Shelley

    2011-01-01

    Technology leaders must participate in strategy creation as well as operational delivery within higher education institutions. The future of higher education--the view to tomorrow--is irrevocably integrated and intertwined with evolving technologies. This article focuses on two specific evolving technologies: (1) alternative IT sourcing; and (2)…

  4. What Technology? Reflections on Evolving Services

    ERIC Educational Resources Information Center

    Collins, Sharon

    2009-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having--or are predicted to have--the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual…

  5. NASA's Space Launch System: An Evolving Capability for Exploration An Evolving Capability for Exploration

    NASA Technical Reports Server (NTRS)

    Creech, Stephen D.; Crumbly, Christopher M.; Robinson, Kimerly F.

    2016-01-01

    A foundational capability for international human deep-space exploration, NASA's Space Launch System (SLS) vehicle represents a new spaceflight infrastructure asset, creating opportunities for mission profiles and space systems that cannot currently be executed. While the primary purpose of SLS, which is making rapid progress towards initial launch readiness in two years, will be to support NASA's Journey to Mars, discussions are already well underway regarding other potential utilization of the vehicle's unique capabilities. In its initial Block 1 configuration, capable of launching 70 metric tons (t) to low Earth orbit (LEO), SLS is capable of propelling the Orion crew vehicle to cislunar space, while also delivering small CubeSat-class spacecraft to deep-space destinations. With the addition of a more powerful upper stage, the Block 1B configuration of SLS will be able to deliver 105 t to LEO and enable more ambitious human missions into the proving ground of space. This configuration offers opportunities for launching co-manifested payloads with the Orion crew vehicle, and a class of secondary payloads, larger than today's CubeSats. Further upgrades to the vehicle, including advanced boosters, will evolve its performance to 130 t in its Block 2 configuration. Both Block 1B and Block 2 also offer the capability to carry 8.4- or 10-m payload fairings, larger than any contemporary launch vehicle. With unmatched mass-lift capability, payload volume, and C3, SLS not only enables spacecraft or mission designs currently impossible with contemporary EELVs, it also offers enhancing benefits, such as reduced risk, operational costs and/or complexity, shorter transit time to destination or launching large systems either monolithically or in fewer components. This paper will discuss both the performance and capabilities of Space Launch System as it evolves, and the current state of SLS utilization planning.

  6. Quantitative Non-canonical Amino Acid Tagging (QuaNCAT) Proteomics Identifies Distinct Patterns of Protein Synthesis Rapidly Induced by Hypertrophic Agents in Cardiomyocytes, Revealing New Aspects of Metabolic Remodeling*

    PubMed Central

    Liu, Rui; Kenney, Justin W.; Manousopoulou, Antigoni; Johnston, Harvey E.; Kamei, Makoto; Woelk, Christopher H.; Xie, Jianling; Schwarzer, Michael; Proud, Christopher G.

    2016-01-01

    Cardiomyocytes undergo growth and remodeling in response to specific pathological or physiological conditions. In the former, myocardial growth is a risk factor for cardiac failure and faster protein synthesis is a major factor driving cardiomyocyte growth. Our goal was to quantify the rapid effects of different pro-hypertrophic stimuli on the synthesis of specific proteins in ARVC and to determine whether such effects are caused by alterations on mRNA abundance or the translation of specific mRNAs. Cardiomyocytes have very low rates of protein synthesis, posing a challenging problem in terms of studying changes in the synthesis of specific proteins, which also applies to other nondividing primary cells. To study the rates of accumulation of specific proteins in these cells, we developed an optimized version of the Quantitative Noncanonical Amino acid Tagging LC/MS proteomic method to label and selectively enrich newly synthesized proteins in these primary cells while eliminating the suppressive effects of pre-existing and highly abundant nonisotope-tagged polypeptides. Our data revealed that a classical pathologic (phenylephrine; PE) and the recently identified insulin stimulus that also contributes to the development of pathological cardiac hypertrophy (insulin), both increased the synthesis of proteins involved in, e.g. glycolysis, the Krebs cycle and beta-oxidation, and sarcomeric components. However, insulin increased synthesis of many metabolic enzymes to a greater extent than PE. Using a novel validation method, we confirmed that synthesis of selected candidates is indeed up-regulated by PE and insulin. Synthesis of all proteins studied was up-regulated by signaling through mammalian target of rapamycin complex 1 without changes in their mRNA levels, showing the key importance of translational control in the rapid effects of hypertrophic stimuli. Expression of PKM2 was up-regulated in rat hearts following TAC. This isoform possesses specific regulatory

  7. An unusually fast-evolving supernova.

    PubMed

    Poznanski, Dovi; Chornock, Ryan; Nugent, Peter E; Bloom, Joshua S; Filippenko, Alexei V; Ganeshalingam, Mohan; Leonard, Douglas C; Li, Weidong; Thomas, Rollin C

    2010-01-01

    Analyses of supernovae (SNe) have revealed two main types of progenitors: exploding white dwarfs and collapsing massive stars. Here we describe SN 2002bj, which stands out as different from any SN reported to date. Its light curve rose and declined very rapidly, yet reached a peak intrinsic brightness greater than -18 magnitude. A spectrum obtained 7 days after discovery shows the presence of helium and intermediate-mass elements, yet no clear hydrogen or iron-peak elements. The spectrum only barely resembles that of a type Ia SN, with added carbon and helium. Its properties suggest that SN 2002bj may be representative of a class of progenitors that previously has been only hypothesized: a helium detonation on a white dwarf, ejecting a small envelope of material. New surveys should find many such objects, despite their scarcity.

  8. The evolving doublecortin (DCX) superfamily.

    PubMed

    Reiner, Orly; Coquelle, Frédéric M; Peter, Bastian; Levy, Talia; Kaplan, Anna; Sapir, Tamar; Orr, Irit; Barkai, Naama; Eichele, Gregor; Bergmann, Sven

    2006-07-26

    Doublecortin (DCX) domains serve as protein-interaction platforms. Mutations in members of this protein superfamily are linked to several genetic diseases. Mutations in the human DCX gene result in abnormal neuronal migration, epilepsy, and mental retardation; mutations in RP1 are associated with a form of inherited blindness, and DCDC2 has been associated with dyslectic reading disabilities. The DCX-repeat gene family is composed of eleven paralogs in human and in mouse. Its evolution was followed across vertebrates, invertebrates, and was traced to unicellular organisms, thus enabling following evolutionary additions and losses of genes or domains. The N-terminal and C-terminal DCX domains have undergone sub-specialization and divergence. Developmental in situ hybridization data for nine genes was generated. In addition, a novel co-expression analysis for most human and mouse DCX superfamily-genes was performed using high-throughput expression data extracted from Unigene. We performed an in-depth study of a complete gene superfamily using several complimentary methods. This study reveals the existence and conservation of multiple members of the DCX superfamily in different species. Sequence analysis combined with expression analysis is likely to be a useful tool to predict correlations between human disease and mouse models. The sub-specialization of some members due to restricted expression patterns and sequence divergence may explain the successful addition of genes to this family throughout evolution.

  9. Tensions inherent in the evolving role of the infection preventionist

    PubMed Central

    Conway, Laurie J.; Raveis, Victoria H.; Pogorzelska-Maziarz, Monika; Uchida, May; Stone, Patricia W.; Larson, Elaine L.

    2014-01-01

    Background The role of infection preventionists (IPs) is expanding in response to demands for quality and transparency in health care. Practice analyses and survey research have demonstrated that IPs spend a majority of their time on surveillance and are increasingly responsible for prevention activities and management; however, deeper qualitative aspects of the IP role have rarely been explored. Methods We conducted a qualitative content analysis of in-depth interviews with 19 IPs at hospitals throughout the United States to describe the current IP role, specifically the ways that IPs effect improvements and the facilitators and barriers they face. Results The narratives document that the IP role is evolving in response to recent changes in the health care landscape and reveal that this progression is associated with friction and uncertainty. Tensions inherent in the evolving role of the IP emerged from the interviews as 4 broad themes: (1) expanding responsibilities outstrip resources, (2) shifting role boundaries create uncertainty, (3) evolving mechanisms of influence involve trade-offs, and (4) the stress of constant change is compounded by chronic recurring challenges. Conclusion Advances in implementation science, data standardization, and training in leadership skills are needed to support IPs in their evolving role. PMID:23880116

  10. Evolving Strategies for Cancer and Autoimmunity: Back to the Future

    PubMed Central

    Lane, Peter J. L.; McConnell, Fiona M.; Anderson, Graham; Nawaf, Maher G.; Gaspal, Fabrina M.; Withers, David R.

    2014-01-01

    Although current thinking has focused on genetic variation between individuals and environmental influences as underpinning susceptibility to both autoimmunity and cancer, an alternative view is that human susceptibility to these diseases is a consequence of the way the immune system evolved. It is important to remember that the immunological genes that we inherit and the systems that they control were shaped by the drive for reproductive success rather than for individual survival. It is our view that human susceptibility to autoimmunity and cancer is the evolutionarily acceptable side effect of the immune adaptations that evolved in early placental mammals to accommodate a fundamental change in reproductive strategy. Studies of immune function in mammals show that high affinity antibodies and CD4 memory, along with its regulation, co-evolved with placentation. By dissection of the immunologically active genes and proteins that evolved to regulate this step change in the mammalian immune system, clues have emerged that may reveal ways of de-tuning both effector and regulatory arms of the immune system to abrogate autoimmune responses whilst preserving protection against infection. Paradoxically, it appears that such a detuned and deregulated immune system is much better equipped to mount anti-tumor immune responses against cancers. PMID:24782861

  11. Evolvability and robustness in populations of RNA virus Φ6

    PubMed Central

    Goldhill, Daniel; Lee, Angela; Williams, Elizabeth S. C. P.; Turner, Paul E.

    2014-01-01

    Microbes can respond quickly to environmental disturbances through adaptation. However, processes determining the constraints on this adaptation are not well understood. One process that could affect the rate of adaptation to environmental perturbations is genetic robustness, the ability to maintain phenotype despite mutation. Genetic robustness has been theoretically linked to evolvability but rarely tested empirically using evolving populations. We used populations of the RNA bacteriophage ϕ6 previously characterized as differing in robustness, and passaged them through a repeated environmental disturbance: periodic 45°C heat shock. The robust populations evolved faster to withstand the disturbance, relative to the less robust (brittle) populations. The robust populations also achieved relatively greater thermotolerance by the end of the experimental evolution. Sequencing revealed that thermotolerance occurred via a key mutation in gene P5 (viral lysis protein), previously shown to be associated with heat shock survival in the virus. Whereas this identical mutation fixed in all of the independently evolving robust populations, it was absent in some brittle populations, which instead fixed a less beneficial mutation. We concluded that robust populations adapted faster to the environmental change, and more easily accessed mutations of large benefit. Our study shows that genetic robustness can play a role in determining the relative ability for microbes to adapt to changing environments. PMID:24550904

  12. Meeting evolving technology education challenges in photonics and optics

    NASA Astrophysics Data System (ADS)

    Woodward, William R.

    2012-10-01

    The rapid evolution of technology places great challenges on educators and employers to train and certify personnel in these technologies in a timely way. A cooperative effort between international standards organizations and the Electronics Technicians Association, International (ETA) is pioneering a new approach to meet the challenges of evolving technology education in the areas of photonics and optics. ETA recently introduced two optics certifications and two photonics certifications. Each of these certifications contains multiple knowledge and hands-on examinations that were developed specifically to meet the needs of industry.

  13. Longitudinal testing of hippocampal plasticity reveals the onset and maintenance of endogenous human Aß-induced synaptic dysfunction in individual freely behaving pre-plaque transgenic rats: rapid reversal by anti-Aß agents.

    PubMed

    Qi, Yingjie; Klyubin, Igor; Harney, Sarah C; Hu, NengWei; Cullen, William K; Grant, Marianne K; Steffen, Julia; Wilson, Edward N; Do Carmo, Sonia; Remy, Stefan; Fuhrmann, Martin; Ashe, Karen H; Cuello, A Claudio; Rowan, Michael J

    2014-12-24

    Long before synaptic loss occurs in Alzheimer's disease significant harbingers of disease may be detected at the functional level. Here we examined if synaptic long-term potentiation is selectively disrupted prior to extracellular deposition of Aß in a very complete model of Alzheimer's disease amyloidosis, the McGill-R-Thy1-APP transgenic rat. Longitudinal studies in freely behaving animals revealed an age-dependent, relatively rapid-onset and persistent inhibition of long-term potentiation without a change in baseline synaptic transmission in the CA1 area of the hippocampus. Thus the ability of a standard 200 Hz conditioning protocol to induce significant NMDA receptor-dependent short- and long-term potentiation was lost at about 3.5 months of age and this deficit persisted for at least another 2-3 months, when plaques start to appear. Consistent with in vitro evidence for a causal role of a selective reduction in NMDA receptor-mediated synaptic currents, the deficit in synaptic plasticity in vivo was associated with a reduction in the synaptic burst response to the conditioning stimulation and was overcome using stronger 400 Hz stimulation. Moreover, intracerebroventricular treatment for 3 days with an N-terminally directed monoclonal anti- human Aß antibody, McSA1, transiently reversed the impairment of synaptic plasticity. Similar brief treatment with the BACE1 inhibitor LY2886721 or the γ-secretase inhibitor MRK-560 was found to have a comparable short-lived ameliorative effect when tracked in individual rats. These findings provide strong evidence that endogenously generated human Aß selectively disrupts the induction of long-term potentiation in a manner that enables potential therapeutic options to be assessed longitudinally at the pre-plaque stage of Alzheimer's disease amyloidosis.

  14. Warning signals evolve to disengage Batesian mimics.

    PubMed

    Franks, Daniel W; Ruxton, Graeme D; Sherratt, Thomas N

    2009-01-01

    Prey that are unprofitable to attack are typically conspicuous in appearance. Conventional theory assumes that these warning signals have evolved in response to predator receiver biases. However, such biases might be a symptom rather than a cause of warning signals. We therefore examine an alternative theory: that conspicuousness evolves in unprofitable prey to avoid confusion with profitable prey. One might wonder why unprofitable prey do not find a cryptic means to be distinct from profitable prey, reducing both their risk of confusion with profitable prey and their rate of detection by predators. Here we present the first coevolutionary model to allow for Batesian mimicry and signals with different levels of detectability. We find that unprofitable prey do indeed evolve ways of distinguishing themselves using cryptic signals, particularly when appearance traits can evolve in multiple dimensions. However, conspicuous warning signals readily evolve in unprofitable prey when there are more ways to look different from the background than to match it. Moreover, the more unprofitable the prey species, the higher its evolved conspicuousness. Our results provide strong support for the argument that unprofitable species evolve conspicuous signals to avoid confusion with profitable prey and indicate that peak shift in conspicuousness-linked traits is a major factor in its establishment.

  15. Modeling and technical use of gas evolving electrodes. Part 2: Modeling of gas-evolving electrolyzers with free electrolyte circulation

    NASA Technical Reports Server (NTRS)

    Schleiff, M.; Thiele, W.; Matschiner, H.

    1983-01-01

    In an electrochemical reactor with gas-evolving electrodes, the transporting action of the gas bubbles can be used to move the electrolyte in a cycle flow, when the structure of the flow channels is suitable. For an electrolysis cell with such a circulation system a mathematic model was set up and evaluated. It is shown that in this manner, a rapid flow through the electrode gap can be achieved without additional energy consumption, in addition to a low gas fraction and a low cell voltage. The cell voltage and the attainable cycle spread are investigated as a function of the geometric parameters for their optimum values.

  16. Neural mechanisms underlying the evolvability of behaviour

    PubMed Central

    Katz, Paul S.

    2011-01-01

    The complexity of nervous systems alters the evolvability of behaviour. Complex nervous systems are phylogenetically constrained; nevertheless particular species-specific behaviours have repeatedly evolved, suggesting a predisposition towards those behaviours. Independently evolved behaviours in animals that share a common neural architecture are generally produced by homologous neural structures, homologous neural pathways and even in the case of some invertebrates, homologous identified neurons. Such parallel evolution has been documented in the chromatic sensitivity of visual systems, motor behaviours and complex social behaviours such as pair-bonding. The appearance of homoplasious behaviours produced by homologous neural substrates suggests that there might be features of these nervous systems that favoured the repeated evolution of particular behaviours. Neuromodulation may be one such feature because it allows anatomically defined neural circuitry to be re-purposed. The developmental, genetic and physiological mechanisms that contribute to nervous system complexity may also bias the evolution of behaviour, thereby affecting the evolvability of species-specific behaviour. PMID:21690127

  17. Evolvability Characterization in the Context of SOA

    NASA Astrophysics Data System (ADS)

    Arciniegas H., Jose L.; Dueñas L., Juan C.

    Service-Oriented Architecture (SOA) is an architectural style which promotes reuse of self-contained services. These self-contained services allow a better consideration of software quality characteristics as they can be independently analyzed. In our work, the evolvability quality characteristic has been considered, due to its impact in the stages of Maintenance and Evolution (M&E) for the software enterprises. Three goals are underlined in this paper: first, the relationship between SOA and quality characteristics focusing on a precise definition of evolvability of a software product from the SOA perspective, second a M&E model for SOA, and finally, some experiences are presented in order to assess evolvability in real software products. Two case studies have been executed: the first one analyzing the evolvability of the OSGi framework. And in the second case, the model is used in local Small and Medium Enterprises (SMEs), where an improvement process has been executed.

  18. Neural mechanisms underlying the evolvability of behaviour.

    PubMed

    Katz, Paul S

    2011-07-27

    The complexity of nervous systems alters the evolvability of behaviour. Complex nervous systems are phylogenetically constrained; nevertheless particular species-specific behaviours have repeatedly evolved, suggesting a predisposition towards those behaviours. Independently evolved behaviours in animals that share a common neural architecture are generally produced by homologous neural structures, homologous neural pathways and even in the case of some invertebrates, homologous identified neurons. Such parallel evolution has been documented in the chromatic sensitivity of visual systems, motor behaviours and complex social behaviours such as pair-bonding. The appearance of homoplasious behaviours produced by homologous neural substrates suggests that there might be features of these nervous systems that favoured the repeated evolution of particular behaviours. Neuromodulation may be one such feature because it allows anatomically defined neural circuitry to be re-purposed. The developmental, genetic and physiological mechanisms that contribute to nervous system complexity may also bias the evolution of behaviour, thereby affecting the evolvability of species-specific behaviour.

  19. Higher rates of sex evolve in spatially heterogeneous environments.

    PubMed

    Becks, Lutz; Agrawal, Aneil F

    2010-11-04

    The evolution and maintenance of sexual reproduction has puzzled biologists for decades. Although this field is rich in hypotheses, experimental evidence is scarce. Some important experiments have demonstrated differences in evolutionary rates between sexual and asexual populations; other experiments have documented evolutionary changes in phenomena related to genetic mixing, such as recombination and selfing. However, direct experiments of the evolution of sex within populations are extremely rare (but see ref. 12). Here we use the rotifer, Brachionus calyciflorus, which is capable of both sexual and asexual reproduction, to test recent theory predicting that there is more opportunity for sex to evolve in spatially heterogeneous environments. Replicated experimental populations of rotifers were maintained in homogeneous environments, composed of either high- or low-quality food habitats, or in heterogeneous environments that consisted of a mix of the two habitats. For populations maintained in either type of homogeneous environment, the rate of sex evolves rapidly towards zero. In contrast, higher rates of sex evolve in populations experiencing spatially heterogeneous environments. The data indicate that the higher level of sex observed under heterogeneity is not due to sex being less costly or selection against sex being less efficient; rather sex is sufficiently advantageous in heterogeneous environments to overwhelm its inherent costs. Counter to some alternative theories for the evolution of sex, there is no evidence that genetic drift plays any part in the evolution of sex in these populations.

  20. Biomimetic molecular design tools that learn, evolve, and adapt

    PubMed Central

    2017-01-01

    A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine. PMID:28694872

  1. Directed evolution to re-adapt a co-evolved network within an enzyme.

    PubMed

    Strafford, John; Payongsri, Panwajee; Hibbert, Edward G; Morris, Phattaraporn; Batth, Sukhjeet S; Steadman, David; Smith, Mark E B; Ward, John M; Hailes, Helen C; Dalby, Paul A

    2012-01-01

    We have previously used targeted active-site saturation mutagenesis to identify a number of transketolase single mutants that improved activity towards either glycolaldehyde (GA), or the non-natural substrate propionaldehyde (PA). Here, all attempts to recombine the singles into double mutants led to unexpected losses of specific activity towards both substrates. A typical trade-off occurred between soluble expression levels and specific activity for all single mutants, but many double mutants decreased both properties more severely suggesting a critical loss of protein stability or native folding. Statistical coupling analysis (SCA) of a large multiple sequence alignment revealed a network of nine co-evolved residues that affected all but one double mutant. Such networks maintain important functional properties such as activity, specificity, folding, stability, and solubility and may be rapidly disrupted by introducing one or more non-naturally occurring mutations. To identify variants of this network that would accept and improve upon our best D469 mutants for activity towards PA, we created a library of random single, double and triple mutants across seven of the co-evolved residues, combining our D469 variants with only naturally occurring mutations at the remaining sites. A triple mutant cluster at D469, E498 and R520 was found to behave synergistically for the specific activity towards PA. Protein expression was severely reduced by E498D and improved by R520Q, yet variants containing both mutations led to improved specific activity and enzyme expression, but with loss of solubility and the formation of inclusion bodies. D469S and R520Q combined synergistically to improve k(cat) 20-fold for PA, more than for any previous transketolase mutant. R520Q also doubled the specific activity of the previously identified D469T to create our most active transketolase mutant to date. Our results show that recombining active-site mutants obtained by saturation mutagenesis

  2. Thermal and Evolved-Gas Analyzer for Phoenix Mars Lander

    NASA Technical Reports Server (NTRS)

    2007-01-01

    NASA's Phoenix Mars Lander carries an instrument to heat and sniff samples of Martian soil and ice to analyze some ingredients.

    The Thermal and Evolved-Gas Analyzer will study substances that are converted to gases by heating samples delivered to this instrument by the lander's robotic arm. It provides two types of information. One of its tools, called a differential scanning calorimeter (on the left in this photograph) monitors how much power is required to increase the temperature of the sample at a constant rate. This reveals which temperatures are transition points from solid to liquid and from liquid to gas for ingredients in the sample. The gases that are released, or 'evolved' by this heating then go to a mass spectrometer (on the right), a tool that can identify the chemicals.

  3. Rapid evolution meets invasive species control: The potential for pesticide resistance in sea lamprey

    USGS Publications Warehouse

    Dunlop, Erin S.; McLaughlin, Robert L.; Adams, Jean V.; Jones, Michael L.; Birceanu, Oana; Christie, Mark R.; Criger, Lori A.; Hinderer, Julia L.M.; Hollingworth, Robert M.; Johnson, Nicholas; Lantz, Stephen R.; Li, Weiming; Miller, James R.; Morrison, Bruce J.; Mota-Sanchez, David; Muir, Andrew M.; Sepulveda, Maria S.; Steeves, Todd B.; Walter, Lisa; Westman, Erin; Wirgin, Isaac; Wilkie, Michael P.

    2017-01-01

    Rapid evolution of pest, pathogen and wildlife populations can have undesirable effects; for example, when insects evolve resistance to pesticides or fishes evolve smaller body size in response to harvest. A destructive invasive species in the Laurentian Great Lakes, the sea lamprey (Petromyzon marinus) has been controlled with the pesticide 3-trifluoromethyl-4-nitrophenol (TFM) since the 1950s. We evaluated the likelihood of sea lamprey evolving resistance to TFM by (1) reviewing sea lamprey life history and control; (2) identifying physiological and behavioural resistance strategies; (3) estimating the strength of selection from TFM; (4) assessing the timeline for evolution; and (5) analyzing historical toxicity data for evidence of resistance. The number of sea lamprey generations exposed to TFM was within the range observed for fish populations where rapid evolution has occurred. Mortality from TFM was estimated as 82-90%, suggesting significant selective pressure. However, 57 years of toxicity data revealed no increase in lethal concentrations of TFM. Vigilance and the development of alternative controls are required to prevent this aquatic invasive species from evolving strategies to evade control.

  4. Recent advances in evolvable systems--ICES 96 (International Conference on Evolvable Systems).

    PubMed

    Frank, I; Manderick, B; Higuchi, T

    1997-01-01

    This paper reviews the developments in evolvable hardware systems presented at the First International Conference on Evolvable Systems (ICES 96). The main body of the review gives an overview of the 34 papers presented orally, splitting them into three broad groups according to whether they involve (1) evolving a fit solution to a problem as a member of a population of competing candidates, (2) evolving solutions that can individually learn from and adapt to their environments, or (3) the embryonic growth of solutions. We also review the discussion sessions of the conference and give pointers to related upcoming events.

  5. Evolving networks in the human epileptic brain

    NASA Astrophysics Data System (ADS)

    Lehnertz, Klaus; Ansmann, Gerrit; Bialonski, Stephan; Dickten, Henning; Geier, Christian; Porz, Stephan

    2014-01-01

    Network theory provides novel concepts that promise an improved characterization of interacting dynamical systems. Within this framework, evolving networks can be considered as being composed of nodes, representing systems, and of time-varying edges, representing interactions between these systems. This approach is highly attractive to further our understanding of the physiological and pathophysiological dynamics in human brain networks. Indeed, there is growing evidence that the epileptic process can be regarded as a large-scale network phenomenon. We here review methodologies for inferring networks from empirical time series and for a characterization of these evolving networks. We summarize recent findings derived from studies that investigate human epileptic brain networks evolving on timescales ranging from few seconds to weeks. We point to possible pitfalls and open issues, and discuss future perspectives.

  6. Quantifying evolvability in small biological networks

    SciTech Connect

    Nemenman, Ilya; Mugler, Andrew; Ziv, Etay; Wiggins, Chris H

    2008-01-01

    The authors introduce a quantitative measure of the capacity of a small biological network to evolve. The measure is applied to a stochastic description of the experimental setup of Guet et al. (Science 2002, 296, pp. 1466), treating chemical inducers as functional inputs to biochemical networks and the expression of a reporter gene as the functional output. The authors take an information-theoretic approach, allowing the system to set parameters that optimise signal processing ability, thus enumerating each network's highest-fidelity functions. All networks studied are highly evolvable by the measure, meaning that change in function has little dependence on change in parameters. Moreover, each network's functions are connected by paths in the parameter space along which information is not significantly lowered, meaning a network may continuously change its functionality without completely losing it along the way. This property further underscores the evolvability of the networks.

  7. Metanetworks of artificially evolved regulatory networks

    NASA Astrophysics Data System (ADS)

    Danacı, Burçin; Erzan, Ayşe

    2016-04-01

    We study metanetworks arising in genotype and phenotype spaces, in the context of a model population of Boolean graphs evolved under selection for short dynamical attractors. We define the adjacency matrix of a graph as its genotype, which gets mutated in the course of evolution, while its phenotype is its set of dynamical attractors. Metanetworks in the genotype and phenotype spaces are formed, respectively, by genetic proximity and by phenotypic similarity, the latter weighted by the sizes of the basins of attraction of the shared attractors. We find that evolved populations of Boolean graphs form tree-like giant clusters in genotype space, while random populations of Boolean graphs are typically so far removed from each other genetically that they cannot form a metanetwork. In phenotype space, the metanetworks of evolved populations are super robust both under the elimination of weak connections and random removal of nodes.

  8. JavaGenes: Evolving Graphs with Crossover

    NASA Technical Reports Server (NTRS)

    Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

    2000-01-01

    Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

  9. THE DECELERATION OF NEBULAR SHELLS IN EVOLVED PLANETARY NEBULAE

    SciTech Connect

    Pereyra, Margarita; Richer, Michael G.; Lopez, Jose Alberto E-mail: richer@astrosen.unam.mx

    2013-07-10

    We have selected a group of 100 evolved planetary nebulae (PNe) and study their kinematics based upon spatially-resolved, long-slit, echelle spectroscopy. The data have been drawn from the San Pedro Martir Kinematic Catalogue of PNe. The aim is to characterize in detail the global kinematics of PNe at advanced stages of evolution with the largest sample of homogenous data used to date for this purpose. The results reveal two groups that share kinematics, morphology, and photo-ionization characteristics of the nebular shell and central star luminosities at the different late stages under study. The typical flow velocities we measure are usually larger than seen in earlier evolutionary stages, with the largest velocities occurring in objects with very weak or absent [N II] {lambda}6584 line emission, by all indications the least evolved objects in our sample. The most evolved objects expand more slowly. This apparent deceleration during the final stage of PNe evolution is predicted by hydrodynamical models, but other explanations are also possible. These results provide a template for comparison with the predictions of theoretical models.

  10. Idiopathic Facial Aseptic Granuloma: Review of an Evolving Clinical Entity.

    PubMed

    Zitelli, Kristine B; Sheil, Amy T; Fleck, Robert; Schwentker, Ann; Lucky, Anne W

    2015-01-01

    Idiopathic facial aseptic granuloma (IFAG), originally termed pyodermite froide du visage, describes a generally asymptomatic facial nodule presenting in childhood with clinical resemblance to pyoderma or cystic, granulomatous, or vascular lesions. Clinical understanding is constantly evolving, with recent observations indicating that IFAG may represent a subtype of childhood rosacea. We present a case of IFAG associated with eyelid chalazions in a 19-month-old boy. Although his clinical course paralleled previously reported IFAG cases, we observed a unique ultrasound variation during initial diagnostic examination. Further delineation of clinical, imaging, and histologic properties of IFAG may reveal insights into etiologic associations and ideal management.

  11. A Stefan problem on an evolving surface

    PubMed Central

    Alphonse, Amal; Elliott, Charles M.

    2015-01-01

    We formulate a Stefan problem on an evolving hypersurface and study the well posedness of weak solutions given L1 data. To do this, we first develop function spaces and results to handle equations on evolving surfaces in order to give a natural treatment of the problem. Then, we consider the existence of solutions for data; this is done by regularization of the nonlinearity. The regularized problem is solved by a fixed point theorem and then uniform estimates are obtained in order to pass to the limit. By using a duality method, we show continuous dependence, which allows us to extend the results to L1 data. PMID:26261364

  12. How the first biopolymers could have evolved.

    PubMed Central

    Abkevich, V I; Gutin, A M; Shakhnovich, E I

    1996-01-01

    In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution. PMID:8570645

  13. Surveying The Digital Landscape: Evolving Technologies 2004. The EDUCAUSE Evolving Technologies Committee

    ERIC Educational Resources Information Center

    EDUCAUSE Review, 2004

    2004-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual conference. This year, under the…

  14. Surveying The Digital Landscape: Evolving Technologies 2004. The EDUCAUSE Evolving Technologies Committee

    ERIC Educational Resources Information Center

    EDUCAUSE Review, 2004

    2004-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual conference. This year, under the…

  15. Rapid Prototyping

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Javelin, a Lone Peak Engineering Inc. Company has introduced the SteamRoller(TM) System as a commercial product. The system was designed by Javelin during a Phase II NASA funded small commercial product. The purpose of the invention was to allow automated-feed of flexible ceramic tapes to the Laminated Object Manufacturing rapid prototyping equipment. The ceramic material that Javelin was working with during the Phase II project is silicon nitride. This engineered ceramic material is of interest for space-based component.

  16. Toward an Evolved Concept of Landrace

    PubMed Central

    Casañas, Francesc; Simó, Joan; Casals, Joan; Prohens, Jaime

    2017-01-01

    The term “landrace” has generally been defined as a cultivated, genetically heterogeneous variety that has evolved in a certain ecogeographical area and is therefore adapted to the edaphic and climatic conditions and to its traditional management and uses. Despite being considered by many to be inalterable, landraces have been and are in a constant state of evolution as a result of natural and artificial selection. Many landraces have disappeared from cultivation but are preserved in gene banks. Using modern selection and breeding technology tools to shape these preserved landraces together with the ones that are still cultivated is a further step in their evolution in order to preserve their agricultural significance. Adapting historical landraces to present agricultural conditions using cutting-edge breeding technology represents a challenging opportunity to use them in a modern sustainable agriculture, as an immediate return on the investment is highly unlikely. Consequently, we propose a more inclusive definition of landraces, namely that they consist of cultivated varieties that have evolved and may continue evolving, using conventional or modern breeding techniques, in traditional or new agricultural environments within a defined ecogeographical area and under the influence of the local human culture. This includes adaptation of landraces to new management systems and the unconscious or conscious selection made by farmers or breeders using available technology. In this respect, a mixed selection system might be established in which farmers and other social agents develop evolved landraces from the variability generated by public entities. PMID:28228769

  17. Apollo 16 Evolved Lithology Sodic Ferrogabbro

    NASA Technical Reports Server (NTRS)

    Zeigler, Ryan; Jolliff, B. L.; Korotev, R. L.

    2014-01-01

    Evolved lunar igneous lithologies, often referred to as the alkali suite, are a minor but important component of the lunar crust. These evolved samples are incompatible-element rich samples, and are, not surprisingly, most common in the Apollo sites in (or near) the incompatible-element rich region of the Moon known as the Procellarum KREEP Terrane (PKT). The most commonly occurring lithologies are granites (A12, A14, A15, A17), monzogabbro (A14, A15), alkali anorthosites (A12, A14), and KREEP basalts (A15, A17). The Feldspathic Highlands Terrane is not entirely devoid of evolved lithologies, and rare clasts of alkali gabbronorite and sodic ferrogabbro (SFG) have been identified in Apollo 16 station 11 breccias 67915 and 67016. Curiously, nearly all pristine evolved lithologies have been found as small clasts or soil particles, exceptions being KREEP basalts 15382/6 and granitic sample 12013 (which is itself a breccia). Here we reexamine the petrography and geochemistry of two SFG-like particles found in a survey of Apollo 16 2-4 mm particles from the Cayley Plains 62283,7-15 and 62243,10-3 (hereafter 7-15 and 10-3 respectively). We will compare these to previously reported SFG samples, including recent analyses on the type specimen of SFG from lunar breccia 67915.

  18. Did Language Evolve Like the Vertebrate Eye?

    ERIC Educational Resources Information Center

    Botha, Rudolf P.

    2002-01-01

    Offers a critical appraisal of the way in which the idea that human language or some of its features evolved like the vertebrate eye by natural selection is articulated in Pinker and Bloom's (1990) selectionist account of language evolution. Argues that this account is less than insightful because it fails to draw some of the conceptual…

  19. The Evolving Leadership Path of Visual Analytics

    SciTech Connect

    Kluse, Michael; Peurrung, Anthony J.; Gracio, Deborah K.

    2012-01-02

    This is a requested book chapter for an internationally authored book on visual analytics and related fields, coordianted by a UK university and to be published by Springer in 2012. This chapter is an overview of the leadship strategies that PNNL's Jim Thomas and other stakeholders used to establish visual analytics as a field, and how those strategies may evolve in the future.

  20. Evolving Neural Networks for Nonlinear Control.

    DTIC Science & Technology

    1996-09-30

    An approach to creating Amorphous Recurrent Neural Networks (ARNN) using Genetic Algorithms (GA) called 2pGA has been developed and shown to be...effective in evolving neural networks for the control and stabilization of both linear and nonlinear plants, the optimal control for a nonlinear regulator

  1. Toward an Evolved Concept of Landrace.

    PubMed

    Casañas, Francesc; Simó, Joan; Casals, Joan; Prohens, Jaime

    2017-01-01

    The term "landrace" has generally been defined as a cultivated, genetically heterogeneous variety that has evolved in a certain ecogeographical area and is therefore adapted to the edaphic and climatic conditions and to its traditional management and uses. Despite being considered by many to be inalterable, landraces have been and are in a constant state of evolution as a result of natural and artificial selection. Many landraces have disappeared from cultivation but are preserved in gene banks. Using modern selection and breeding technology tools to shape these preserved landraces together with the ones that are still cultivated is a further step in their evolution in order to preserve their agricultural significance. Adapting historical landraces to present agricultural conditions using cutting-edge breeding technology represents a challenging opportunity to use them in a modern sustainable agriculture, as an immediate return on the investment is highly unlikely. Consequently, we propose a more inclusive definition of landraces, namely that they consist of cultivated varieties that have evolved and may continue evolving, using conventional or modern breeding techniques, in traditional or new agricultural environments within a defined ecogeographical area and under the influence of the local human culture. This includes adaptation of landraces to new management systems and the unconscious or conscious selection made by farmers or breeders using available technology. In this respect, a mixed selection system might be established in which farmers and other social agents develop evolved landraces from the variability generated by public entities.

  2. Did Language Evolve Like the Vertebrate Eye?

    ERIC Educational Resources Information Center

    Botha, Rudolf P.

    2002-01-01

    Offers a critical appraisal of the way in which the idea that human language or some of its features evolved like the vertebrate eye by natural selection is articulated in Pinker and Bloom's (1990) selectionist account of language evolution. Argues that this account is less than insightful because it fails to draw some of the conceptual…

  3. Thermal and Evolved-Gas Analyzer Illustration

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This is a computer-aided drawing of the Thermal and Evolved-Gas Analyzer, or TEGA, on NASA's Phoenix Mars Lander.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  4. The Evolving Office of the Registrar

    ERIC Educational Resources Information Center

    Pace, Harold L.

    2011-01-01

    A healthy registrar's office will continue to evolve as it considers student, faculty, and institutional needs; staff talents and expectations; technological opportunities; economic realities; space issues; work environments; and where the strategic plan is taking the institution in support of the mission. Several recognized leaders in the field…

  5. A Course Evolves-Physical Anthropology.

    ERIC Educational Resources Information Center

    O'Neil, Dennis

    2001-01-01

    Describes the development of an online physical anthropology course at Palomar College (California) that evolved from online tutorials. Discusses the ability to update materials on the Web more quickly than in traditional textbooks; creating Web pages that are readable by most Web browsers; test security issues; and clarifying ownership of online…

  6. Apology and forgiveness evolve to resolve failures in cooperative agreements.

    PubMed

    Martinez-Vaquero, Luis A; Han, The Anh; Pereira, Luís Moniz; Lenaerts, Tom

    2015-06-09

    Making agreements on how to behave has been shown to be an evolutionarily viable strategy in one-shot social dilemmas. However, in many situations agreements aim to establish long-term mutually beneficial interactions. Our analytical and numerical results reveal for the first time under which conditions revenge, apology and forgiveness can evolve and deal with mistakes within ongoing agreements in the context of the Iterated Prisoners Dilemma. We show that, when the agreement fails, participants prefer to take revenge by defecting in the subsisting encounters. Incorporating costly apology and forgiveness reveals that, even when mistakes are frequent, there exists a sincerity threshold for which mistakes will not lead to the destruction of the agreement, inducing even higher levels of cooperation. In short, even when to err is human, revenge, apology and forgiveness are evolutionarily viable strategies which play an important role in inducing cooperation in repeated dilemmas.

  7. Apology and forgiveness evolve to resolve failures in cooperative agreements

    PubMed Central

    Martinez-Vaquero, Luis A.; Han, The Anh; Pereira, Luís Moniz; Lenaerts, Tom

    2015-01-01

    Making agreements on how to behave has been shown to be an evolutionarily viable strategy in one-shot social dilemmas. However, in many situations agreements aim to establish long-term mutually beneficial interactions. Our analytical and numerical results reveal for the first time under which conditions revenge, apology and forgiveness can evolve and deal with mistakes within ongoing agreements in the context of the Iterated Prisoners Dilemma. We show that, when the agreement fails, participants prefer to take revenge by defecting in the subsisting encounters. Incorporating costly apology and forgiveness reveals that, even when mistakes are frequent, there exists a sincerity threshold for which mistakes will not lead to the destruction of the agreement, inducing even higher levels of cooperation. In short, even when to err is human, revenge, apology and forgiveness are evolutionarily viable strategies which play an important role in inducing cooperation in repeated dilemmas. PMID:26057819

  8. A More Rapid, Rapid Response.

    PubMed

    Robison, Justin; Slamon, Nicholas B

    2016-09-01

    Critical care physicians' standard for arrival to a rapid response team activation is 10 minutes or less at this institution. This study proposes that a FaceTime (Apple, Cupertino, CA) video call between the staff at the bedside and the critical care physician will allow the implementation of potentially life-saving therapies earlier than the current average response (4.5 min). Prospective cohort study. Freestanding, tertiary-care children's hospital. Pediatric patients ages 0-17. Six units were chosen as matched pairs. In the telemedicine units, after notification of an rapid response team, the critical care intensivist established a FaceTime video call with the nurse at the bedside and gathered history, visually assessed the patient, and suggested interventions. Simultaneously, the rapid response nurse, respiratory therapist, and fellow were dispatched to respond to the bedside. After the video call, the intensivist also reported to the bedside. The control units followed the standard rapid response team protocol: the intensivist physically responded to the bedside. Differences in response time, number of interventions, Pediatric Early Warning System scores, and disposition were measured, and the PICU course of those transferred was evaluated. The telemedicine group's average time to establish FaceTime interface was 2.6 minutes and arrival at bedside was 3.7 minutes. The control group average arrival time was 3.6 minutes. The difference between FaceTime interface and physical arrival in the control group was statistically significant (p = 0.012). Physical arrival times between the telemedicine and control groups remained consistent. Fifty-eight percent of the telemedicine patients and 73% of the control patients were admitted to the PICU (p = 0.13). Of patients transferred to the PICU, there was no difference in rate of intubation, initiation of bilevel positive airway pressure, central line placement, or vasopressors. The study group averaged 1.4 interventions

  9. Why, when, and how did yeast evolve alcoholic fermentation?

    PubMed

    Dashko, Sofia; Zhou, Nerve; Compagno, Concetta; Piškur, Jure

    2014-09-01

    The origin of modern fruits brought to microbial communities an abundant source of rich food based on simple sugars. Yeasts, especially Saccharomyces cerevisiae, usually become the predominant group in these niches. One of the most prominent and unique features and likely a winning trait of these yeasts is their ability to rapidly convert sugars to ethanol at both anaerobic and aerobic conditions. Why, when, and how did yeasts remodel their carbon metabolism to be able to accumulate ethanol under aerobic conditions and at the expense of decreasing biomass production? We hereby review the recent data on the carbon metabolism in Saccharomycetaceae species and attempt to reconstruct the ancient environment, which could promote the evolution of alcoholic fermentation. We speculate that the first step toward the so-called fermentative lifestyle was the exploration of anaerobic niches resulting in an increased metabolic capacity to degrade sugar to ethanol. The strengthened glycolytic flow had in parallel a beneficial effect on the microbial competition outcome and later evolved as a "new" tool promoting the yeast competition ability under aerobic conditions. The basic aerobic alcoholic fermentation ability was subsequently "upgraded" in several lineages by evolving additional regulatory steps, such as glucose repression in the S. cerevisiae clade, to achieve a more precise metabolic control.

  10. Evolving technologies drive the new roles of Biomedical Engineering.

    PubMed

    Frisch, P H; St Germain, J; Lui, W

    2008-01-01

    Rapidly changing technology coupled with the financial impact of organized health care, has required hospital Biomedical Engineering organizations to augment their traditional operational and business models to increase their role in developing enhanced clinical applications utilizing new and evolving technologies. The deployment of these technology based applications has required Biomedical Engineering organizations to re-organize to optimize the manner in which they provide and manage services. Memorial Sloan-Kettering Cancer Center has implemented a strategy to explore evolving technologies integrating them into enhanced clinical applications while optimally utilizing the expertise of the traditional Biomedical Engineering component (Clinical Engineering) to provide expanded support in technology / equipment management, device repair, preventive maintenance and integration with legacy clinical systems. Specifically, Biomedical Engineering is an integral component of the Medical Physics Department which provides comprehensive and integrated support to the Center in advanced physical, technical and engineering technology. This organizational structure emphasizes the integration and collaboration between a spectrum of technical expertise for clinical support and equipment management roles. The high cost of clinical equipment purchases coupled with the increasing cost of service has driven equipment management responsibilities to include significant business and financial aspects to provide a cost effective service model. This case study details the dynamics of these expanded roles, future initiatives and benefits for Biomedical Engineering and Memorial Sloan Kettering Cancer Center.

  11. Nuclear transit study in children with chronic faecal soiling after Hirschsprung disease (HSCR) surgery has revealed a group with rapid proximal colonic treatment and possible adverse reactions to food.

    PubMed

    Stathopoulos, Lefteris; King, Sebastian K; Southwell, Bridget R; Hutson, John M

    2016-08-01

    Long-term problems with faecal incontinence occur in up to 50 % of patients after pull-through for Hirschsprung disease (HSCR). The cause often remains unknown, leading to empirical treatments. Using nuclear transit study, we found some patients surprisingly had rapid proximal colonic transit, suspicious of occult diarrhoea. We aimed to assess whether these patients had unrecognized adverse reactions to food. Patients (n = 10, all males, 9.6 year; 4.25-15.5 years) with persistent faecal incontinence following pull-through for HSCR referred to the senior author and after exclusion of anatomical defects, underwent nuclear transit studies. Most (8) subsequently underwent breath hydrogen tests for sugar malabsorption and were tested for adverse reactions to food. Exclusion diets for protein allergens, lactose or fructose were then trialed. Of the 10 patients with rapid intestinal transit proven on nuclear transit study, breath hydrogen tests for fructose and/or lactose malabsorption were done in 8, and were positive in 7/8 patients. Exclusion diets contributed to either resolution or improvement in faecal incontinence in 9/10 patients. Rapid transit in the proximal, ganglionated colon may be present in children with faecal incontinence following pull-through for HSCR, possibly secondary to adverse reactions to food. This study suggests that children with post-operative soiling may benefit from a transit study and hydrogen breath tests to diagnose adverse reactions to food caused by sugar malabsorption.

  12. Sixteen Years of Bt Maize in the EU Hotspot: Why Has Resistance Not Evolved?

    PubMed Central

    Castañera, Pedro; Farinós, Gema P.; Ortego, Félix; Andow, David A.

    2016-01-01

    The majority of Bt maize production in the European Union (EU) is concentrated in northeast Spain, which is Europe’s only hotspot where resistance might evolve, and the main target pest, Sesamia nonagrioides, has been exposed to Cry1Ab maize continuously since 1998. The cropping system in northeast Spain has some similar characteristics to those that probably led to rapid resistance failures in two other target noctuid maize pests. These include repeated cultivation of Bt maize in the same fields, low use of refuges, recurring exposure of larvae to non-high dose concentrations of Cry1Ab toxin during the first years of cultivation, low migratory potential, and production concentrated in an irrigated region with few alternative hosts. Available data reveal no evidence of resistance in S. nonagrioides after 16 years of use. We explore the possible reasons for this resistance management success using evolutionary models to consider factors expected to accelerate resistance, and those expected to delay resistance. Low initial adoption rates and the EU policy decision to replace Event 176 with MON 810 Bt maize were key to delaying resistance evolution. Model results suggest that if refuge compliance continues at the present 90%, Bt maize might be used sustainably in northeast Spain for at least 20 more years before resistance might occur. However, obtaining good estimates of the present R allele frequency and level of local assortative mating are crucial to reduce uncertainty about the future success of resistance management. PMID:27144535

  13. Flow, Morphology and Sedimentology of an Evolving Chute Cutoff on the Wabash River, IL-in.

    NASA Astrophysics Data System (ADS)

    Zinger, J. A.; Best, J.; Rhoads, B. L.; Larson, T. H.

    2014-12-01

    The development of chute cutoffs and the resulting abandonment of meander bends have a substantial influence on the sedimentary dynamics of floodplains. The incision of a chute cutoff channel can rapidly mobilize a large volume of floodplain sediment. On the other hand, bar formation during bend abandonment and the subsequent deposition of sediment within the oxbow lake are key processes in the production of a heterogeneous floodplain sedimentary architecture. This paper describes the evolution of two recent chute cutoffs on the Wabash River, IL-IN. We follow these cutoffs from their initial incision in 2008-2009 through the early stages of bend abandonment. The volume of floodplain sediment mobilized by erosion of the two cutoff channels is estimated using channel bankline positions determined from RTK-GPS surveys and aerial orthophotographs; this flux is then assessed within the context of the sediment mobilized by lateral migration of bends. Repeat bathymetric surveys and aerial photography capture the evolution of bar forms associated with the chute cutoff, and data from ground-penetrating radar reveal the subsurface structure of the complex assemblage of bars that developed as the chute cutoff system shifted from a predominantly erosional to a mixed depositional-erosional phase. These results are combined with knowledge of chute cutoff hydrodynamics to develop an understanding of the dynamics of sediment exchange between river channels and floodplains at evolving meander bend cutoffs.

  14. Sixteen Years of Bt Maize in the EU Hotspot: Why Has Resistance Not Evolved?

    PubMed

    Castañera, Pedro; Farinós, Gema P; Ortego, Félix; Andow, David A

    2016-01-01

    The majority of Bt maize production in the European Union (EU) is concentrated in northeast Spain, which is Europe's only hotspot where resistance might evolve, and the main target pest, Sesamia nonagrioides, has been exposed to Cry1Ab maize continuously since 1998. The cropping system in northeast Spain has some similar characteristics to those that probably led to rapid resistance failures in two other target noctuid maize pests. These include repeated cultivation of Bt maize in the same fields, low use of refuges, recurring exposure of larvae to non-high dose concentrations of Cry1Ab toxin during the first years of cultivation, low migratory potential, and production concentrated in an irrigated region with few alternative hosts. Available data reveal no evidence of resistance in S. nonagrioides after 16 years of use. We explore the possible reasons for this resistance management success using evolutionary models to consider factors expected to accelerate resistance, and those expected to delay resistance. Low initial adoption rates and the EU policy decision to replace Event 176 with MON 810 Bt maize were key to delaying resistance evolution. Model results suggest that if refuge compliance continues at the present 90%, Bt maize might be used sustainably in northeast Spain for at least 20 more years before resistance might occur. However, obtaining good estimates of the present R allele frequency and level of local assortative mating are crucial to reduce uncertainty about the future success of resistance management.

  15. Evolving treatment plan quality criteria from institution-specific experience.

    PubMed

    Ruan, D; Shao, W; Demarco, J; Tenn, S; King, C; Low, D; Kupelian, P; Steinberg, M

    2012-05-01

    The dosimetric aspects of radiation therapy treatment plan quality are usually evaluated and reported with dose volume histogram (DVH) endpoints. For clinical practicality, a small number of representative quantities derived from the DVH are often used as dose endpoints to summarize the plan quality. National guidelines on reference values for such quantities for some standard treatment approaches are often used as acceptance criteria to trigger treatment plan review. On the other hand, treatment prescription and planning approaches specific to each institution warrants the need to report plan quality in terms of practice consistency and with respect to institution-specific experience. The purpose of this study is to investigate and develop a systematic approach to record and characterize the institution-specific plan experience and use such information to guide the design of plan quality criteria. In the clinical setting, this approach will assist in (1) improving overall plan quality and consistency and (2) detecting abnormal plan behavior for retrospective analysis. The authors propose a self-evolving methodology and have developed an in-house prototype software suite that (1) extracts the dose endpoints from a treatment plan and evaluates them against both national standard and institution-specific criteria and (2) evolves the statistics for the dose endpoints and updates institution-specific criteria. The validity of the proposed methodology was demonstrated with a database of prostate stereotactic body radiotherapy cases. As more data sets are accumulated, the evolving institution-specific criteria can serve as a reliable and stable consistency measure for plan quality and reveals the potential use of the "tighter" criteria than national standards or projected criteria, leading to practice that may push to shrink the gap between plans deemed acceptable and the underlying unknown optimality. The authors have developed a rationale to improve plan quality and

  16. Dust obscuration by an evolving galaxy population

    NASA Technical Reports Server (NTRS)

    Najita, Joan; Silk, Joseph; Wachter, Kenneth W.

    1990-01-01

    The effect of an evolving luminosity function (LF) on the ability of foreground galaxies to obscure background sources is discussed, using the Press-Schechter/CDM standard evolving LF model. Galaxies are modeled as simplified versions of local spirals and Poisson statistics are used to estimate the fraction of sky covered by intervening dusty galaxies and the mean optical depths due to these galaxies. The results are compared to those obtained in the case of nonevolving luminosity function in a low-density universe. It is found that evolution of the galaxy LF does not allow the quasar dust obscuration hypothesis to be sustained for dust disks with plausible sizes. Even in a low-density universe, where evolution at z = less than 10 is unimportant, large disk radii are needed to achieve the desired obscuring effect. The mean fraction of sky covered is presented as a function of the redshift z along with adequate diagram illustrations.

  17. The management of evolving bronchopulmonary dysplasia.

    PubMed

    Schulzke, Sven M; Pillow, J Jane

    2010-09-01

    Bronchopulmonary dysplasia (BPD) is associated with increased mortality and significant long-term cardiorespiratory and neurodevelopmental sequelae. Treatment of evolving BPD in the neonatal intensive care unit (NICU) is challenging due to the complex interplay of contributing risk factors which include preterm birth per se, supplemental oxygen, positive pressure ventilation, patent ductus arterious, and pre- and postnatal infection. Management of evolving BPD requires a multimodal approach including adequate nutrition, careful fluid management, effective and safe pharmacotherapy, and respiratory support aiming at minimal lung injury. Among pharmacological interventions, caffeine has the best risk-benefit profile. Systemic postnatal corticosteroids should be reserved to ventilated infants at highest risk of BPD who cannot be weaned from the ventilator. Several ongoing randomised trials are evaluating optimal oxygen saturation targets in preterm infants. The most beneficial respiratory support strategy to minimise lung injury remains unclear and requires further investigation. Copyright 2009 Elsevier Ltd. All rights reserved.

  18. Evolved gas analysis of secondary organic aerosols

    SciTech Connect

    Grosjean, D.; Williams, E.L. II; Grosjean, E. ); Novakov, T. )

    1994-11-01

    Secondary organic aerosols have been characterized by evolved gas analysis (EGA). Hydrocarbons selected as aerosol precursors were representative of anthropogenic emissions (cyclohexene, cyclopentene, 1-decene and 1-dodecene, n-dodecane, o-xylene, and 1,3,5-trimethylbenzene) and of biogenic emissions (the terpenes [alpha]-pinene, [beta]-pinene and d-limonene and the sesquiterpene trans-caryophyllene). Also analyzed by EGA were samples of secondary, primary (highway tunnel), and ambient (urban) aerosols before and after exposure to ozone and other photochemical oxidants. The major features of the EGA thermograms (amount of CO[sub 2] evolved as a function of temperature) are described. The usefulness and limitations of EGA data for source apportionment of atmospheric particulate carbon are briefly discussed. 28 refs., 7 figs., 4 tabs.

  19. [Families and psychiatry: models and evolving links].

    PubMed

    Frankhauser, Adeline

    2016-01-01

    The role of the families of persons with severe psychiatric disorders (schizophrenia in particular) in the care of their relatives has recently evolved: once seen as pathogenic to be kept at a distance, the family is now recognised by professionals as a partner in the care process. The links between families and psychiatric institutions remain complex and marked by ambivalence and paradoxes. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  20. Design Space Issues for Intrinsic Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    Hereford, James; Gwaltney, David

    2004-01-01

    This paper discusses the problem of increased programming time for intrinsic evolvable hardware (EM) as the complexity of the circuit grows. As the circuit becomes more complex, then more components will be required and a longer programming string, L, is required. We develop equations for the size of the population, n, and the number of generations required for the population to converge, based on L. Our analytical results show that even though the design search space grows as 2L (assuming a binary programming string), the number of circuit evaluations, n*ngen, only grows as O(Lg3), or slightly less than O(L). This makes evolvable techniques a good tool for exploring large design spaces. The major hurdle for intrinsic EHW is evaluation time for each possible circuit. The evaluation time involves downloading the bit string to the device, updating the device configuration, measuring the output and then transferring the output data to the control processor. Each of these steps must be done for each member of the population. The processing time of the computer becomes negligible since the selection/crossover/mutation steps are only done once per generation. Evaluation time presently limits intrinsic evolvable hardware techniques to designing only small or medium-sized circuits. To evolve large or complicated circuits, several researchers have proposed using hierarchical design or reuse techniques where submodules are combined together to form complex circuits. However, these practical approaches limit the search space of available designs and preclude utilizing parasitic coupling or other effects within the programmable device. The practical approaches also raise the issue of why intrinsic EHW techniques do not easily apply to large design spaces, since the analytical results show only an O(L) complexity growth.

  1. The evolving definition of systemic arterial hypertension.

    PubMed

    Ram, C Venkata S; Giles, Thomas D

    2010-05-01

    Systemic hypertension is an important risk factor for premature cardiovascular disease. Hypertension also contributes to excessive morbidity and mortality. Whereas excellent therapeutic options are available to treat hypertension, there is an unsettled issue about the very definition of hypertension. At what level of blood pressure should we treat hypertension? Does the definition of hypertension change in the presence of co-morbid conditions? This article covers in detail the evolving concepts in the diagnosis and management of hypertension.

  2. Quantum games on evolving random networks

    NASA Astrophysics Data System (ADS)

    Pawela, Łukasz

    2016-09-01

    We study the advantages of quantum strategies in evolutionary social dilemmas on evolving random networks. We focus our study on the two-player games: prisoner's dilemma, snowdrift and stag-hunt games. The obtained result show the benefits of quantum strategies for the prisoner's dilemma game. For the other two games, we obtain regions of parameters where the quantum strategies dominate, as well as regions where the classical strategies coexist.

  3. Nursing administration research: an evolving science.

    PubMed

    Murphy, Lyn Stankiewicz; Scott, Elaine S; Warshawsky, Nora E

    2014-12-01

    The nature and focus of nursing administrative research have evolved over time. Recently, the research agenda has primarily reflected the national health policy agenda. Although nursing research has traditionally been dominated by clinical interests, nursing administrative research has historically addressed the interface of reimbursement, quality, and care delivery systems. This article traces the evolution of nursing administrative research to answer questions relevant to scope, practice, and policy and suggests future directions.

  4. Evolving specialization of the arthropod nervous system.

    PubMed

    Jarvis, Erin; Bruce, Heather S; Patel, Nipam H

    2012-06-26

    The diverse array of body plans possessed by arthropods is created by generating variations upon a design of repeated segments formed during development, using a relatively small "toolbox" of conserved patterning genes. These attributes make the arthropod body plan a valuable model for elucidating how changes in development create diversity of form. As increasingly specialized segments and appendages evolved in arthropods, the nervous systems of these animals also evolved to control the function of these structures. Although there is a remarkable degree of conservation in neural development both between individual segments in any given species and between the nervous systems of different arthropod groups, the differences that do exist are informative for inferring general principles about the holistic evolution of body plans. This review describes developmental processes controlling neural segmentation and regionalization, highlighting segmentation mechanisms that create both ectodermal and neural segments, as well as recent studies of the role of Hox genes in generating regional specification within the central nervous system. We argue that this system generates a modular design that allows the nervous system to evolve in concert with the body segments and their associated appendages. This information will be useful in future studies of macroevolutionary changes in arthropod body plans, especially in understanding how these transformations can be made in a way that retains the function of appendages during evolutionary transitions in morphology.

  5. Rapid outer pore movements after opening in a KV1 potassium channel are revealed by TMRM fluorescence from the S3-S4 linker, and modulated by extracellular potassium.

    PubMed

    Vaid, Moninder; Horne, Andrew; Claydon, Thomas; Fedida, David

    2009-01-01

    Fluorescence-based approaches provide powerful techniques to directly report structural dynamics underlying gating processes in Shaker KV channels. Here, following on from work carried out in Shaker channels, we have used voltage clamp fluorimetry for the first time to study voltage sensor motions in mammalian KV1.5 channels, by attaching TMRM fluorescent probes to substituted cysteine residues in the S3-S4 linker of KV1.5 (A397C). Compared with the Shaker channel, there are significant differences in the fluorescence signals that occur on activation of the channel. In addition to a well-understood fluorescence quenching signal associated with S4 movement, we have recorded a unique partial recovery of fluorescence after the quenching that is attributable to gating events at the outer pore mouth, that is not seen in Shaker despite significant homology between it and KV1.5 channels in the S5-P loop-S6 region. Extracellular potassium is known to modulate C-type inactivation in Shaker and KV channels at sites in the outer pore mouth, and so here we have measured the concentration-dependence of potassium effects on the fluorescence recovery signals from A397C. Elevation of extracellular K+ inhibits the rapid fluorescence recovery, with complete abolition at 99 mM K+, and an IC50 of 29 mM K+o. These experiments suggest that the rapid fluorescence recovery reflects early gating movements associated with inactivation, modulated by extracellular K+, and further support the idea that outer pore motions occur rapidly after KV1.5 channel opening and can be observed by fluorophores attached to the S3-S4 linker.

  6. eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.

    PubMed

    Brylinski, Michal

    2013-07-31

    Many structural bioinformatics approaches employ sequence profile-based threading techniques. To improve fold recognition rates, homology searching may include artificially evolved amino acid sequences, which were demonstrated to enhance the sensitivity of protein threading in targeting midnight zone templates. We describe implementation details of eVolver, an optimization algorithm that evolves protein sequences to stabilize the respective structures by a variety of potentials, which are compatible with those commonly used in protein threading. In a case study focusing on LARG PDZ domain, we show that artificially evolved sequences have quite high capabilities to recognize the correct protein structures using standard sequence profile-based fold recognition. Computationally design protein sequences can be incorporated in existing sequence profile-based threading approaches to increase their sensitivity. They also provide a desired linkage between protein structure and function in in silico experiments that relate to e.g. the completeness of protein structure space, the origin of folds and protein universe. eVolver is freely available as a user-friendly webserver and a well-documented stand-alone software distribution at http://www.brylinski.org/evolver.

  7. Escape from bacterial iron piracy through rapid evolution of transferrin

    PubMed Central

    Barber, Matthew F.; Elde, Nels C.

    2015-01-01

    Iron sequestration provides an innate defense termed nutritional immunity, leading pathogens to scavenge iron from hosts. Although the molecular basis of this battle for iron is established, its potential as a force for evolution at host-pathogen interfaces is unknown. We show that the iron transport protein transferrin is engaged in ancient and ongoing evolutionary conflicts with TbpA, a transferrin surface receptor from bacteria. Single substitutions in transferrin at rapidly evolving sites reverse TbpA binding, providing a mechanism to counteract bacterial iron piracy among great apes. Furthermore, the C2 transferrin polymorphism in humans evades TbpA variants from Haemophilus influenzae, revealing a functional basis for standing genetic variation. These findings identify a central role for nutritional immunity in the persistent evolutionary conflicts between primates and bacterial pathogens. PMID:25504720

  8. Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection.

    PubMed

    Janković, Srdja; Ćirković, Milan M

    2016-03-01

    Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.

  9. Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection

    NASA Astrophysics Data System (ADS)

    Janković, Srdja; Ćirković, Milan M.

    2016-03-01

    Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.

  10. Production and decay of evolving horizons

    NASA Astrophysics Data System (ADS)

    Nielsen, Alex B.; Visser, Matt

    2006-07-01

    We consider a simple physical model for an evolving horizon that is strongly interacting with its environment, exchanging arbitrarily large quantities of matter with its environment in the form of both infalling material and outgoing Hawking radiation. We permit fluxes of both lightlike and timelike particles to cross the horizon, and ask how the horizon grows and shrinks in response to such flows. We place a premium on providing a clear and straightforward exposition with simple formulae. To be able to handle such a highly dynamical situation in a simple manner we make one significant physical restriction—that of spherical symmetry—and two technical mathematical restrictions: (1) we choose to slice the spacetime in such a way that the spacetime foliations (and hence the horizons) are always spherically symmetric. (2) Furthermore, we adopt Painlevé Gullstrand coordinates (which are well suited to the problem because they are nonsingular at the horizon) in order to simplify the relevant calculations. Of course physics results are ultimately independent of the choice of coordinates, but this particular coordinate system yields a clean physical interpretation of the relevant physics. We find particularly simple forms for surface gravity, and for the first and second law of black hole thermodynamics, in this general evolving horizon situation. Furthermore, we relate our results to Hawking's apparent horizon, Ashtekar and co-worker's isolated and dynamical horizons, and Hayward's trapping horizon. The evolving black hole model discussed here will be of interest, both from an astrophysical viewpoint in terms of discussing growing black holes and from a purely theoretical viewpoint in discussing black hole evaporation via Hawking radiation.

  11. Risky prey behavior evolves in risky habitats

    PubMed Central

    Urban, Mark C.

    2007-01-01

    Longstanding theory in behavioral ecology predicts that prey should evolve decreased foraging rates under high predation threat. However, an alternative perspective suggests that growth into a size refuge from gape-limited predation and the future benefits of large size can outweigh the initial survival costs of intense foraging. Here, I evaluate the relative contributions of selection from a gape-limited predator (Ambystoma opacum) and spatial location to explanations of variation in foraging, growth, and survival in 10 populations of salamander larvae (Ambystoma maculatum). Salamander larvae from populations naturally exposed to intense A. opacum predation risk foraged more actively under common garden conditions. Higher foraging rates were associated with low survival in populations exposed to free-ranging A. opacum larvae. Results demonstrate that risky foraging activity can evolve in high predation-risk habitats when the dominant predators are gape-limited. This finding invites the further exploration of diverse patterns of prey foraging behavior that depends on natural variation in predator size-selectivity. In particular, prey should adopt riskier behaviors under predation threat than expected under existing risk allocation models if foraging effort directly reduces the duration of risk by growth into a size refuge. Moreover, evidence from this study suggests that foraging has evolved over microgeographic scales despite substantial modification by regional gene flow. This interaction between local selection and spatial location suggests a joint role for adaptation and maladaptation in shaping species interactions across natural landscapes, which is a finding with implications for dynamics at the population, community, and metacommunity levels. PMID:17724339

  12. Risky prey behavior evolves in risky habitats.

    PubMed

    Urban, Mark C

    2007-09-04

    Longstanding theory in behavioral ecology predicts that prey should evolve decreased foraging rates under high predation threat. However, an alternative perspective suggests that growth into a size refuge from gape-limited predation and the future benefits of large size can outweigh the initial survival costs of intense foraging. Here, I evaluate the relative contributions of selection from a gape-limited predator (Ambystoma opacum) and spatial location to explanations of variation in foraging, growth, and survival in 10 populations of salamander larvae (Ambystoma maculatum). Salamander larvae from populations naturally exposed to intense A. opacum predation risk foraged more actively under common garden conditions. Higher foraging rates were associated with low survival in populations exposed to free-ranging A. opacum larvae. Results demonstrate that risky foraging activity can evolve in high predation-risk habitats when the dominant predators are gape-limited. This finding invites the further exploration of diverse patterns of prey foraging behavior that depends on natural variation in predator size-selectivity. In particular, prey should adopt riskier behaviors under predation threat than expected under existing risk allocation models if foraging effort directly reduces the duration of risk by growth into a size refuge. Moreover, evidence from this study suggests that foraging has evolved over microgeographic scales despite substantial modification by regional gene flow. This interaction between local selection and spatial location suggests a joint role for adaptation and maladaptation in shaping species interactions across natural landscapes, which is a finding with implications for dynamics at the population, community, and metacommunity levels.

  13. Functional modules of sigma factor regulons guarantee adaptability and evolvability

    NASA Astrophysics Data System (ADS)

    Binder, Sebastian C.; Eckweiler, Denitsa; Schulz, Sebastian; Bielecka, Agata; Nicolai, Tanja; Franke, Raimo; Häussler, Susanne; Meyer-Hermann, Michael

    2016-02-01

    The focus of modern molecular biology turns from assigning functions to individual genes towards understanding the expression and regulation of complex sets of molecules. Here, we provide evidence that alternative sigma factor regulons in the pathogen Pseudomonas aeruginosa largely represent insulated functional modules which provide a critical level of biological organization involved in general adaptation and survival processes. Analysis of the operational state of the sigma factor network revealed that transcription factors functionally couple the sigma factor regulons and significantly modulate the transcription levels in the face of challenging environments. The threshold quality of newly evolved transcription factors was reached faster and more robustly in in silico testing when the structural organization of sigma factor networks was taken into account. These results indicate that the modular structures of alternative sigma factor regulons provide P. aeruginosa with a robust framework to function adequately in its environment and at the same time facilitate evolutionary change. Our data support the view that widespread modularity guarantees robustness of biological networks and is a key driver of evolvability.

  14. Functional modules of sigma factor regulons guarantee adaptability and evolvability

    PubMed Central

    Binder, Sebastian C.; Eckweiler, Denitsa; Schulz, Sebastian; Bielecka, Agata; Nicolai, Tanja; Franke, Raimo; Häussler, Susanne; Meyer-Hermann, Michael

    2016-01-01

    The focus of modern molecular biology turns from assigning functions to individual genes towards understanding the expression and regulation of complex sets of molecules. Here, we provide evidence that alternative sigma factor regulons in the pathogen Pseudomonas aeruginosa largely represent insulated functional modules which provide a critical level of biological organization involved in general adaptation and survival processes. Analysis of the operational state of the sigma factor network revealed that transcription factors functionally couple the sigma factor regulons and significantly modulate the transcription levels in the face of challenging environments. The threshold quality of newly evolved transcription factors was reached faster and more robustly in in silico testing when the structural organization of sigma factor networks was taken into account. These results indicate that the modular structures of alternative sigma factor regulons provide P. aeruginosa with a robust framework to function adequately in its environment and at the same time facilitate evolutionary change. Our data support the view that widespread modularity guarantees robustness of biological networks and is a key driver of evolvability. PMID:26915971

  15. Evolving communicative complexity: insights from rodents and beyond.

    PubMed

    Pollard, Kimberly A; Blumstein, Daniel T

    2012-07-05

    Social living goes hand in hand with communication, but the details of this relationship are rarely simple. Complex communication may be described by attributes as diverse as a species' entire repertoire, signallers' individualistic signatures, or complex acoustic phenomena within single calls. Similarly, attributes of social complexity are diverse and may include group size, social role diversity, or networks of interactions and relationships. How these different attributes of social and communicative complexity co-evolve is an active question in behavioural ecology. Sciurid rodents (ground squirrels, prairie dogs and marmots) provide an excellent model system for studying these questions. Sciurid studies have found that demographic role complexity predicts alarm call repertoire size, while social group size predicts alarm call individuality. Along with other taxa, sciurids reveal an important insight: different attributes of sociality are linked to different attributes of communication. By breaking social and communicative complexity down to different attributes, focused studies can better untangle the underlying evolutionary relationships and move us closer to a comprehensive theory of how sociality and communication evolve.

  16. Evolving communicative complexity: insights from rodents and beyond

    PubMed Central

    Pollard, Kimberly A.; Blumstein, Daniel T.

    2012-01-01

    Social living goes hand in hand with communication, but the details of this relationship are rarely simple. Complex communication may be described by attributes as diverse as a species' entire repertoire, signallers' individualistic signatures, or complex acoustic phenomena within single calls. Similarly, attributes of social complexity are diverse and may include group size, social role diversity, or networks of interactions and relationships. How these different attributes of social and communicative complexity co-evolve is an active question in behavioural ecology. Sciurid rodents (ground squirrels, prairie dogs and marmots) provide an excellent model system for studying these questions. Sciurid studies have found that demographic role complexity predicts alarm call repertoire size, while social group size predicts alarm call individuality. Along with other taxa, sciurids reveal an important insight: different attributes of sociality are linked to different attributes of communication. By breaking social and communicative complexity down to different attributes, focused studies can better untangle the underlying evolutionary relationships and move us closer to a comprehensive theory of how sociality and communication evolve. PMID:22641825

  17. Constrained evolvability of interferon suppression in an RNA virus.

    PubMed

    Garijo, Raquel; Cuevas, José M; Briz, Álvaro; Sanjuán, Rafael

    2016-04-21

    Innate immunity responses controlled by interferon (IFN) are believed to constitute a major selective pressure shaping viral evolution. Viruses encode a variety of IFN suppressors, but these are often multifunctional proteins that also play essential roles in other steps of the viral infection cycle, possibly limiting their evolvability. Here, we experimentally evolved a vesicular stomatitis virus (VSV) mutant carrying a defect in the matrix protein (M∆51) that abolishes IFN suppression and that has been previously used in the context of oncolytic virotherapy. Serial transfers of this virus in normal, IFN-secreting cells led to a modest recovery of IFN blocking capacity and to weak increases in viral fitness. Full-genome ultra-deep sequencing and phenotypic analysis of population variants revealed that the anti-IFN function of the matrix protein was not restored, and that the Mdelta51 defect was instead compensated by changes in the viral phosphoprotein. We also show that adaptation to IFN-secreting cells can be driven by the selection of fast-growing viruses with no IFN suppression capacity, and that these population variants can be trans-complemented by other, IFN-suppressing variants. Our results thus suggest that virus-virus interactions and alternative strategies of innate immunity evasion can determine the evolution of IFN suppression in a virus.

  18. Evolvable circuit with transistor-level reconfigurability

    NASA Technical Reports Server (NTRS)

    Stoica, Adrian (Inventor); Salazar-Lazaro, Carlos Harold (Inventor)

    2004-01-01

    An evolvable circuit includes a plurality of reconfigurable switches, a plurality of transistors within a region of the circuit, the plurality of transistors having terminals, the plurality of transistors being coupled between a power source terminal and a power sink terminal so as to be capable of admitting power between the power source terminal and the power sink terminal, the plurality of transistors being coupled so that every transistor terminal to transistor terminal coupling within the region of the circuit comprises a reconfigurable switch.

  19. Present weather and climate: evolving conditions

    USGS Publications Warehouse

    Hoerling, Martin P; Dettinger, Michael; Wolter, Klaus; Lukas, Jeff; Eischeid, Jon K.; Nemani, Rama; Liebmann, Brant; Kunkel, Kenneth E.

    2013-01-01

    This chapter assesses weather and climate variability and trends in the Southwest, using observed climate and paleoclimate records. It analyzes the last 100 years of climate variability in comparison to the last 1,000 years, and links the important features of evolving climate conditions to river flow variability in four of the region’s major drainage basins. The chapter closes with an assessment of the monitoring and scientific research needed to increase confidence in understanding when climate episodes, events, and phenomena are attributable to human-caused climate change.

  20. Cobalt-phosphate oxygen-evolving compound.

    PubMed

    Kanan, Matthew W; Surendranath, Yogesh; Nocera, Daniel G

    2009-01-01

    The utilization of solar energy on a large scale requires efficient storage. Solar-to-fuels has the capacity to meet large scale storage needs as demonstrated by natural photosynthesis. This process uses sunlight to rearrange the bonds of water to furnish O2 and an H2-equivalent. We present a tutorial review of our efforts to develop an amorphous cobalt-phosphate catalyst that oxidizes water to O2. The use of earth-abundant materials, operation in water at neutral pH, and the formation of the catalyst in situ captures functional elements of the oxygen evolving complex of Photosystem II.

  1. An evolving paradigm for the secretory pathway?

    PubMed Central

    Lippincott-Schwartz, Jennifer

    2011-01-01

    The paradigm that the secretory pathway consists of a stable endoplasmic reticulum and Golgi apparatus, using discrete transport vesicles to exchange their contents, gained important support from groundbreaking biochemical and genetic studies during the 1980s. However, the subsequent development of new imaging technologies with green fluorescent protein introduced data on dynamic processes not fully accounted for by the paradigm. As a result, we may be seeing an example of how a paradigm is evolving to account for the results of new technologies and their new ways of describing cellular processes. PMID:22039065

  2. Mobile computing acceptance grows as applications evolve.

    PubMed

    Porn, Louis M; Patrick, Kelly

    2002-01-01

    Handheld devices are becoming more cost-effective to own, and their use in healthcare environments is increasing. Handheld devices currently are being used for e-prescribing, charge capture, and accessing daily schedules and reference tools. Future applications may include education on medications, dictation, order entry, and test-results reporting. Selecting the right handheld device requires careful analysis of current and future applications, as well as vendor expertise. It is important to recognize the technology will continue to evolve over the next three years.

  3. Time evolving fluid from Vaidya spacetime

    NASA Astrophysics Data System (ADS)

    Wu, Bin; Hao, Xin; Zhao, Liu

    2017-08-01

    A time evolving fluid system is constructed on a timelike boundary hypersurface at finite cutoff in Vaidya spacetime. The approach used to construct the fluid equations is a direct extension of the ordinary gravity/fluid correspondence under the constrained fluctuation obeying Petrov type I conditions. The explicit relationships between the time dependent fluctuation modes and the fluid quantities such as density, velocity field and kinematic viscosity parameters are established, and the resulting fluid system is governed by a system of a sourced continuity equation and a compressible Navier-Stokes equation with nontrivial time evolution.

  4. SALT Spectroscopy of Evolved Massive Stars

    NASA Astrophysics Data System (ADS)

    Kniazev, A. Y.; Gvaramadze, V. V.; Berdnikov, L. N.

    2017-06-01

    Long-slit spectroscopy with the Southern African Large Telescope (SALT) of central stars of mid-infrared nebulae detected with the Spitzer Space Telescope and Wide-Field Infrared Survey Explorer (WISE) led to the discovery of numerous candidate luminous blue variables (cLBVs) and other rare evolved massive stars. With the recent advent of the SALT fiber-fed high-resolution echelle spectrograph (HRS), a new perspective for the study of these interesting objects is appeared. Using the HRS we obtained spectra of a dozen newly identified massive stars. Some results on the recently identified cLBV Hen 3-729 are presented.

  5. Investigating Evolved Compositions Around Wolf Crater

    NASA Technical Reports Server (NTRS)

    Greenhagen, B. T.; Cahill, J. T. S.; Jolliff, B. L.; Lawrence, S. J.; Glotch, T. D.

    2017-01-01

    Wolf crater is an irregularly shaped, approximately 25 km crater in the south-central portion of Mare Nubium on the lunar nearside. While not previously identified as a lunar "red spot", Wolf crater was identified as a Th anomaly by Lawrence and coworkers. We have used data from the Lunar Reconnaissance Orbiter (LRO) to determine the area surrounding Wolf crater has composition more similar to highly evolved, non-mare volcanic structures than typical lunar crustal lithology. In this presentation, we will investigate the geomorphology and composition of the Wolf crater and discuss implications for the origin of the anomalous terrain.

  6. f( R) gravity solutions for evolving wormholes

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Subhra; Chakraborty, Subenoy

    2017-08-01

    The scalar-tensor f( R) theory of gravity is considered in the framework of a simple inhomogeneous space-time model. In this research we use the reconstruction technique to look for possible evolving wormhole solutions within viable f( R) gravity formalism. These f( R) models are then constrained so that they are consistent with existing experimental data. Energy conditions related to the matter threading the wormhole are analyzed graphically and are in general found to obey the null energy conditions (NEC) in regions around the throat, while in the limit f(R)=R, NEC can be violated at large in regions around the throat.

  7. Salmonella Rapidly Regulates Membrane Permeability To Survive Oxidative Stress.

    PubMed

    van der Heijden, Joris; Reynolds, Lisa A; Deng, Wanyin; Mills, Allan; Scholz, Roland; Imami, Koshi; Foster, Leonard J; Duong, Franck; Finlay, B Brett

    2016-08-09

    The outer membrane (OM) of Gram-negative bacteria provides protection against toxic molecules, including reactive oxygen species (ROS). Decreased OM permeability can promote bacterial survival under harsh circumstances and protects against antibiotics. To better understand the regulation of OM permeability, we studied the real-time influx of hydrogen peroxide in Salmonella bacteria and discovered two novel mechanisms by which they rapidly control OM permeability. We found that pores in two major OM proteins, OmpA and OmpC, could be rapidly opened or closed when oxidative stress is encountered and that the underlying mechanisms rely on the formation of disulfide bonds in the periplasmic domain of OmpA and TrxA, respectively. Additionally, we found that a Salmonella mutant showing increased OM permeability was killed more effectively by treatment with antibiotics. Together, these results demonstrate that Gram-negative bacteria regulate the influx of ROS for defense against oxidative stress and reveal novel targets that can be therapeutically targeted to increase bacterial killing by conventional antibiotics. Pathogenic bacteria have evolved ways to circumvent inflammatory immune responses. A decrease in bacterial outer membrane permeability during infection helps protect bacteria from toxic molecules produced by the host immune system and allows for effective colonization of the host. In this report, we reveal molecular mechanisms that rapidly alter outer membrane pores and their permeability in response to hydrogen peroxide and oxidative stress. These mechanisms are the first examples of pores that are rapidly opened or closed in response to reactive oxygen species. Moreover, one of these mechanisms can be targeted to artificially increase membrane permeability and thereby increase bacterial killing by the antibiotic cefotaxime during in vitro experiments and in a mouse model of infection. We envision that a better understanding of the regulation of membrane

  8. Rapid prototype and test

    SciTech Connect

    Gregory, D.L.; Hansche, B.D.

    1996-06-01

    In order to support advanced manufacturing, Sandia has acquired the capability to produce plastic prototypes using stereolithography. Currently, these prototypes are used mainly to verify part geometry and ``fit and form`` checks. This project investigates methods for rapidly testing these plastic prototypes, and inferring from prototype test data actual metal part performance and behavior. Performances examined include static load/stress response, and structural dynamic (modal) and vibration behavior. The integration of advanced non-contacting measurement techniques including scanning laser velocimetry, laser holography, and thermoelasticity into testing of these prototypes is described. Photoelastic properties of the epoxy prototypes to reveal full field stress/strain fields are also explored.

  9. The emotion system promotes diversity and evolvability

    PubMed Central

    Giske, Jarl; Eliassen, Sigrunn; Fiksen, Øyvind; Jakobsen, Per J.; Aksnes, Dag L.; Mangel, Marc; Jørgensen, Christian

    2014-01-01

    Studies on the relationship between the optimal phenotype and its environment have had limited focus on genotype-to-phenotype pathways and their evolutionary consequences. Here, we study how multi-layered trait architecture and its associated constraints prescribe diversity. Using an idealized model of the emotion system in fish, we find that trait architecture yields genetic and phenotypic diversity even in absence of frequency-dependent selection or environmental variation. That is, for a given environment, phenotype frequency distributions are predictable while gene pools are not. The conservation of phenotypic traits among these genetically different populations is due to the multi-layered trait architecture, in which one adaptation at a higher architectural level can be achieved by several different adaptations at a lower level. Our results emphasize the role of convergent evolution and the organismal level of selection. While trait architecture makes individuals more constrained than what has been assumed in optimization theory, the resulting populations are genetically more diverse and adaptable. The emotion system in animals may thus have evolved by natural selection because it simultaneously enhances three important functions, the behavioural robustness of individuals, the evolvability of gene pools and the rate of evolutionary innovation at several architectural levels. PMID:25100697

  10. Early formation of evolved asteroidal crust.

    PubMed

    Day, James M D; Ash, Richard D; Liu, Yang; Bellucci, Jeremy J; Rumble, Douglas; McDonough, William F; Walker, Richard J; Taylor, Lawrence A

    2009-01-08

    Mechanisms for the formation of crust on planetary bodies remain poorly understood. It is generally accepted that Earth's andesitic continental crust is the product of plate tectonics, whereas the Moon acquired its feldspar-rich crust by way of plagioclase flotation in a magma ocean. Basaltic meteorites provide evidence that, like the terrestrial planets, some asteroids generated crust and underwent large-scale differentiation processes. Until now, however, no evolved felsic asteroidal crust has been sampled or observed. Here we report age and compositional data for the newly discovered, paired and differentiated meteorites Graves Nunatak (GRA) 06128 and GRA 06129. These meteorites are feldspar-rich, with andesite bulk compositions. Their age of 4.52 +/- 0.06 Gyr demonstrates formation early in Solar System history. The isotopic and elemental compositions, degree of metamorphic re-equilibration and sulphide-rich nature of the meteorites are most consistent with an origin as partial melts from a volatile-rich, oxidized asteroid. GRA 06128 and 06129 are the result of a newly recognized style of evolved crust formation, bearing witness to incomplete differentiation of their parent asteroid and to previously unrecognized diversity of early-formed materials in the Solar System.

  11. The evolving role of the transfusion practitioner.

    PubMed

    Miller, Kristy; Akers, Christine; Davis, Amanda K; Wood, Erica; Hennessy, Clare; Bielby, Linley

    2015-04-01

    Much of the recent work in transfusion practice has shifted to focus on the patient, after efforts over previous decades to ensure the quality and safety of blood products. After the commencement of hemovigilance and transfusion practice improvement programs, the introduction of transfusion practitioners (TP) into health care services and blood centers has continued to increase worldwide. Since this relatively new role was introduced, much work of the TP has focused on patient and staff education, adverse events, transfusion governance, and monitoring of transfusion practices within organizations. The complex nature of the transfusion process makes the TP an integral link in the transfusion chain. Together with hospital transfusion teams and committees, the TP works collaboratively to facilitate the transfusion change management programs and initiatives. Recently, the TP role has evolved to include an emphasis on patient blood management and, to some extent, is shaped by national standards and regulations. These established roles of the TP, together with the ever-changing field of transfusion medicine, provide new opportunities and challenges for a role that is continuing to evolve worldwide. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. BOOK REVIEW: OPENING SCIENCE, THE EVOLVING GUIDE ...

    EPA Pesticide Factsheets

    The way we get our funding, collaborate, do our research, and get the word out has evolved over hundreds of years but we can imagine a more open science world, largely facilitated by the internet. The movement towards this more open way of doing and presenting science is coming, and it is not taking hundreds of years. If you are interested in these trends, and would like to find out more about where this is all headed and what it means to you, consider downloding Opening Science, edited by Sönke Bartling and Sascha Friesike, subtitled The Evolving Guide on How the Internet is Changing Research, Collaboration, and Scholarly Publishing. In 26 chapters by various authors from a range of disciplines the book explores the developing world of open science, starting from the first scientific revolution and bringing us to the next scientific revolution, sometimes referred to as “Science 2.0”. Some of the articles deal with the impact of the changing landscape of how science is done, looking at the impact of open science on Academia, or journal publishing, or medical research. Many of the articles look at the uses, pitfalls, and impact of specific tools, like microblogging (think Twitter), social networking, and reference management. There is lots of discussion and definition of terms you might use or misuse like “altmetrics” and “impact factor”. Science will probably never be completely open, and Twitter will probably never replace the journal article,

  13. Evolving Dark Energy with w =/ -1

    SciTech Connect

    Hall, Lawrence J.; Nomura, Yasunori; Oliver, Steven J.

    2005-03-31

    Theories of evolving quintessence are constructed that generically lead to deviations from the w = -1 prediction of non-evolving dark energy. The small mass scale that governs evolution, m_\\phi \\approx 10^-33 eV, is radiatively stable, and the"Why Now?'' problem is solved. These results rest crucially on seesaw cosmology: in broad outline, fundamental physics and cosmology can be understood from only two mass scales, the weak scale, v, and the Planck scale, M. Requiring a scale of dark energy \\rho_DE^1/4 governed by v^2/M, and a radiatively stable evolution rate m_\\phi given by v^4/M^3, leads to a distinctive form for the equation of state w(z) that follows from a cosine quintessence potential. An explicit hidden axion model is constructed. Dark energy resides in the potential of the axion field which is generated by a new QCD-like force that gets strong at the scale \\Lambda \\approx v^2/M \\approx \\rho_DE^1/4. The evolution rate is given by a second seesaw that leads to the axion mass, m_\\phi \\approx \\Lambda^2/f, with f \\approx M.

  14. Novel cooperation experimentally evolved between species.

    PubMed

    Harcombe, William

    2010-07-01

    Cooperation violates the view of "nature red in tooth and claw" that prevails in our understanding of evolution, yet examples of cooperation abound. Most work has focused on maintenance of cooperation within a single species through mechanisms such as kin selection. The factors necessary for the evolutionary origin of aiding unrelated individuals such as members of another species have not been experimentally tested. Here, I demonstrate that cooperation between species can be evolved in the laboratory if (1) there is preexisting reciprocation or feedback for cooperation, and (2) reciprocation is preferentially received by cooperative genotypes. I used a two species system involving Salmonella enterica ser. Typhimurium and an Escherichia coli mutant unable to synthesize an essential amino acid. In lactose media Salmonella consumes metabolic waste from E. coli, thus creating a mechanism of reciprocation for cooperation. Growth in a spatially structured environment assured that the benefits of cooperation were preferentially received by cooperative genotypes. Salmonella evolved to aid E. coli by excreting a costly amino acid, however this novel cooperation disappeared if the waste consumption or spatial structure were removed. This study builds on previous work to demonstrate an experimental origin of interspecific cooperation, and to test the factors necessary for such interactions to arise.

  15. Shaping the outflows of evolved stars

    NASA Astrophysics Data System (ADS)

    Mohamed, Shazrene

    2015-08-01

    Both hot and cool evolved stars, e.g., red (super)giants and Wolf-Rayet stars, lose copious amounts of mass, momentum and mechanical energy through powerful, dense stellar winds. The interaction of these outflows with their surroundings results in highly structured and complex circumstellar environments, often featuring knots, arcs, shells and spirals. Recent improvements in computational power and techniques have led to the development of detailed, multi-dimensional simulations that have given new insight into the origin of these structures, and better understanding of the physical mechanisms driving their formation. In this talk, I will discuss three of the main mechanisms that shape the outflows of evolved stars:- interaction with the interstellar medium (ISM), i.e., wind-ISM interactions- interaction with a stellar wind, either from a previous phase of evolution or the wind from a companion star, i.e., wind-wind interactions- and interaction with a companion star that has a weak or insignicant outflow (e.g., a compact companion such as a neutron star or black hole), i.e., wind-companion interactions.I will also highlight the broader implications and impact of these stellar wind interactions for other phenomena, e.g, for symbiotic and X-ray binaries, supernovae and Gamma-ray bursts.

  16. Hierarchical decomposition of dynamically evolving regulatory networks.

    PubMed

    Ay, Ahmet; Gong, Dihong; Kahveci, Tamer

    2015-05-15

    Gene regulatory networks describe the interplay between genes and their products. These networks control almost every biological activity in the cell through interactions. The hierarchy of genes in these networks as defined by their interactions gives important insights into how these functions are governed. Accurately determining the hierarchy of genes is however a computationally difficult problem. This problem is further complicated by the fact that an intrinsic characteristic of regulatory networks is that the wiring of interactions can change over time. Determining how the hierarchy in the gene regulatory networks changes with dynamically evolving network topology remains to be an unsolved challenge. In this study, we develop a new method, named D-HIDEN (Dynamic-HIerarchical DEcomposition of Networks) to find the hierarchy of the genes in dynamically evolving gene regulatory network topologies. Unlike earlier methods, which recompute the hierarchy from scratch when the network topology changes, our method adapts the hierarchy based on the wiring of the interactions only for the nodes which have the potential to move in the hierarchy. We compare D-HIDEN to five currently available hierarchical decomposition methods on synthetic and real gene regulatory networks. Our experiments demonstrate that D-HIDEN significantly outperforms existing methods in running time, accuracy, or both. Furthermore, our method is robust against dynamic changes in hierarchy. Our experiments on human gene regulatory networks suggest that our method may be used to reconstruct hierarchy in gene regulatory networks.

  17. Evolving MEMS Resonator Designs for Fabrication

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.; Kraus, William F.; Lohn, Jason D.

    2008-01-01

    Because of their small size and high reliability, microelectromechanical (MEMS) devices have the potential to revolution many areas of engineering. As with conventionally-sized engineering design, there is likely to be a demand for the automated design of MEMS devices. This paper describes our current status as we progress toward our ultimate goal of using an evolutionary algorithm and a generative representation to produce designs of a MEMS device and successfully demonstrate its transfer to an actual chip. To produce designs that are likely to transfer to reality, we present two ways to modify evaluation of designs. The first is to add location noise, differences between the actual dimensions of the design and the design blueprint, which