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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. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. The functions of the multiproduct and rapidly evolving dec-1 eggshell gene are conserved between evolutionarily distant species of Drosophila.

    PubMed Central

    Badciong, J C; Otto, J M; Waring, G L

    2001-01-01

    The Drosophila dec-1 gene encodes multiple proteins that are required for female fertility and proper eggshell morphogenesis. Genetic and immunolocalization data suggest that the different DEC-1 proteins are functionally distinct. To identify regions within the proteins with potential biological significance, we cloned and sequenced the D. yakuba and D. virilis dec-1 homologs. Interspecies comparisons of the predicted translation products revealed rapidly evolving sequences punctuated by blocks of conserved amino acids. Despite extensive amino acid variability, the proteins produced by the different dec-1 homologs were functionally interchangeable. The introduction of transgenes containing either the D. yakuba or the D. virilis dec-1 open reading frames into a D. melanogaster DEC-1 protein null mutant was sufficient to restore female fertility and wild-type eggshell morphology. Normal expression and extracellular processing of the DEC-1 proteins was correlated with the phenotypic rescue. The nature of the conserved features highlighted by the evolutionary comparison and the molecular resemblance of some of these features to those found in other extracellular proteins suggests functional correlates for some of the multiple DEC-1 derivatives. PMID:11729155

  13. 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

  14. 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.

  15. 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

  16. 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.

  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.

  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. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  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. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. How rapidly can maternal behavior affecting primary sex ratio evolve in a reptile with environmental sex determination?

    PubMed

    Morjan, Carrie L

    2003-08-01

    Theoretical models identify maternal behavior as critical for the maintenance and evolution of sex ratios in organisms with environmental sex determination (ESD). Maternal choice of nest site is generally thought to respond more rapidly to sex ratio selection than environmental sensitivity of offspring sex (threshold temperatures) in reptiles with temperature-dependent sex determination (TSD, a form of ESD). However, knowledge of the evolutionary potential for either of these traits in a field setting is limited. I developed a simulation model using local climate data and observed levels of phenotypic variation for nest-site choice and threshold temperatures in painted turtles (Chrysemys picta) with TSD. Both nest-site choice and threshold temperatures, and hence sex ratios, evolved slowly to simulated climate change scenarios. In contrast to expectations from previous models, nest-site choice evolved more slowly than threshold temperatures because of large climatic effects on nest temperatures and indirect selection on maternally expressed traits. A variant of the model, assuming inheritance of nest-site choice through natal imprinting, demonstrated that natal imprinting inhibited adaptive responses in female nest-site choice to climate change. These results predict that females have relatively low potential to adaptively adjust sex ratios through nest-site choice.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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...

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  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. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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

    2016-12-05

    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. [Bayesian; BEAST; morphological clock; morphology

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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).

  3. 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

  4. 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

  5. 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

  6. 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).

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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?

  11. 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.

  12. 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

  13. 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

    2017-12-01

    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.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. Analyzing Evolving Social Network 2 (EVOLVE2)

    DTIC Science & Technology

    2015-04-01

    over time, and how changes in topology affect evolution of influence and groups -Understand the impact of dynamics and network flows on the...incorporate time. The research had two major threads: • Understand how networks evolve over time, and how changes in topology affect evolution of...1958 14 Meissner Effect 1958 307 Random-Phase Approximation ... Superconductivity 1959 40 Evidence for Anisotropy of the Superconducting Energy... 1989

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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…

  11. 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.

  12. [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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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…

  7. "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…

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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…

  6. 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.

  7. 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

  8. 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…

  9. 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.

  10. 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…

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Evolved Expendable Launch Vehicle (EELV)

    DTIC Science & Technology

    2015-12-15

    potential NSS mission processing timelines. SpaceX is now eligible for an award of specified NSS missions to include the GPS III-2 launch service... SpaceX has also evolved their Falcon 9v1.1 configuration into the Falcon 9 Upgrade. To update the certification baseline, SpaceX and AF built Joint Work...9 v1.1 commercial launch experienced an in-flight mishap resulting in loss of vehicle on June 28, 2015. An official investigation was led by a SpaceX

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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…

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  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. 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.

  17. 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.

  18. 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.

  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. 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.

  1. 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

  2. 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

  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. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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…

  14. Directional Communication in Evolved Multiagent Teams

    DTIC Science & Technology

    2013-06-10

    only a fraction of the observable state of the environment. In such tasks, communication facilitates sharing information among team members to...architecture is becoming increasingly important for evolving autonomous multiagent systems. Directional reception of signals, a design feature of communication ...Title ABSTRACT How to best design a communication architecture is becoming increasingly important for evolving autonomous multiagent systems. Directional

  15. 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)…

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  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. 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.

  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. 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

  10. 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.

  11. 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…

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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…

  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. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  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. 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.

  9. 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.

  10. 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.

  11. Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales

    PubMed Central

    Zhang, Lu; Wu, Wei; Yan, Hai-Fei; Ge, Xue-Jun

    2015-01-01

    Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data. PMID:26819541

  12. 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.

  13. 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.

  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. 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.

  16. 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.

  17. 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.

  18. Exon-specific northern analysis and rapid amplification of cDNA ends (RACE) reveal that the proximal promoter II (PII) is responsible for aromatase cytochrome P450 (CYP19) expression in human ovary.

    PubMed

    Jenkins, C; Michael, D; Mahendroo, M; Simpson, E

    1993-11-01

    Estrogens are synthesized from C19 steroids by a unique form of cytochrome P450, aromatase cytochrome P-450 (P-450AROM; the product of the CYP19 gene). We have shown that tissue-specific expression of human P-450AROM is determined, in part, by the use of alternative promoters. Previous methods of analysis for determining the specific 5'-termini of the different transcripts included S1 nuclease protection, primer extension, and Northern analysis. In the present study we have used the RACE procedure (rapid amplification of cDNA ends) to amplify and clone the 5' termini of P-450AROM transcripts expressed in human corpus luteum (CL). Sequencing of the resulting clones supports the results of the previously performed studies. Specifically, the proximal promoter, PII, is the predominant promoter utilized in CL, such that the start of transcription occurs 26 bp downstream of the putative TATA sequence. A minority of the clones possess an alternative 5'-end, namely I.3. Exon-specific Northern analysis confirms that the majority of the P-450AROM transcripts in CL tissue contain sequence specific for promoter II. Similarly, exon-specific Northern analysis indicates that transcripts in human follicles, as well as granulosa cells in culture, contain primarily sequence specific for promoter II.

  19. 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.

  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. 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.

  2. 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

  3. 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.

  4. Bed bugs evolved unique adaptive strategy to resist pyrethroid insecticides.

    PubMed

    Zhu, Fang; Gujar, Hemant; Gordon, Jennifer R; Haynes, Kenneth F; Potter, Michael F; Palli, Subba R

    2013-01-01

    Recent advances in genomic and post-genomic technologies have facilitated a genome-wide analysis of the insecticide resistance-associated genes in insects. Through bed bug, Cimex lectularius transcriptome analysis, we identified 14 molecular markers associated with pyrethroid resistance. Our studies revealed that most of the resistance-associated genes functioning in diverse mechanisms are expressed in the epidermal layer of the integument, which could prevent or slow down the toxin from reaching the target sites on nerve cells, where an additional layer of resistance (kdr) is possible. This strategy evolved in bed bugs is based on their unique morphological, physiological and behavioral characteristics and has not been reported in any other insect species. RNA interference-aided knockdown of resistance associated genes showed the relative contribution of each mechanism towards overall resistance development. Understanding the complexity of adaptive strategies employed by bed bugs will help in designing the most effective and sustainable bed bug control methods.

  5. Bed bugs evolved unique adaptive strategy to resist pyrethroid insecticides

    PubMed Central

    Zhu, Fang; Gujar, Hemant; Gordon, Jennifer R.; Haynes, Kenneth F.; Potter, Michael F.; Palli, Subba R.

    2013-01-01

    Recent advances in genomic and post-genomic technologies have facilitated a genome-wide analysis of the insecticide resistance-associated genes in insects. Through bed bug, Cimex lectularius transcriptome analysis, we identified 14 molecular markers associated with pyrethroid resistance. Our studies revealed that most of the resistance-associated genes functioning in diverse mechanisms are expressed in the epidermal layer of the integument, which could prevent or slow down the toxin from reaching the target sites on nerve cells, where an additional layer of resistance (kdr) is possible. This strategy evolved in bed bugs is based on their unique morphological, physiological and behavioral characteristics and has not been reported in any other insect species. RNA interference-aided knockdown of resistance associated genes showed the relative contribution of each mechanism towards overall resistance development. Understanding the complexity of adaptive strategies employed by bed bugs will help in designing the most effective and sustainable bed bug control methods. PMID:23492626

  6. Evolvability and hierarchy in rewired bacterial gene networks

    PubMed Central

    Isalan, Mark; Lemerle, Caroline; Michalodimitrakis, Konstantinos; Beltrao, Pedro; Horn, Carsten; Raineri, Emanuele; Garriga-Canut, Mireia; Serrano, Luis

    2009-01-01

    Sequencing DNA from several organisms has revealed that duplication and drift of existing genes have primarily molded the contents of a given genome. Though the effect of knocking out or over-expressing a particular gene has been studied in many organisms, no study has systematically explored the effect of adding new links in a biological network. To explore network evolvability, we constructed 598 recombinations of promoters (including regulatory regions) with different transcription or σ-factor genes in Escherichia coli, added over a wild-type genetic background. Here we show that ~95% of new networks are tolerated by the bacteria, that very few alter growth, and that expression level correlates with factor position in the wild-type network hierarchy. Most importantly, we find that certain networks consistently survive over the wild-type under various selection pressures. Therefore new links in the network are rarely a barrier for evolution and can even confer a fitness advantage. PMID:18421347

  7. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus

    DOE PAGES

    Lund, C. H.; Bromley, J. R.; Stenbaek, A.; ...

    2014-10-18

    A growing body of evidence suggests that protein–protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. Wemore » tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. In conclusion, our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta.« less

  8. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus

    SciTech Connect

    Lund, C. H.; Bromley, J. R.; Stenbaek, A.; Rasmussen, R. E.; Scheller, H. V.; Sakuragi, Y.

    2014-10-18

    A growing body of evidence suggests that protein–protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. In conclusion, our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta.

  9. A reversible Renilla luciferase protein complementation assay for rapid identification of protein-protein interactions reveals the existence of an interaction network involved in xyloglucan biosynthesis in the plant Golgi apparatus.

    PubMed

    Lund, Christian H; Bromley, Jennifer R; Stenbæk, Anne; Rasmussen, Randi E; Scheller, Henrik V; Sakuragi, Yumiko

    2015-01-01

    A growing body of evidence suggests that protein-protein interactions (PPIs) occur amongst glycosyltransferases (GTs) required for plant glycan biosynthesis (e.g. cell wall polysaccharides and N-glycans) in the Golgi apparatus, and may control the functions of these enzymes. However, identification of PPIs in the endomembrane system in a relatively fast and simple fashion is technically challenging, hampering the progress in understanding the functional coordination of the enzymes in Golgi glycan biosynthesis. To solve the challenges, we adapted and streamlined a reversible Renilla luciferase protein complementation assay (Rluc-PCA), originally reported for use in human cells, for transient expression in Nicotiana benthamiana. We tested Rluc-PCA and successfully identified luminescence complementation amongst Golgi-localizing GTs known to form a heterodimer (GAUT1 and GAUT7) and those which homooligomerize (ARAD1). In contrast, no interaction was shown between negative controls (e.g. GAUT7, ARAD1, IRX9). Rluc-PCA was used to investigate PPIs amongst Golgi-localizing GTs involved in biosynthesis of hemicelluloses. Although no PPI was identified among six GTs involved in xylan biosynthesis, Rluc-PCA confirmed three previously proposed interactions and identified seven novel PPIs amongst GTs involved in xyloglucan biosynthesis. Notably, three of the novel PPIs were confirmed by a yeast-based split-ubiquitin assay. Finally, Gateway-enabled expression vectors were generated, allowing rapid construction of fusion proteins to the Rluc reporters and epitope tags. Our results show that Rluc-PCA coupled with transient expression in N. benthamiana is a fast and versatile method suitable for analysis of PPIs between Golgi resident proteins in an easy and mid-throughput fashion in planta.

  10. Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

    PubMed Central

    2013-01-01

    Background As one of the fastest-growing lignocellulose-abundant plants on Earth, bamboos can reach their final height quickly due to the expansion of individual internodes already present in the buds; however, the molecular processes underlying this phenomenon remain unclear. Moso bamboo (Phyllostachys heterocycla cv. Pubescens) internodes from four different developmental stages and three different internodes within the same stage were used in our study to investigate the molecular processes at the transcriptome and post-transcriptome level. Results Our anatomical observations indicated the development of culms was dominated by cell division in the initial stages and by cell elongation in the middle and late stages. The four major endogenous hormones appeared to actively promote culm development. Using next-generation sequencing-based RNA-Seq, mRNA and microRNA expression profiling technology, we produced a transcriptome and post-transcriptome in possession of a large fraction of annotated Moso bamboo genes, and provided a molecular basis underlying the phenomenon of sequentially elongated internodes from the base to the top. Several key pathways such as environmental adaptation, signal transduction, translation, transport and many metabolisms were identified as involved in the rapid elongation of bamboo culms. Conclusions This is the first report on the temporal and spatial transcriptome and gene expression and microRNA profiling in a developing bamboo culms. In addition to gaining more insight into the unique growth characteristics of bamboo, we provide a good case study to analyze gene, microRNA expression and profiling of non-model plant species using high-throughput short-read sequencing. Also, we demonstrate that the integrated analysis of our multi-omics data, including transcriptome, post-transcriptome, proteome, yield more complete representations and additional biological insights, especially the complex dynamic processes occurring in Moso bamboo culms

  11. 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

  12. Have plants evolved to self-immolate?

    PubMed Central

    Bowman, David M. J. S.; French, Ben J.; Prior, Lynda D.

    2014-01-01

    By definition fire prone ecosystems have highly combustible plants, leading to the hypothesis, first formally stated by Mutch in 1970, that community flammability is the product of natural selection of flammable traits. However, proving the “Mutch hypothesis” has presented an enormous challenge for fire ecologists given the difficulty in establishing cause and effect between landscape fire and flammable plant traits. Individual plant traits (such as leaf moisture content, retention of dead branches and foliage, oil rich foliage) are known to affect the flammability of plants but there is no evidence these characters evolved specifically to self-immolate, although some of these traits may have been secondarily modified to increase the propensity to burn. Demonstrating individual benefits from self-immolation is extraordinarily difficult, given the intersection of the physical environmental factors that control landscape fire (fuel production, dryness and ignitions) with community flammability properties that emerge from numerous traits of multiple species (canopy cover and litter bed bulk density). It is more parsimonious to conclude plants have evolved mechanisms to tolerate, but not promote, landscape fire. PMID:25414710

  13. The Comet Cometh: Evolving Developmental Systems.

    PubMed

    Jaeger, Johannes; Laubichler, Manfred; Callebaut, Werner

    In a recent opinion piece, Denis Duboule has claimed that the increasing shift towards systems biology is driving evolutionary and developmental biology apart, and that a true reunification of these two disciplines within the framework of evolutionary developmental biology (EvoDevo) may easily take another 100 years. He identifies methodological, epistemological, and social differences as causes for this supposed separation. Our article provides a contrasting view. We argue that Duboule's prediction is based on a one-sided understanding of systems biology as a science that is only interested in functional, not evolutionary, aspects of biological processes. Instead, we propose a research program for an evolutionary systems biology, which is based on local exploration of the configuration space in evolving developmental systems. We call this approach-which is based on reverse engineering, simulation, and mathematical analysis-the natural history of configuration space. We discuss a number of illustrative examples that demonstrate the past success of local exploration, as opposed to global mapping, in different biological contexts. We argue that this pragmatic mode of inquiry can be extended and applied to the mathematical analysis of the developmental repertoire and evolutionary potential of evolving developmental mechanisms and that evolutionary systems biology so conceived provides a pragmatic epistemological framework for the EvoDevo synthesis.

  14. 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 is a technique we have used for our work in evolving antennas and robots. The second method is to add prestress to model the warping that occurs during the extreme heat of fabrication. In future we expect to fabricate and test some MEMS resonators that are evolved in this way.

  15. 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.

  16. 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.

  17. Collapse of cooperation in evolving games

    PubMed Central

    Stewart, Alexander J.; Plotkin, Joshua B.

    2014-01-01

    Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner’s Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players’ payoffs as well as their strategies to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the coevolution of strategies and payoffs in arbitrary iterated games. We show that, when there is a tradeoff between the benefits and costs of cooperation, coevolution often leads to a dramatic loss of cooperation in the Iterated Prisoner’s Dilemma. The collapse of cooperation is so extreme that the average payoff in a population can decline even as the potential reward for mutual cooperation increases. Depending upon the form of tradeoffs, evolution may even move away from the Iterated Prisoner’s Dilemma game altogether. Our work offers a new perspective on the Prisoner’s Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the coevolution of strategies and payoffs in iterated interactions. PMID:25422421

  18. Caterpillars evolved from onychophorans by hybridogenesis.

    PubMed

    Williamson, Donald I

    2009-11-24

    I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals. "Caterpillars," the name for eruciforms with thoracic and abdominal legs, are larvae of lepidopterans, hymenopterans, and mecopterans (scorpionflies). Grubs and maggots, including the larvae of beetles, bees, and flies, evolved from caterpillars by loss of legs. Caterpillar larval organs are dismantled and reconstructed in the pupal phase. Such indirect developmental patterns (metamorphoses) did not originate solely by accumulation of random mutations followed by natural selection; rather they are fully consistent with my concept of evolution by hybridogenesis. Members of the phylum Onychophora (velvet worms) are proposed as the evolutionary source of caterpillars and their grub or maggot descendants. I present a molecular biological research proposal to test my thesis. By my hypothesis 2 recognizable sets of genes are detectable in the genomes of all insects with caterpillar grub- or maggot-like larvae: (i) onychophoran genes that code for proteins determining larval morphology/physiology and (ii) sequentially expressed insect genes that code for adult proteins. The genomes of insects and other animals that, by contrast, entirely lack larvae comprise recognizable sets of genes from single animal common ancestors.

  19. 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,

  20. Collapse of cooperation in evolving games.

    PubMed

    Stewart, Alexander J; Plotkin, Joshua B

    2014-12-09

    Game theory provides a quantitative framework for analyzing the behavior of rational agents. The Iterated Prisoner's Dilemma in particular has become a standard model for studying cooperation and cheating, with cooperation often emerging as a robust outcome in evolving populations. Here we extend evolutionary game theory by allowing players' payoffs as well as their strategies to evolve in response to selection on heritable mutations. In nature, many organisms engage in mutually beneficial interactions and individuals may seek to change the ratio of risk to reward for cooperation by altering the resources they commit to cooperative interactions. To study this, we construct a general framework for the coevolution of strategies and payoffs in arbitrary iterated games. We show that, when there is a tradeoff between the benefits and costs of cooperation, coevolution often leads to a dramatic loss of cooperation in the Iterated Prisoner's Dilemma. The collapse of cooperation is so extreme that the average payoff in a population can decline even as the potential reward for mutual cooperation increases. Depending upon the form of tradeoffs, evolution may even move away from the Iterated Prisoner's Dilemma game altogether. Our work offers a new perspective on the Prisoner's Dilemma and its predictions for cooperation in natural populations; and it provides a general framework to understand the coevolution of strategies and payoffs in iterated interactions.

  1. The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery.

    PubMed

    Davidovich, Chen; Belousoff, Matthew; Bashan, Anat; Yonath, Ada

    2009-09-01

    Structural analysis supported by biochemical, mutagenesis and computational evidence, revealed that the contemporary ribosome's active site is a universal symmetrical pocket made of ribosomal RNA. This pocket seems to be the remnant of the proto-ribosome, a dimeric RNA assembly evolved by gene duplication, capable of autonomously catalyzing peptide bond formation and non-coded amino acid polymerization.

  2. Transforming Research in Oceanography through Education, Ethnography and Rapidly Evolving Technologies: An NSF-INSPIRE project.

    NASA Astrophysics Data System (ADS)

    German, C. R.; Croff Bell, K. L.; Pallant, A.; Mirmalek, Z.; Jasanoff, S.; Rajan, K.

    2014-12-01

    This paper will discuss a new NSF-INSPIRE project that brings together research conducted in the fields of Ocean Sciences, Education & Human Resources and Computer and Information Science & Engineering. Specifically, our objective is to investigate new methods by which telepresence can be used to conduct cutting edge research and provide authentic educational experiences to undergraduate students, remotely. We choose to conduct this research in an Oceanographic context for two reasons: first with the move toward smaller research ships in the national Oceanographic research fleet, we anticipate that access to berth space at sea will continue to be at a premium. Any component of traditional oceanographic research that can be ported to shore without loss of effectiveness would be of immediate benefit to the Ocean Sciences. Equally, however, we argue that any improvements to work place and/or education practices that we can identify while delivering research and education from the bottom of the deep ocean should be readily mappable to any other scientific or engineering activities that seek to make use of telepresence in less extreme remote environments. Work on our TREET project, to-date, has included recruitment of 6 early career scientists keen to take advantage of the research opportunity provided, together with two senior science mentors with experience using Telepresence and a cohort of undergraduate students at three of the ECS partner Universities, spanning 4 time zones across the continental US. Following a 12-week synchronous on-line seminar series taught in Spring-Summer 2014, the entire team joined together at the Inner Space Center in Sept-Oct 2014 to participate, virtually, in a cruise of research and exploration to the Kick'Em Jenny underwater volcano and adjacent cold seep sites, conducted by the Ocean Exploration Trust's ROV Hercules aboard the Exploration Vessel Nautilus. Our presentation will include preliminary results from that cruise.

  3. The Information Technology Program Manager’s Dilemma: Rapidly Evolving Technology and Stagnant Processes

    DTIC Science & Technology

    2010-08-01

    18. NUMBER OF PAGES 5 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard...Objectives for Infor- mation and related Technology ( COBIT ) and the Informa- tion Technology Infrastructure Library (ITIL), both of which recognize the

  4. A great earthquake rupture across a rapidly evolving three-plate boundary.

    PubMed

    Furlong, Kevin P; Lay, Thorne; Ammon, Charles J

    2009-04-10

    On 1 April 2007 a great, tsunamigenic earthquake (moment magnitude 8.1) ruptured the Solomon Islands subduction zone at the triple junction where the Australia and Solomon Sea-Woodlark Basin plates simultaneously underthrust the Pacific plate with different slip directions. The associated abrupt change in slip direction during the great earthquake drove convergent anelastic deformation of the upper Pacific plate, which generated localized uplift in the forearc above the subducting Simbo fault, potentially amplifying local tsunami amplitude. Elastic deformation during the seismic cycle appears to be primarily accommodated by the overriding Pacific forearc. This earthquake demonstrates the seismogenic potential of extremely young subducting oceanic lithosphere, the ability of ruptures to traverse substantial geologic boundaries, and the consequences of complex coseismic slip for uplift and tsunamigenesis.

  5. Provenance and sediment-dispersal system in tectonically active rapidly evolving foreland basin, Western Interior

    SciTech Connect

    Khandaker, N.I.; Vondra, C.F.

    1989-03-01

    The Upper Cretaceous Frontier Formation, along the mobile edge of the Western Interior foreland basin, is composed mainly of clastic sediments and was deposited during the initial Late Cretaceous transgressive-regressive phases of the Western Interior seaway across Wyoming. The formation contains many persistent bentonite beds and several sandstone packages in its lower part and a thin, lenticular lithic wacke-polymictic conglomerate association at its upper contact (Torchlight Sandstone Member). Abundant granule to cobble-sized clasts of andesite, granite, chert, and quartzite are set in a poorly sorted sand-to-granule grade volcaniclastic matrix. There is a lithologic continuity of this volcaniclastic unit across the Bighorn Mountains into the Powder River basin. A high-energy distributary complex of sizable areal extent is invoked for the deposition of this linear conglomerate facies. Geochemical investigations of the whole-rock andesite clasts and bentonite allowed more precise definition of character, tectonic setting, and evolutionary stages of sedimentary distributive provinces. Bentonites and andesites are strongly enriched in strontium and barium, but only mildly enriched in heavy rare earth elements and high field-strength elements. These analyzed rocks have trace element characteristics similar in a general way to those of typical orogenic volcanics; they show some significant differences in detail. Composition of volcaniclasts and paleocurrent data indicate a proximal sediment source for the extrabasinal detritus within the Frontier Formation. The possibility of a contribution from a Mesozoic volcanic center in the neighborhood of southwestern Montana is strongly favored. The products of this volcanism constitute an assemblage of deep crustal to mantle( ) derived rocks, and their composition record time-integrated enrichment in light over heavy rare earth elements.

  6. Challenges in Developing Data Collection Systems in a Rapidly Evolving Higher Education Environment

    ERIC Educational Resources Information Center

    Borden, Victor M. H.; Calderon, Angel; Fourie, Neels; Lepori, Benedetto; Bonaccorsi, Andrea

    2013-01-01

    Efforts to develop common higher education data standards are expanding both within and across countries. The institutional research (IR) community plays a critical role in assuring that these efforts capture the diverse manifestations of the postsecondary and tertiary education systems and promote responsible comparisons. This chapter provides…

  7. Evolving force balance at Columbia Glacier, Alaska, during its rapid retreat

    USGS Publications Warehouse

    O'Neel, S.; Pfeffer, W.T.; Krimmel, R.; Meier, M.

    2005-01-01

    Changes in driving and resistive stresses play an essential role in governing the buoyancy forces that are important controls on the speed and irreversibility of tidewater glacier retreats. We describe changes in geometry, velocity, and strain rate and present a top-down force balance analysis performed over the lower reach of Columbia Glacier. Our analysis uses new measurements and estimates of basal topography and photogrammetric surface velocity measurements made between 1977 and 2001, while assuming depth-independent strain. Sensitivity tests show that the method is robust and insensitive to small changes in the calculation parameters. Spatial distributions of ice speed show little correspondence with driving stress. Instead, spatial patterns of ice speed exhibit a nonlinear correspondence with basal drag. Primary resistance to flow comes from basal drag, but lateral drag becomes increasingly more important throughout the retreat, which may account for observed increases in speed. Maximum basal drag is always located in a prominent constriction located ~12 km upstream from the preretreat terminus. Once the terminus retreated into deep water off the terminal moraine marking the modern maximum extent, the upstream location of this maximum basal drag helped to promote thinning and decrease effective pressure in the lower region by limiting replenishing ice flow from upstream. An increase in both ice velocity and calving resulted, initiating what appears to be an irreversible retreat. Copyright 2005 by the American Geophysical Union.

  8. Induced Seismicity: Balancing the Scientific Process With the Need for Rapid Communication of Evolving Seismic Hazards

    NASA Astrophysics Data System (ADS)

    Cochran, E. S.; Ellsworth, W. L.; Llenos, A. L.; Rubinstein, J. L.

    2014-12-01

    In this presentation, we outline the USGS response to dramatically increased earthquake activity in the central and eastern US, with a focus on Oklahoma. Using the November 2011 Prague, OK earthquake sequence as an example, we describe the tensions between the need to conduct thorough scientific investigations while providing timely information to local, state, and federal government agencies, and the public. In the early morning hours of November 5, 2011 a M4.8 earthquake struck near the town of Prague, Oklahoma and was followed by a M5.6 earthquake just over 20 hours later. The mainshock was widely felt across the central US, causing damage to homes close to the epicenter and injuring at least 2 people. Within hours of the initial event several portable instruments were installed and following the mainshock a larger seismic deployment was mounted (Keranen et al., 2013). A sizeable earthquake in the central or eastern US is always of scientific interest due to the dearth of seismic data available for assessing seismic hazard. The Prague sequence garnered especially strong scientific and public interest when a link between the sequence and injection of wastewater at several local deep wells was postulated. Therefore, there was a need to provide immediate information as it became available. However, in the first few days to months it was impossible to confidently confirm or refute whether the seismicity was linked to injection, but it was known that the foreshock occurred close to several deep injection wells and many of the events were shallow; thus, the sequence warranted further study. Over the course of the next few years, several studies built the case that the Prague sequence was likely induced by wastewater injection (Keranen et al., 2013; Sumy et al., 2014; McGarr, 2014) and additional studies suggested that the changes in seismicity throughout Oklahoma were not due to natural variations in seismicity rates (Llenos and Michael, 2013; Ellsworth, 2013). These studies changed the public discourse from providing primary information about the on-going earthquake sequences to how to mitigate the hazard associated with wastewater injection. And, scientific studies are now focused on how to include the impact of induced events within the National Seismic Hazard Maps (e.g. Peterson et al., 2014).

  9. Study of cell kinetics within evolving secondary Haversian systems.

    PubMed Central

    Jaworski, Z F; Hooper, C

    1980-01-01

    A study of the origin, proliferation rate and migration of cells within the secondary evolving Haversian systems was undertaken in young adult Beagle dogs. Autoradiographs of serial longitudinal sections prepared from rib biopsies taken from one hour to eleven days after the injection of tritiated thymidine were subjected to semiquantitative analysis as to the time of appearance, number, location and transformation of various labelled cells. Numerous labelled osteoblasts appeared early (at 14-24 hours) in the most proximal closing cone. With time, this zone was seen to have been left behind the advancing cutting cone and the successive generations of osteoblasts. The first labelled osteocytes were seen at nine days after injection, in the distal closing cone. Labelled nuclei within the osteoclasts were few and appeared late (none before 24 hours). It is apparent that each self renewing cell population within these systems (i.e. osteoclasts, osteoblasts and endothelial cells) derives from its own immediate precursor and evolves at its own speed. The mononuclear osteoclasts' precursors divide locally and infrequently and the turnover of osteoclastic nuclei appears to be slow; consequently their life span and that of the osteoclasts appears to be longer than the time of the observation, i.e. 11 days. The proliferation of osteoblasts' precursors and osteoblasts recruitment is rapid. The life span of osteoblasts was found to be indeterminate; some osteoblasts may become osteocytes within a few days while others may continue to deposit bone for several weeks. Since the recruitment of osteoclastic nuclei is slow while that of the osteoblasts is fast, it is unlikely that the osteoclasts in the sites of lamellar bone remodelling modulate into osteoblasts. Images Fig. 2(cont.) Fig. 2 Fig. 3(cont.) Fig. 3 Fig. 4 Fig. 5 PMID:7440406

  10. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity.

    PubMed

    Parra, Gabriel I; Squires, R Burke; Karangwa, Consolee K; Johnson, Jordan A; Lepore, Cara J; Sosnovtsev, Stanislav V; Green, Kim Y

    2017-01-01

    Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining "static") and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification ("static" versus "evolving"), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as "immunotypes". We propose that "immunotypes" and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population.

  11. NASA's Space Launch System: An Evolving Capability for Exploration

    NASA Technical Reports Server (NTRS)

    Creech, Stephen D.; Robinson, Kimberly 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 will propel 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.

  12. Simple Moving Average: A Method of Reporting Evolving Complication Rates.

    PubMed

    Harmsen, Samuel M; Chang, Yu-Hui H; Hattrup, Steven J

    2016-09-01

    Surgeons often cite published complication rates when discussing surgery with patients. However, these rates may not truly represent current results or an individual surgeon's experience with a given procedure. This study proposes a novel method to more accurately report current complication trends that may better represent the patient's potential experience: simple moving average. Reverse shoulder arthroplasty (RSA) is an increasingly popular and rapidly evolving procedure with highly variable reported complication rates. The authors used an RSA model to test and evaluate the usefulness of simple moving average. This study reviewed 297 consecutive RSA procedures performed by a single surgeon and noted complications in 50 patients (16.8%). Simple moving average for total complications as well as minor, major, acute, and chronic complications was then calculated using various lag intervals. These findings showed trends toward fewer total, major, and chronic complications over time, and these trends were represented best with a lag of 75 patients. Average follow-up within this lag was 26.2 months. Rates for total complications decreased from 17.3% to 8% at the most recent simple moving average. The authors' traditional complication rate with RSA (16.8%) is consistent with reported rates. However, the use of simple moving average shows that this complication rate decreased over time, with current trends (8%) markedly lower, giving the senior author a more accurate picture of his evolving complication trends with RSA. Compared with traditional methods, simple moving average can be used to better reflect current trends in complication rates associated with a surgical procedure and may better represent the patient's potential experience. [Orthopedics.2016; 39(5):e869-e876.].

  13. Chemically Induced Conditional Rescue of the Reduced Epidermal Fluorescence8 Mutant of Arabidopsis Reveals Rapid Restoration of Growth and Selective Turnover of Secondary Metabolite Pools1[C][OPEN

    PubMed Central

    Kim, Jeong Im; Ciesielski, Peter N.; Donohoe, Bryon S.; Chapple, Clint; Li, Xu

    2014-01-01

    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. PMID:24381065

  14. Ultra-fast in-situ X-ray studies of evolving columnar dendrites in solidifying steel weld pools

    NASA Astrophysics Data System (ADS)

    Mirihanage, W. U.; Di Michiel, M.; Mathiesen, R. H.

    2015-06-01

    High-brilliance polychromatic synchrotron radiation has been used to conduct in-situ studies of the solidification microstructure evolution during simulated welding. The welding simulations were realized by rapidly fusing ∼ 5 mm spot in Fe-Cr-Ni steel. During the solid- liquid-solid phase transformations, a section of the weld pool was placed in an incident 50-150 keV polychromatic synchrotron X-ray beam, in a near-horizontal position at a very low inclination angle. Multiple high-resolution 2D detectors with very high frame rates were utilized to capture time resolved X-ray diffraction data from suitably oriented solid dendrites evolving in the weld pool. Comprehensive analysis of the diffraction data revealed individual and overall dendritic growth characteristics and relevant melt and solid flow dynamics during weld pool solidification, which was completed within 1.5 s. Columnar dendrite tip velocities were estimated from the experimental data and during early stages of solidification were exceeded 4 mm/s. The most remarkable observation revealed through the time-resolved reciprocal space observations are correlated to significant tilting of columnar type dendrites at their root during solidification, presumably caused by convective currents in the weld pool. When the columnar dendrite tilting are transformed to respective metric linear tilting velocities at the dendrite tip; tilting velocities are found to be in the same order of magnitude as the columnar tip growth velocities, suggesting a highly transient nature of growth conditions.

  15. Evolving Digital Publishing Opportunities across Composition Studies

    ERIC Educational Resources Information Center

    Hawishler, Gail E.; Selfe, Cynthia L.

    2014-01-01

    In this article, the authors report since the early 1980s, the profession has seen plenty of changes in the arena of digital scholarly publishing: during this time, while the specific challenges have seldom remained the same, the presence and the pressures of rapid technological change endure. In fact, as an editorial team that has, in part,…

  16. Analysis of an evolving email network

    NASA Astrophysics Data System (ADS)

    Zhu, Chaopin; Kuh, Anthony; Wang, Juan; de Wilde, Philippe

    2006-10-01

    In this paper we study an evolving email network model first introduced by Wang and De Wilde, to the best of our knowledge. The model is analyzed by formulating the network topology as a random process and studying the dynamics of the process. Our analytical results show a number of steady state properties about the email traffic between different nodes and the aggregate networking behavior (i.e., degree distribution, clustering coefficient, average path length, and phase transition), and also confirm the empirical results obtained by Wang and De Wilde. We also conducted simulations confirming the analytical results. Extensive simulations were run to evaluate email traffic behavior at the link and network levels, phase transition phenomena, and also studying the behavior of email traffic in a hierarchical network. The methods established here are also applicable to many other practical networks including sensor networks and social networks.

  17. Pulmonary Sporotrichosis: An Evolving Clinical Paradigm.

    PubMed

    Aung, Ar K; Spelman, Denis W; Thompson, Philip J

    2015-10-01

    In recent decades, sporotrichosis, caused by thermally dimorphic fungi Sporothrix schenckii complex, has become an emerging infection in many parts of the world. Pulmonary infection with S. schenckii still remains relatively uncommon, possibly due to underrecognition. Pulmonary sporotrichosis presents with distinct clinical and radiological patterns in both immunocompetent and immunocompromised hosts and can often result in significant morbidity and mortality despite treatment. Current understanding regarding S. schenckii biology, epidemiology, immunopathology, clinical diagnostics, and treatment options has been evolving in the recent years with increased availability of molecular sequencing techniques. However, this changing knowledge has not yet been fully translated into a better understanding of the clinical aspects of pulmonary sporotrichosis, as such current management guidelines remain unsupported by high-level clinical evidence. This article examines recent advances in the knowledge of sporotrichosis and its application to the difficult challenges of managing pulmonary sporotrichosis.

  18. Evolving resistance among Gram-positive pathogens.

    PubMed

    Munita, Jose M; Bayer, Arnold S; Arias, Cesar A

    2015-09-15

    Antimicrobial therapy is a key component of modern medical practice and a cornerstone for the development of complex clinical interventions in critically ill patients. Unfortunately, the increasing problem of antimicrobial resistance is now recognized as a major public health threat jeopardizing the care of thousands of patients worldwide. Gram-positive pathogens exhibit an immense genetic repertoire to adapt and develop resistance to virtually all antimicrobials clinically available. As more molecules become available to treat resistant gram-positive infections, resistance emerges as an evolutionary response. Thus, antimicrobial resistance has to be envisaged as an evolving phenomenon that demands constant surveillance and continuous efforts to identify emerging mechanisms of resistance to optimize the use of antibiotics and create strategies to circumvent this problem. Here, we will provide a broad perspective on the clinical aspects of antibiotic resistance in relevant gram-positive pathogens with emphasis on the mechanistic strategies used by these organisms to avoid being killed by commonly used antimicrobial agents.

  19. The distances of highly evolved planetary nebulae

    NASA Astrophysics Data System (ADS)

    Phillips, J. P.

    2005-02-01

    The central stars of highly evolved planetary nebulae (PNe) are expected to have closely similar absolute visual magnitudes MV. This enables us to determine approximate distances to these sources where one knows their central star visual magnitudes, and levels of extinction. We find that such an analysis implies values of D which are similar to those determined by Phillips; Cahn, Kaler & Stanghellin; Acker, and Daub. However, our distances are very much smaller than those of Zhang; Bensby & Lundstrom, and van de Steene & Zijlstra. The reasons for these differences are discussed, and can be traced to errors in the assumed relation between brightness temperature and radius. Finally, we determine that the binary companions of such stars can be no brighter than MV~ 6mag, implying a spectral type of K0 or later in the case of main-sequence stars.

  20. Synchronization in evolving snowdrift game model

    NASA Astrophysics Data System (ADS)

    Huang, Y.; Wu, L.; Zhu, S. Q.

    2009-06-01

    The interaction between the evolution of the game and the underlying network structure with evolving snowdrift game model is investigated. The constructed network follows a power-law degree distribution typically showing scale-free feature. The topological features of average path length, clustering coefficient, degree-degree correlations and the dynamical feature of synchronizability are studied. The synchronizability of the constructed networks changes by the interaction. It will converge to a certain value when sufficient new nodes are added. It is found that initial payoffs of nodes greatly affect the synchronizability. When initial payoffs for players are equal, low common initial payoffs may lead to more heterogeneity of the network and good synchronizability. When initial payoffs follow certain distributions, better synchronizability is obtained compared to equal initial payoff. The result is also true for phase synchronization of nonidentical oscillators.

  1. Design Space Issues for Intrinsic Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    Hereford, James; Gwaltney, David

    2004-01-01

    This paper discuss the problem of increased programming time for intrinsic evolvable hardware (EHW) as the complexity of the circuit grows. We develop equations for the size of the population, n, and the number of generations required for the population to converge, ngen, based on L, the length of the programming string. We show that the processing time of the computer becomes negligible for intrinsic EHW since the selection/crossover/mutation steps are only done once per generation, suggesting there is room for use of more complex evolutionary algorithms m intrinsic EHW. F i y , we review the state of the practice and discuss the notion of a system design approach for intrinsic EHW.

  2. Evolving unipolar memristor spiking neural networks

    NASA Astrophysics Data System (ADS)

    Howard, David; Bull, Larry; De Lacy Costello, Ben

    2015-10-01

    Neuromorphic computing - brain-like computing in hardware - typically requires myriad complimentary metal oxide semiconductor spiking neurons interconnected by a dense mesh of nanoscale plastic synapses. Memristors are frequently cited as strong synapse candidates due to their statefulness and potential for low-power implementations. To date, plentiful research has focused on the bipolar memristor synapse, which is capable of incremental weight alterations and can provide adaptive self-organisation under a Hebbian learning scheme. In this paper, we consider the unipolar memristor synapse - a device capable of non-Hebbian switching between only two states (conductive and resistive) through application of a suitable input voltage - and discuss its suitability for neuromorphic systems. A self-adaptive evolutionary process is used to autonomously find highly fit network configurations. Experimentation on two robotics tasks shows that unipolar memristor networks evolve task-solving controllers faster than both bipolar memristor networks and networks containing constant non-plastic connections whilst performing at least comparably.

  3. Life cycle planning: An evolving concept

    SciTech Connect

    Moore, P.J.R.; Gorman, I.G.

    1994-12-31

    Life-cycle planning is an evolving concept in the management of oil and gas projects. BHP Petroleum now interprets this idea to include all development planning from discovery and field appraisal to final abandonment and includes safety, environmental, technical, plant, regulatory, and staffing issues. This article describes in the context of the Timor Sea, how despite initial successes and continuing facilities upgrades, BHPP came to perceive that current operations could be the victim of early development successes, particularly in the areas of corrosion and maintenance. The search for analogies elsewhere lead to the UK North Sea, including the experiences of Britoil and BP, both of which performed detailed Life of Field studies in the later eighties. These materials have been used to construct a format and content for total Life-cycle plans in general and the social changes required to ensure their successful application in Timor Sea operations and deployment throughout Australia.

  4. Modelling of the Evolving Stable Boundary Layer

    NASA Astrophysics Data System (ADS)

    Sorbjan, Zbigniew

    2014-06-01

    A single-column model of the evolving stable boundary layer (SBL) is tested for self-similar properties of the flow and effects of ambient forcing. The turbulence closure of the model is diagnostic, based on the K-theory approach, with a semi-empirical form of the mixing length, and empirical stability functions of the Richardson number. The model results, expressed in terms of local similarity scales, are universal functions, satisfied in the entire SBL. Based on similarity expression, a realizability condition is derived for the minimum allowable turbulent heat flux in the SBL. Numerical experiments show that the development of "horse-shoe" shaped, fixed-elevation hodographs in the interior of the SBL around sunrise is controlled by effects imposed by surface thermal forcing.

  5. Language as a coordination tool evolves slowly

    PubMed Central

    2016-01-01

    Social living ultimately depends on coordination between group members, and communication is necessary to make this possible. We suggest that this might have been the key selection pressure acting on the evolution of language in humans and use a behavioural coordination model to explore the impact of communication efficiency on social group coordination. We show that when language production is expensive but there is an individual benefit to the efficiency with which individuals coordinate their behaviour, the evolution of efficient communication is selected for. Contrary to some views of language evolution, the speed of evolution is necessarily slow because there is no advantage in some individuals evolving communication abilities that much exceed those of the community at large. However, once a threshold competence has been achieved, evolution of higher order language skills may indeed be precipitate. PMID:28083091

  6. Regulatory mechanisms link phenotypic plasticity to evolvability.

    PubMed

    van Gestel, Jordi; Weissing, Franz J

    2016-04-18

    Organisms have a remarkable capacity to respond to environmental change. They can either respond directly, by means of phenotypic plasticity, or they can slowly adapt through evolution. Yet, how phenotypic plasticity links to evolutionary adaptability is largely unknown. Current studies of plasticity tend to adopt a phenomenological reaction norm (RN) approach, which neglects the mechanisms underlying plasticity. Focusing on a concrete question - the optimal timing of bacterial sporulation - we here also consider a mechanistic approach, the evolution of a gene regulatory network (GRN) underlying plasticity. Using individual-based simulations, we compare the RN and GRN approach and find a number of striking differences. Most importantly, the GRN model results in a much higher diversity of responsive strategies than the RN model. We show that each of the evolved strategies is pre-adapted to a unique set of unseen environmental conditions. The regulatory mechanisms that control plasticity therefore critically link phenotypic plasticity to the adaptive potential of biological populations.

  7. Evolving surgical approaches in liver transplantation.

    PubMed

    Petrowsky, Henrik; Busuttil, Ronald W

    2009-02-01

    The growing discrepancy between the need and the availability of donor livers has resulted in evolving surgical approaches in liver transplantation during the last two decades to expand the donor pool. One approach is to transplant partial grafts, obtained either from a living donor or splitting a cadaveric donor liver. For both surgical methods, it is important to obtain a minimal viable graft volume to prevent small-for-size syndrome and graft failure. This minimal volume, expressed as graft-to-whole body ratio, must be between 0.8 and 1%. Living donor liver transplantation (LDLT) became the primary transplant option in many Asian countries and is increasingly performed as an adjunct transplant option in countries with low donation rates. Split liver transplantation (SLT) is a surgical method that creates two allografts from one deceased donor. The most widely used splitting technique is the division of the liver into a left lateral sectoral graft (segments 2 and 3) for a pediatric patient and a right trisegmental graft (segments 1 and 4 to 8) for an adult patient. Both LDLT and SLT are also important and established methods for the treatment of pediatric patients. Another evolving surgical approach is auxiliary liver transplantation, which describes the transplanting a whole or partial graft with preservation of the partial native liver. This bridging technique is applied in patients with fulminate liver failure and should allow the regeneration of the injured liver with the potential to discontinue immunosuppression. Other methods such as xenotransplantation, as well as hepatocyte and stem cell transplantation, are promising approaches that are still in experimental phases.

  8. How evolved psychological mechanisms empower cultural group selection.

    PubMed

    Henrich, Joseph; Boyd, Robert

    2016-01-01

    Driven by intergroup competition, social norms, beliefs, and practices can evolve in ways that more effectively tap into a wide variety of evolved psychological mechanisms to foster group-beneficial behavior. The more powerful such evolved mechanisms are, the more effectively culture can potentially harness and manipulate them to generate greater phenotypic variation across groups, thereby fueling cultural group selection.

  9. Genetics of Rapid and Extreme Size Evolution in Island Mice.

    PubMed

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

    2015-09-01

    Organisms on islands provide a revealing window into the process of adaptation. Populations that colonize islands often evolve substantial differences in body size from their mainland relatives. Although the ecological drivers of this phenomenon have received considerable attention, its genetic basis remains poorly understood. We use house mice (subspecies: Mus musculus domesticus) from remote Gough Island to provide a genetic portrait of rapid and extreme size evolution. In just a few hundred generations, Gough Island mice evolved the largest body size among wild house mice from around the world. Through comparisons with a smaller-bodied wild-derived strain from the same subspecies (WSB/EiJ), we demonstrate that Gough Island mice achieve their exceptional body weight primarily by growing faster during the 6 weeks after birth. We use genetic mapping in large F(2) intercrosses between Gough Island mice and WSB/EiJ to identify 19 quantitative trait loci (QTL) responsible for the evolution of 16-week weight trajectories: 8 QTL for body weight and 11 QTL for growth rate. QTL exhibit modest effects that are mostly additive. We conclude that body size evolution on islands can be genetically complex, even when substantial size changes occur rapidly. In comparisons to published studies of laboratory strains of mice that were artificially selected for divergent body sizes, we discover that the overall genetic profile of size evolution in nature and in the laboratory is similar, but many contributing loci are distinct. Our results underscore the power of genetically characterizing the entire growth trajectory in wild populations and lay the foundation necessary for identifying the mutations responsible for extreme body size evolution in nature.

  10. Genetics of Rapid and Extreme Size Evolution in Island Mice

    PubMed Central

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

    2015-01-01

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

  11. Genetic structure and evolved malaria resistance in Hawaiian honeycreepers

    USGS Publications Warehouse

    Foster, J.T.; Woodworth, B.L.; Eggert, L.E.; Hart, P.J.; Palmer, D.; Duffy, D.C.; Fleischer, R.C.

    2007-01-01

    Infectious diseases now threaten wildlife populations worldwide but population recovery following local extinction has rarely been observed. In such a case, do resistant individuals recolonize from a central remnant population, or do they spread from small, perhaps overlooked, populations of resistant individuals? Introduced avian malaria (Plasmodium relictum) has devastated low-elevation populations of native birds in Hawaii, but at least one species (Hawaii amakihi, Hemignathus virens) that was greatly reduced at elevations below about 1000 m tolerates malaria and has initiated a remarkable and rapid recovery. We assessed mitochondrial and nuclear DNA markers from amakihi and two other Hawaiian honeycreepers, apapane (Himatione sanguinea) and iiwi (Vestiaria coccinea), at nine primary study sites from 2001 to 2003 to determine the source of re-establishing birds. In addition, we obtained sequences from tissue from amakihi museum study skins (1898 and 1948-49) to assess temporal changes in allele distributions. We found that amakihi in lowland areas are, and have historically been, differentiated from birds at high elevations and had unique alleles retained through time; that is, their genetic signature was not a subset of the genetic variation at higher elevations. We suggest that high disease pressure rapidly selected for resistance to malaria at low elevation, leaving small pockets of resistant birds, and this resistance spread outward from the scattered remnant populations. Low-elevation amakihi are currently isolated from higher elevations (> 1000 m) where disease emergence and transmission rates appear to vary seasonally and annually. In contrast to results from amakihi, no genetic differentiation between elevations was found in apapane and iiwi, indicating that slight variation in genetic or life-history attributes can determine disease resistance and population recovery. Determining the conditions that allow for the development of resistance to disease is

  12. The Evolving Structure of Young Volcanic Eruption Clouds

    NASA Astrophysics Data System (ADS)

    Carn, S. A.; Bursik, M. I.

    2015-12-01

    Processes acting in nascent volcanic clouds within seconds to hours of eruption (e.g., ash aggregation, ice nucleation, gravity waves) set the stage for subsequent advection and diffusion of volcanic ash, hence strongly influence aviation hazards and atmospheric impacts, but are very difficult to observe. Young plumes initially spread by gravity in the crosswind direction due to density differences with the surrounding stratified atmosphere. Subsequently, plumes lose their density contrast with the atmosphere and are advected as lenses of aerosol and gas, slowly thinning, spreading and dispersing as shearing and small scale turbulence act at their margins, and as fine ash settles out. Since 2006, satellite observations from NASA's A-Train constellation, including the CALIOP lidar and CloudSat radar, have provided tantalizing glimpses of young volcanic clouds in the first few hours of atmospheric residence. These unique observations, although spatially limited, provide insight into the evolving structure of young volcanic clouds from an optically thick, vertically extensive initial state to thin layers confined to a limited altitude range. Layered volcanic clouds may develop due to the existence of alternating turbulent and stable layers in the free troposphere and stratosphere. Turbulent layers retain particles longer than do quiescent layers because the turbulence retains particles in suspension. Particles fall more rapidly through the quiescent layers by single particle settling, or more rapidly because of convective sedimentation. The result is a distinct, banded ash cloud structure. We present A-Train satellite observations of volcanic clouds at various stages of evolution from several recent eruptions (including Kelut, Redoubt, Chaitén, Eyjafjallajökull, Okmok and Kasatochi) and also show the results of preliminary model simulations of the development of volcanic cloud layering.

  13. The evolving quality of frictional contact with graphene.

    PubMed

    Li, Suzhi; Li, Qunyang; Carpick, Robert W; Gumbsch, Peter; Liu, Xin Z; Ding, Xiangdong; Sun, Jun; Li, Ju

    2016-11-24

    Graphite and other lamellar materials are used as dry lubricants for macroscale metallic sliding components and high-pressure contacts. It has been shown experimentally that monolayer graphene exhibits higher friction than multilayer graphene and graphite, and that this friction increases with continued sliding, but the mechanism behind this remains subject to debate. It has long been conjectured that the true contact area between two rough bodies controls interfacial friction. The true contact area, defined for example by the number of atoms within the range of interatomic forces, is difficult to visualize directly but characterizes the quantity of contact. However, there is emerging evidence that, for a given pair of materials, the quality of the contact can change, and that this can also strongly affect interfacial friction. Recently, it has been found that the frictional behaviour of two-dimensional materials exhibits traits unlike those of conventional bulk materials. This includes the abovementioned finding that for few-layer two-dimensional materials the static friction force gradually strengthens for a few initial atomic periods before reaching a constant value. Such transient behaviour, and the associated enhancement of steady-state friction, diminishes as the number of two-dimensional layers increases, and was observed only when the two-dimensional material was loosely adhering to a substrate. This layer-dependent transient phenomenon has not been captured by any simulations. Here, using atomistic simulations, we reproduce the experimental observations of layer-dependent friction and transient frictional strengthening on graphene. Atomic force analysis reveals that the evolution of static friction is a manifestation of the natural tendency for thinner and less-constrained graphene to re-adjust its configuration as a direct consequence of its greater flexibility. That is, the tip atoms become more strongly pinned, and show greater synchrony in their stick

  14. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  15. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder.

    PubMed

    Ziats, Mark N; Rennert, Owen M

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome.

  16. Evolving Requirements for Magnetic Tape Data Storage Systems

    NASA Technical Reports Server (NTRS)

    Gniewek, John J.

    1996-01-01

    Magnetic tape data storage systems have evolved in an environment where the major applications have been back-up/restore, disaster recovery, and long term archive. Coincident with the rapidly improving price-performance of disk storage systems, the prime requirements for tape storage systems have remained: (1) low cost per MB, (2) a data rate balanced to the remaining system components. Little emphasis was given to configuring the technology components to optimize retrieval of the stored data. Emerging new applications such as network attached high speed memory (HSM), and digital libraries, place additional emphasis and requirements on the retrieval of the stored data. It is therefore desirable to consider the system to be defined both by STorage And Retrieval System (STARS) requirements. It is possible to provide comparative performance analysis of different STARS by incorporating parameters related to (1) device characteristics, and (2) application characteristics in combination with queuing theory analysis. Results of these analyses are presented here in the form of response time as a function of system configuration for two different types of devices and for a variety of applications.

  17. Meiosis evolves: adaptation to external and internal environments.

    PubMed

    Bomblies, Kirsten; Higgins, James D; Yant, Levi

    2015-10-01

    306 I. 306 II. 307 III. 312 IV. 317 V. 318 319 References 319 SUMMARY: Meiosis is essential for the fertility of most eukaryotes and its structures and progression are conserved across kingdoms. Yet many of its core proteins show evidence of rapid or adaptive evolution. What drives the evolution of meiosis proteins? How can constrained meiotic processes be modified in response to challenges without compromising their essential functions? In surveying the literature, we found evidence of two especially potent challenges to meiotic chromosome segregation that probably necessitate adaptive evolutionary responses: whole-genome duplication and abiotic environment, especially temperature. Evolutionary solutions to both kinds of challenge are likely to involve modification of homologous recombination and synapsis, probably via adjustments of core structural components important in meiosis I. Synthesizing these findings with broader patterns of meiosis gene evolution suggests that the structural components of meiosis coevolve as adaptive modules that may change in primary sequence and function while maintaining three-dimensional structures and protein interactions. The often sharp divergence of these genes among species probably reflects periodic modification of entire multiprotein complexes driven by genomic or environmental changes. We suggest that the pressures that cause meiosis to evolve to maintain fertility may cause pleiotropic alterations of global crossover rates. We highlight several important areas for future research.

  18. Mitotic Exit Control as an Evolved Complex System

    SciTech Connect

    Bosl, W; Li, R

    2005-04-25

    The exit from mitosis is the last critical decision a cell has to make during a division cycle. A complex regulatory system has evolved to evaluate the success of mitotic events and control this decision. Whereas outstanding genetic work in yeast has led to rapid discovery of a large number of interacting genes involved in the control of mitotic exit, it has also become increasingly difficult to comprehend the logic and mechanistic features embedded in the complex molecular network. Our view is that this difficulty stems in part from the attempt to explain mitotic exit control using concepts from traditional top-down engineering design, and that exciting new results from evolutionary engineering design applied to networks and electronic circuits may lend better insights. We focus on four particularly intriguing features of the mitotic exit control system: the two-stepped release of Cdc14; the self-activating nature of Tem1 GTPase; the spatial sensor associated with the spindle pole body; and the extensive redundancy in the mitotic exit network. We attempt to examine these design features from the perspective of evolutionary design and complex system engineering.

  19. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder

    PubMed Central

    Ziats, Mark N.; Rennert, Owen M.

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome. PMID:27200076

  20. Advances in the Study of Moving Sediments and Evolving Seabeds

    NASA Astrophysics Data System (ADS)

    Davies, Alan G.; Thorne, Peter D.

    2008-01-01

    Sands and mud are continually being transported around the world’s coastal seas due to the action of tides, wind and waves. The transport of these sediments modifies the boundary between the land and the sea, changing and reshaping its form. Sometimes the nearshore bathymetry evolves slowly over long time periods, at other times more rapidly due to natural episodic events or the introduction of manmade structures at the shoreline. For over half a century we have been trying to understand the physics of sediment transport processes and formulate predictive models. Although significant progress has been made, our capability to forecast the future behaviour of the coastal zone from basic principles is still relatively poor. However, innovative acoustic techniques for studying the fundamentals of sediment movement experimentally are now providing new insights, and it is expected that such observations, coupled with developing theoretical works, will allow us to take further steps towards the goal of predicting the evolution of coastlines and coastal bathymetry. This paper presents an overview of our existing predictive capabilities, primarily in the field of non-cohesive sediment transport, and highlights how new acoustic techniques are enabling our modelling efforts to achieve greater sophistication and accuracy. The paper is aimed at coastal scientists and managers seeking to understand how detailed physical studies can contribute to the improvement of coastal area models and, hence, inform coastal zone management strategies.

  1. Epidemic spreading on evolving signed networks

    NASA Astrophysics Data System (ADS)

    Saeedian, M.; Azimi-Tafreshi, N.; Jafari, G. R.; Kertesz, J.

    2017-02-01

    Most studies of disease spreading consider the underlying social network as obtained without the contagion, though epidemic influences people's willingness to contact others: A "friendly" contact may be turned to "unfriendly" to avoid infection. We study the susceptible-infected disease-spreading model on signed networks, in which each edge is associated with a positive or negative sign representing the friendly or unfriendly relation between its end nodes. In a signed network, according to Heider's theory, edge signs evolve such that finally a state of structural balance is achieved, corresponding to no frustration in physics terms. However, the danger of infection affects the evolution of its edge signs. To describe the coupled problem of the sign evolution and disease spreading, we generalize the notion of structural balance by taking into account the state of the nodes. We introduce an energy function and carry out Monte Carlo simulations on complete networks to test the energy landscape, where we find local minima corresponding to the so-called jammed states. We study the effect of the ratio of initial friendly to unfriendly connections on the propagation of disease. The steady state can be balanced or a jammed state such that a coexistence occurs between susceptible and infected nodes in the system.

  2. The evolved function of the oedipal conflict.

    PubMed

    Josephs, Lawrence

    2010-08-01

    Freud based his oedipal theory on three clinical observations of adult romantic relationships: (1) Adults tend to split love and lust; (2) There tend to be sex differences in the ways that men and women split love and lust; (3) Adult romantic relationships are unconsciously structured by the dynamics of love triangles in which dramas of seduction and betrayal unfold. Freud believed that these aspects of adult romantic relationships were derivative expressions of a childhood oedipal conflict that has been repressed. Recent research conducted by evolutionary psychologists supports many of Freud's original observations and suggests that Freud's oedipal conflict may have evolved as a sexually selected adaptation for reproductive advantage. The evolution of bi-parental care based on sexually exclusive romantic bonds made humans vulnerable to the costs of sexual infidelity, a situation of danger that seriously threatens monogamous bonds. A childhood oedipal conflict enables humans to better adapt to this longstanding evolutionary problem by providing the child with an opportunity to develop working models of love triangles. On the one hand, the oedipal conflict facilitates monogamous resolutions by creating intense anxiety about the dangers of sexual infidelity and mate poaching. On the other hand, the oedipal conflict in humans may facilitate successful cheating and mate poaching by cultivating a talent for hiding our true sexual intentions from others and even from ourselves. The oedipal conflict in humans may be disguised by evolutionary design in order to facilitate tactical deception in adult romantic relationships.

  3. Evolving application of biomimetic nanostructured hydroxyapatite

    PubMed Central

    Roveri, Norberto; Iafisco, Michele

    2010-01-01

    By mimicking Nature, we can design and synthesize inorganic smart materials that are reactive to biological tissues. These smart materials can be utilized to design innovative third-generation biomaterials, which are able to not only optimize their interaction with biological tissues and environment, but also mimic biogenic materials in their functionalities. The biomedical applications involve increasing the biomimetic levels from chemical composition, structural organization, morphology, mechanical behavior, nanostructure, and bulk and surface chemical–physical properties until the surface becomes bioreactive and stimulates cellular materials. The chemical–physical characteristics of biogenic hydroxyapatites from bone and tooth have been described, in order to point out the elective sides, which are important to reproduce the design of a new biomimetic synthetic hydroxyapatite. This review outlines the evolving applications of biomimetic synthetic calcium phosphates, details the main characteristics of bone and tooth, where the calcium phosphates are present, and discusses the chemical–physical characteristics of biomimetic calcium phosphates, methods of synthesizing them, and some of their biomedical applications. PMID:24198477

  4. Evolving Galaxies in a Hierachical Universe

    NASA Astrophysics Data System (ADS)

    Hahn, Changhoon

    2017-01-01

    Observations of galaxies using large surveys (SDSS, COSMOS, PRIMUS, etc.) have firmly established a global view of galaxy properties out to z~1. Galaxies are broadly divided into two classes: blue, typically disk-like star forming galaxies and red, typically elliptical quiescent ones with little star formation. The star formation rates (SFR) and stellar masses of star forming galaxies form an empirical relationship referred to as the "star formation main sequence". Over cosmic time, this sequence undergoes significant decline in SFR and causes the overall cosmic star formation decline. Simultaneously, physical processes cause significant fractions of star forming galaxies to "quench" their star formation. Hierarchical structure formation and cosmological models provide precise predictions of the evolution of the underying dark matter, which serve as the foundation for these detailed trends and their evolution. Whatever trends we observe in galaxy properties can be interpreted within the narrative of the underlying dark matter and halo occupation framework. More importantly, through careful statistical treatment and precise measurements, this connection can be utilized to better constrain and understand key elements of galaxy evolution. In this spirit, for my dissertation I connect observations of evolving galaxy properties to the framework of the hierarchical Universe and use it to better understand physical processes responsible for the cessation of star formation in galaxies. For instance, through this approach, I constrain the quenching timescale of central galaxies and find that they are significantly longer than the quenching timescale of satellite galaxies.

  5. On the Discovery of Evolving Truth.

    PubMed

    Li, Yaliang; Li, Qi; Gao, Jing; Su, Lu; Zhao, Bo; Fan, Wei; Han, Jiawei

    2015-08-01

    In the era of big data, information regarding the same objects can be collected from increasingly more sources. Unfortunately, there usually exist conflicts among the information coming from different sources. To tackle this challenge, truth discovery, i.e., to integrate multi-source noisy information by estimating the reliability of each source, has emerged as a hot topic. In many real world applications, however, the information may come sequentially, and as a consequence, the truth of objects as well as the reliability of sources may be dynamically evolving. Existing truth discovery methods, unfortunately, cannot handle such scenarios. To address this problem, we investigate the temporal relations among both object truths and source reliability, and propose an incremental truth discovery framework that can dynamically update object truths and source weights upon the arrival of new data. Theoretical analysis is provided to show that the proposed method is guaranteed to converge at a fast rate. The experiments on three real world applications and a set of synthetic data demonstrate the advantages of the proposed method over state-of-the-art truth discovery methods.

  6. Women's oral health: the evolving science.

    PubMed

    Sinkford, Jeanne C; Valachovic, Richard W; Harrison, Sonja G

    2008-02-01

    The evidence base for women's oral health is emerging from legislative action, clinical research, and survey documentation. The Women's Health in the Dental School Curriculum study (1999) followed a similar study (1996) of medical school curricula. Both of these major efforts resulted from statutory mandates in the National Institutes of Health Revitalization Act of 1993 (updated October 2000). A major study of the Institute of Medicine (IOM) National Academy of Sciences in 2001 concluded that "the study of sex differences is evolving into a mature science." This IOM study documented the scientific basis for gender-related policy and research and challenged the dental research enterprise to conduct collaborative, cross-disciplinary research on gender-related issues in oral health, disease, and disparities. This report chronicles some of the factors that have and continue to influence concepts of women's oral health in dental education, research, and practice. Gender issues related to women's health are no longer restricted to reproductive issues but are being considered across the life span and include psychosocial factors that impact women's health and treatment outcomes.

  7. Speciation genetics: current status and evolving approaches

    PubMed Central

    Wolf, Jochen B. W.; Lindell, Johan; Backström, Niclas

    2010-01-01

    The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues. PMID:20439277

  8. Extreme insular dwarfism evolved in a mammoth.

    PubMed

    Herridge, Victoria L; Lister, Adrian M

    2012-08-22

    The insular dwarfism seen in Pleistocene elephants has come to epitomize the island rule; yet our understanding of this phenomenon is hampered by poor taxonomy. For Mediterranean dwarf elephants, where the most extreme cases of insular dwarfism are observed, a key systematic question remains unresolved: are all taxa phyletic dwarfs of a single mainland species Palaeoloxodon antiquus (straight-tusked elephant), or are some referable to Mammuthus (mammoths)? Ancient DNA and geochronological evidence have been used to support a Mammuthus origin for the Cretan 'Palaeoloxodon' creticus, but these studies have been shown to be flawed. On the basis of existing collections and recent field discoveries, we present new, morphological evidence for the taxonomic status of 'P'. creticus, and show that it is indeed a mammoth, most probably derived from Early Pleistocene Mammuthus meridionalis or possibly Late Pliocene Mammuthus rumanus. We also show that Mammuthus creticus is smaller than other known insular dwarf mammoths, and is similar in size to the smallest dwarf Palaeoloxodon species from Sicily and Malta, making it the smallest mammoth species known to have existed. These findings indicate that extreme insular dwarfism has evolved to a similar degree independently in two elephant lineages.

  9. Consensus in evolving networks of mobile agents

    NASA Astrophysics Data System (ADS)

    Baronchelli, Andrea; Díaz-Guilera, Albert

    2012-02-01

    Populations of mobile and communicating agents describe a vast array of technological and natural systems, ranging from sensor networks to animal groups. Here, we investigate how a group-level agreement may emerge in the continuously evolving networks defined by the local interactions of the moving individuals. We adopt a general scheme of motion in two dimensions and we let the individuals interact through the minimal naming game, a prototypical scheme to investigate social consensus. We distinguish different regimes of convergence determined by the emission range of the agents and by their mobility, and we identify the corresponding scaling behaviors of the consensus time. In the same way, we rationalize also the behavior of the maximum memory used during the convergence process, which determines the minimum cognitive/storage capacity needed by the individuals. Overall, we believe that the simple and general model presented in this talk can represent a helpful reference for a better understanding of the behavior of populations of mobile agents.

  10. Metapopulation capacity of evolving fluvial landscapes

    NASA Astrophysics Data System (ADS)

    Bertuzzo, Enrico; Rodriguez-Iturbe, Ignacio; Rinaldo, Andrea

    2015-04-01

    The form of fluvial landscapes is known to attain stationary network configurations that settle in dynamically accessible minima of total energy dissipation by landscape-forming discharges. Recent studies have highlighted the role of the dendritic structure of river networks in controlling population dynamics of the species they host and large-scale biodiversity patterns. Here, we systematically investigate the relation between energy dissipation, the physical driver for the evolution of river networks, and the ecological dynamics of their embedded biota. To that end, we use the concept of metapopulation capacity, a measure to link landscape structures with the population dynamics they host. Technically, metapopulation capacity is the leading eigenvalue λM of an appropriate "landscape" matrix subsuming whether a given species is predicted to persist in the long run. λM can conveniently be used to rank different landscapes in terms of their capacity to support viable metapopulations. We study how λM changes in response to the evolving network configurations of spanning trees. Such sequence of configurations is theoretically known to relate network selection to general landscape evolution equations through imperfect searches for dynamically accessible states frustrated by the vagaries of Nature. Results show that the process shaping the metric and the topological properties of river networks, prescribed by physical constraints, leads to a progressive increase in the corresponding metapopulation capacity and therefore on the landscape capacity to support metapopulations—with implications on biodiversity in fluvial ecosystems.

  11. Tearing Mode Stability of Evolving Toroidal Equilibria

    NASA Astrophysics Data System (ADS)

    Pletzer, A.; McCune, D.; Manickam, J.; Jardin, S. C.

    2000-10-01

    There are a number of toroidal equilibrium (such as JSOLVER, ESC, EFIT, and VMEC) and transport codes (such as TRANSP, BALDUR, and TSC) in our community that utilize differing equilibrium representations. There are also many heating and current drive (LSC and TORRAY), and stability (PEST1-3, GATO, NOVA, MARS, DCON, M3D) codes that require this equilibrium information. In an effort to provide seamless compatibility between the codes that produce and need these equilibria, we have developed two Fortran 90 modules, MEQ and XPLASMA, that serve as common interfaces between these two classes of codes. XPLASMA provides a common equilibrium representation for the heating and current drive applications while MEQ provides common equilibrium and associated metric information needed by MHD stability codes. We illustrate the utility of this approach by presenting results of PEST-3 tearing stability calculations of an NSTX discharge performed on profiles provided by the TRANSP code. Using the MEQ module, the TRANSP equilibrium data are stored in a Fortran 90 derived type and passed to PEST3 as a subroutine argument. All calculations are performed on the fly, as the profiles evolve.

  12. Origins of stereoselectivity in evolved ketoreductases.

    PubMed

    Noey, Elizabeth L; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W; Tang, Yi; Houk, Kendall N

    2015-12-22

    Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP(+)-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation.

  13. Origins of stereoselectivity in evolved ketoreductases

    PubMed Central

    Noey, Elizabeth L.; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M.; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W.; Tang, Yi; Houk, Kendall N.

    2015-01-01

    Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP+-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation. PMID:26644568

  14. Evolving paradigms in multifocal breast cancer.

    PubMed

    Salgado, Roberto; Aftimos, Philippe; Sotiriou, Christos; Desmedt, Christine

    2015-04-01

    The 7th edition of the TNM defines multifocal breast cancer as multiple simultaneous ipsilateral and synchronous breast cancer lesions, provided they are macroscopically distinct and measurable using current traditional pathological and clinical tools. According to the College of American Pathologists (CAP), the characterization of only the largest lesion is considered sufficient, unless the grade and/or histology are different between the lesions. Here, we review three potentially clinically relevant aspects of multifocal breast cancers: first, the importance of a different intrinsic breast cancer subtype of the various lesions; second, the emerging awareness of inter-lesion heterogeneity; and last but not least, the potential introduction of bias in clinical trials due to the unrecognized biological diversity of these cancers. Although the current strategy to assess the lesion with the largest diameter has clearly its advantages in terms of costs and feasibility, this recommendation may not be sustainable in time and might need to be adapted to be compliant with new evolving paradigms in breast cancer.

  15. Speciation genetics: current status and evolving approaches.

    PubMed

    Wolf, Jochen B W; Lindell, Johan; Backström, Niclas

    2010-06-12

    The view of species as entities subjected to natural selection and amenable to change put forth by Charles Darwin and Alfred Wallace laid the conceptual foundation for understanding speciation. Initially marred by a rudimental understanding of hereditary principles, evolutionists gained appreciation of the mechanistic underpinnings of speciation following the merger of Mendelian genetic principles with Darwinian evolution. Only recently have we entered an era where deciphering the molecular basis of speciation is within reach. Much focus has been devoted to the genetic basis of intrinsic postzygotic isolation in model organisms and several hybrid incompatibility genes have been successfully identified. However, concomitant with the recent technological advancements in genome analysis and a newfound interest in the role of ecology in the differentiation process, speciation genetic research is becoming increasingly open to non-model organisms. This development will expand speciation research beyond the traditional boundaries and unveil the genetic basis of speciation from manifold perspectives and at various stages of the splitting process. This review aims at providing an extensive overview of speciation genetics. Starting from key historical developments and core concepts of speciation genetics, we focus much of our attention on evolving approaches and introduce promising methodological approaches for future research venues.

  16. An evolving model of online bipartite networks

    NASA Astrophysics Data System (ADS)

    Zhang, Chu-Xu; Zhang, Zi-Ke; Liu, Chuang

    2013-12-01

    Understanding the structure and evolution of online bipartite networks is a significant task since they play a crucial role in various e-commerce services nowadays. Recently, various attempts have been tried to propose different models, resulting in either power-law or exponential degree distributions. However, many empirical results show that the user degree distribution actually follows a shifted power-law distribution, the so-called Mandelbrot’s law, which cannot be fully described by previous models. In this paper, we propose an evolving model, considering two different user behaviors: random and preferential attachment. Extensive empirical results on two real bipartite networks, Delicious and CiteULike, show that the theoretical model can well characterize the structure of real networks for both user and object degree distributions. In addition, we introduce a structural parameter p, to demonstrate that the hybrid user behavior leads to the shifted power-law degree distribution, and the region of power-law tail will increase with the increment of p. The proposed model might shed some lights in understanding the underlying laws governing the structure of real online bipartite networks.

  17. How does cognition evolve? Phylogenetic comparative psychology.

    PubMed

    MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

    2012-03-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

  18. Fast evolving pair-instability supernovae

    DOE PAGES

    Kozyreva, Alexandra; Gilmer, Matthew; Hirschi, Raphael; ...

    2016-10-06

    With an increasing number of superluminous supernovae (SLSNe) discovered the ques- tion of their origin remains open and causes heated debates in the supernova commu- nity. Currently, there are three proposed mechanisms for SLSNe: (1) pair-instability supernovae (PISN), (2) magnetar-driven supernovae, and (3) models in which the su- pernova ejecta interacts with a circumstellar material ejected before the explosion. Based on current observations of SLSNe, the PISN origin has been disfavoured for a number of reasons. Many PISN models provide overly broad light curves and too reddened spectra, because of massive ejecta and a high amount of nickel. In themore » cur- rent study we re-examine PISN properties using progenitor models computed with the GENEC code. We calculate supernova explosions with FLASH and light curve evolu- tion with the radiation hydrodynamics code STELLA. We find that high-mass models (200 M⊙ and 250 M⊙) at relatively high metallicity (Z=0.001) do not retain hydro- gen in the outer layers and produce relatively fast evolving PISNe Type I and might be suitable to explain some SLSNe. We also investigate uncertainties in light curve modelling due to codes, opacities, the nickel-bubble effect and progenitor structure and composition.« less

  19. Fast evolving pair-instability supernovae

    SciTech Connect

    Kozyreva, Alexandra; Gilmer, Matthew; Hirschi, Raphael; Frohlich, Carla; Blinnikov, Sergey; Wollaeger, Ryan Thomas; Noebauer, Ulrich M.; van Rossum, Daniel R.; Heger, Alexander; Even, Wesley Paul; Waldman, Roni; Tolstov, Alexey; Chatzopoulos, Emmanouil; Sorokina, Elena

    2016-10-06

    With an increasing number of superluminous supernovae (SLSNe) discovered the ques- tion of their origin remains open and causes heated debates in the supernova commu- nity. Currently, there are three proposed mechanisms for SLSNe: (1) pair-instability supernovae (PISN), (2) magnetar-driven supernovae, and (3) models in which the su- pernova ejecta interacts with a circumstellar material ejected before the explosion. Based on current observations of SLSNe, the PISN origin has been disfavoured for a number of reasons. Many PISN models provide overly broad light curves and too reddened spectra, because of massive ejecta and a high amount of nickel. In the cur- rent study we re-examine PISN properties using progenitor models computed with the GENEC code. We calculate supernova explosions with FLASH and light curve evolu- tion with the radiation hydrodynamics code STELLA. We find that high-mass models (200 M⊙ and 250 M⊙) at relatively high metallicity (Z=0.001) do not retain hydro- gen in the outer layers and produce relatively fast evolving PISNe Type I and might be suitable to explain some SLSNe. We also investigate uncertainties in light curve modelling due to codes, opacities, the nickel-bubble effect and progenitor structure and composition.

  20. On the Discovery of Evolving Truth

    PubMed Central

    Li, Yaliang; Li, Qi; Gao, Jing; Su, Lu; Zhao, Bo; Fan, Wei; Han, Jiawei

    2015-01-01

    In the era of big data, information regarding the same objects can be collected from increasingly more sources. Unfortunately, there usually exist conflicts among the information coming from different sources. To tackle this challenge, truth discovery, i.e., to integrate multi-source noisy information by estimating the reliability of each source, has emerged as a hot topic. In many real world applications, however, the information may come sequentially, and as a consequence, the truth of objects as well as the reliability of sources may be dynamically evolving. Existing truth discovery methods, unfortunately, cannot handle such scenarios. To address this problem, we investigate the temporal relations among both object truths and source reliability, and propose an incremental truth discovery framework that can dynamically update object truths and source weights upon the arrival of new data. Theoretical analysis is provided to show that the proposed method is guaranteed to converge at a fast rate. The experiments on three real world applications and a set of synthetic data demonstrate the advantages of the proposed method over state-of-the-art truth discovery methods. PMID:26705502

  1. Extreme insular dwarfism evolved in a mammoth

    PubMed Central

    Herridge, Victoria L.; Lister, Adrian M.

    2012-01-01

    The insular dwarfism seen in Pleistocene elephants has come to epitomize the island rule; yet our understanding of this phenomenon is hampered by poor taxonomy. For Mediterranean dwarf elephants, where the most extreme cases of insular dwarfism are observed, a key systematic question remains unresolved: are all taxa phyletic dwarfs of a single mainland species Palaeoloxodon antiquus (straight-tusked elephant), or are some referable to Mammuthus (mammoths)? Ancient DNA and geochronological evidence have been used to support a Mammuthus origin for the Cretan ‘Palaeoloxodon’ creticus, but these studies have been shown to be flawed. On the basis of existing collections and recent field discoveries, we present new, morphological evidence for the taxonomic status of ‘P’. creticus, and show that it is indeed a mammoth, most probably derived from Early Pleistocene Mammuthus meridionalis or possibly Late Pliocene Mammuthus rumanus. We also show that Mammuthus creticus is smaller than other known insular dwarf mammoths, and is similar in size to the smallest dwarf Palaeoloxodon species from Sicily and Malta, making it the smallest mammoth species known to have existed. These findings indicate that extreme insular dwarfism has evolved to a similar degree independently in two elephant lineages. PMID:22572206

  2. Evolving the ingredients for reciprocity and spite

    PubMed Central

    Hauser, Marc; McAuliffe, Katherine; Blake, Peter R.

    2009-01-01

    Darwin never provided a satisfactory account of altruism, but posed the problem beautifully in light of the logic of natural selection. Hamilton and Williams delivered the necessary satisfaction by appealing to kinship, and Trivers showed that kinship was not necessary as long as the originally altruistic act was conditionally reciprocated. From the late 1970s to the present, the kinship theories in particular have been supported by considerable empirical data and elaborated to explore a number of other social interactions such as cooperation, selfishness and punishment, giving us what is now a rich description of the nature of social relationships among organisms. There are, however, two forms of theoretically possible social interactions—reciprocity and spite—that appear absent or nearly so in non-human vertebrates, despite considerable research efforts on a wide diversity of species. We suggest that the rather weak comparative evidence for these interactions is predicted once we consider the requisite socioecological pressures and psychological mechanisms. That is, a consideration of ultimate demands and proximate prerequisites leads to the prediction that reciprocity and spite should be rare in non-human animals, and common in humans. In particular, reciprocity and spite evolved in humans because of adaptive demands on cooperation among unrelated individuals living in large groups, and the integrative capacities of inequity detection, future-oriented decision-making and inhibitory control. PMID:19805432

  3. Evolving dynamic web pages using web mining

    NASA Astrophysics Data System (ADS)

    Menon, Kartik; Dagli, Cihan H.

    2003-08-01

    The heterogeneity and the lack of structure that permeates much of the ever expanding information sources on the WWW makes it difficult for the user to properly and efficiently access different web pages. Different users have different needs from the same web page. It is necessary to train the system to understand the needs and demands of the users. In other words there is a need for efficient and proper web mining. In this paper issues and possible ways of training the system and providing high level of organization for semi structured data available on the web is discussed. Web pages can be evolved based on history of query searches, browsing, links traversed and observation of the user behavior like book marking and time spent on viewing. Fuzzy clustering techniques help in grouping natural users and groups, neural networks, association rules and web traversals patterns help in efficient sequential anaysis based on previous searches and queries by the user. In this paper we analyze web server logs using above mentioned techniques to know more about user interactions. Analyzing these web server logs help to closely understand the user behavior and his/her web access pattern.

  4. Generative Representations for Evolving Families of Designs

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.

    2003-01-01

    Since typical evolutionary design systems encode only a single artifact with each individual, each time the objective changes a new set of individuals must be evolved. When this objective varies in a way that can be parameterized, a more general method is to use a representation in which a single individual encodes an entire class of artifacts. In addition to saving time by preventing the need for multiple evolutionary runs, the evolution of parameter-controlled designs can create families of artifacts with the same style and a reuse of parts between members of the family. In this paper an evolutionary design system is described which uses a generative representation to encode families of designs. Because a generative representation is an algorithmic encoding of a design, its input parameters are a way to control aspects of the design it generates. By evaluating individuals multiple times with different input parameters the evolutionary design system creates individuals in which the input parameter controls specific aspects of a design. This system is demonstrated on two design substrates: neural-networks which solve the 3/5/7-parity problem and three-dimensional tables of varying heights.

  5. Lower mass limit of an evolving interstellar cloud and chemistry in an evolving oscillatory cloud

    NASA Technical Reports Server (NTRS)

    Tarafdar, S. P.

    1986-01-01

    Simultaneous solution of the equation of motion, equation of state and energy equation including heating and cooling processes for interstellar medium gives for a collapsing cloud a lower mass limit which is significantly smaller than the Jeans mass for the same initial density. The clouds with higher mass than this limiting mass collapse whereas clouds with smaller than critical mass pass through a maximum central density giving apparently similar clouds (i.e., same Av, size and central density) at two different phases of its evolution (i.e., with different life time). Preliminary results of chemistry in such an evolving oscillatory cloud show significant difference in abundances of some of the molecules in two physically similar clouds with different life times. The problems of depletion and short life time of evolving clouds appear to be less severe in such an oscillatory cloud.

  6. Rapid shallow breathing

    MedlinePlus

    Tachypnea; Breathing - rapid and shallow; Fast shallow breathing; Respiratory rate - rapid and shallow ... Shallow, rapid breathing has many possible medical causes, including: Asthma Blood clot in an artery in the lung Choking Chronic obstructive ...

  7. Rapid Decisions From Experience

    PubMed Central

    Zeigenfuse, Matthew D.; Pleskac, Timothy J.; Liu, Taosheng

    2014-01-01

    In many everyday decisions, people quickly integrate noisy samples of information to form a preference among alternatives that offer uncertain rewards. Here, we investigated this decision process using the Flash Gambling Task (FGT), in which participants made a series of choices between a certain payoff and an uncertain alternative that produced a normal distribution of payoffs. For each choice, participants experienced the distribution of payoffs via rapid samples updated every 50 ms. We show that people can make these rapid decisions from experience and that the decision process is consistent with a sequential sampling process. Results also reveal a dissociation between these preferential decisions and equivalent perceptual decisions where participants had to determine which alternatives contained more dots on average. To account for this dissociation, we developed a sequential sampling rank-dependent utility model, which showed that participants in the FGT attended more to larger potential payoffs than participants in the perceptual task despite being given equivalent information. We discuss the implications of these findings in terms of computational models of preferential choice and a more complete understanding of experience-based decision making. PMID:24549141

  8. Ploidy dynamics and evolvability in fungi.

    PubMed

    Wertheimer, Noa Blutraich; Stone, Neil; Berman, Judith

    2016-12-05

    Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.

  9. Ploidy dynamics and evolvability in fungi

    PubMed Central

    Stone, Neil

    2016-01-01

    Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival. Furthermore, the stress of exposure to an antifungal drug can induce elevated levels of LOH and can promote the formation of aneuploids. This occurs via mitotic defects that first produce tetraploid progeny with extra spindles, followed by chromosome mis-segregation. Thus, drug exposure induces elevated levels of aneuploidy, which can alter the copy number of genes that improve survival in a given stress or drug. Selection then acts to increase the proportion of adaptive aneuploids in the population. Because aneuploidy is a common property of many pathogenic fungi, including those posing emerging threats to plants, animals and humans, we propose that aneuploid formation and LOH often accompanying it contribute to the rapid generation of diversity that can facilitate the emergence of fungal pathogens to new environmental niches and/or new hosts, as well as promote antifungal drug resistance that makes emerging fungal infections ever more difficult to contain. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’. PMID:28080987

  10. Innovations in scholarly publishing. Evolving trends in research communication in a digital age: examples from the BMJ.

    PubMed

    Jain, Anita

    2014-01-01

    As technology and communication evolve rapidly in this digital age, scholarly publishing is also undergoing a makeover to match the diverse needs of researchers and clinicians. The BMJ has been at the forefront of innovating the presentation of research to increase its readabillty and usefulness. This article presents some of recent formats used for research communication at the BMJ.

  11. Potassium channels and their evolving gates.

    PubMed

    Jan, L Y; Jan, Y N

    1994-09-08

    Potassium channels allow potassium ions to flow across the membrane and play a key role in maintaining membrane potential. Recent research has begun to reveal how these channels transport potassium in preference to other ions, how their activity is controlled, and how they are related to other channels.

  12. BUBBLE DYNAMICS AT GAS-EVOLVING ELECTRODES

    SciTech Connect

    Sides, Paul J.

    1980-12-01

    Nucleation of bubbles, their growth by diffusion of dissolved gas to the bubble surface and by coalescence, and their detachment from the electrode are all very fast phenomena; furthermore, electrolytically generated bubbles range in size from ten to a few hundred microns; therefore, magnification and high speed cinematography are required to observe bubbles and the phenomena of their growth on the electrode surface. Viewing the action from the front side (the surface on which the bubbles form) is complicated because the most important events occur close to the surface and are obscured by other bubbles passing between the camera and the electrode; therefore, oxygen was evolved on a transparent tin oxide "window" electrode and the events were viewed from the backside. The movies showed that coalescence of bubbles is very important for determining the size of bubbles and in the chain of transport processes; growth by diffusion and by coalescence proceeds in series and parallel; coalescing bubbles cause significant fluid motion close to the electrode; bubbles can leave and reattach; and bubbles evolve in a cycle of growth by diffusion and different modes of coalescence. An analytical solution for the primary potential and current distribution around a spherical bubble in contact with a plane electrode is presented. Zero at the contact point, the current density reaches only one percent of its undisturbed value at 30 percent of the radius from that point and goes through a shallow maximum two radii away. The solution obtained for spherical bubbles is shown to apply for the small bubbles of electrolytic processes. The incremental resistance in ohms caused by sparse arrays of bubbles is given by {Delta}R = 1.352 af/kS where f is the void fraction of gas in the bubble layer, a is the bubble layer thickness, k is the conductivity of gas free electrolyte, and S is the electrode area. A densely populated gas bubble layer on an electrode was modeled as a hexagonal array of

  13. Evolving Recommendations on Prostate Cancer Screening.

    PubMed

    Brawley, Otis W; Thompson, Ian M; Grönberg, Henrik

    2016-01-01

    Results of a number of studies demonstrate that the serum prostate-specific antigen (PSA) in and of itself is an inadequate screening test. Today, one of the most pressing questions in prostate cancer medicine is how can screening be honed to identify those who have life-threatening disease and need aggressive treatment. A number of efforts are underway. One such effort is the assessment of men in the landmark Prostate Cancer Prevention Trial that has led to a prostate cancer risk calculator (PCPTRC), which is available online. PCPTRC version 2.0 predicts the probability of the diagnosis of no cancer, low-grade cancer, or high-grade cancer when variables such as PSA, age, race, family history, and physical findings are input. Modern biomarker development promises to provide tests with fewer false positives and improved ability to find high-grade cancers. Stockholm III (STHLM3) is a prospective, population-based, paired, screen-positive, prostate cancer diagnostic study assessing a combination of plasma protein biomarkers along with age, family history, previous biopsy, and prostate examination for prediction of prostate cancer. Multiparametric MRI incorporates anatomic and functional imaging to better characterize and predict future behavior of tumors within the prostate. After diagnosis of cancer, several genomic tests promise to better distinguish the cancers that need treatment versus those that need observation. Although the new technologies are promising, there is an urgent need for evaluation of these new tests in high-quality, large population-based studies. Until these technologies are proven, most professional organizations have evolved to a recommendation of informed or shared decision making in which there is a discussion between the doctor and patient.

  14. Emergent spacetime in stochastically evolving dimensions

    NASA Astrophysics Data System (ADS)

    Afshordi, Niayesh; Stojkovic, Dejan

    2014-12-01

    Changing the dimensionality of the space-time at the smallest and largest distances has manifold theoretical advantages. If the space is lower dimensional in the high energy regime, then there are no ultraviolet divergencies in field theories, it is possible to quantize gravity, and the theory of matter plus gravity is free of divergencies or renormalizable. If the space is higher dimensional at cosmological scales, then some cosmological problems (including the cosmological constant problem) can be attacked from a completely new perspective. In this paper, we construct an explicit model of "evolving dimensions" in which the dimensions open up as the temperature of the universe drops. We adopt the string theory framework in which the dimensions are fields that live on the string worldsheet, and add temperature dependent mass terms for them. At the Big Bang, all the dimensions are very heavy and are not excited. As the universe cools down, dimensions open up one by one. Thus, the dimensionality of the space we live in depends on the energy or temperature that we are probing. In particular, we provide a kinematic Brandenberger-Vafa argument for how a discrete causal set, and eventually a continuum (3 + 1)-dim spacetime along with Einstein gravity emerges in the Infrared from the worldsheet action. The (3 + 1)-dim Planck mass and the string scale become directly related, without any compactification. Amongst other predictions, we argue that LHC might be blind to new physics even if it comes at the TeV scale. In contrast, cosmic ray experiments, especially those that can register the very beginning of the shower, and collisions with high multiplicity and density of particles, might be sensitive to the dimensional cross-over.

  15. Evolvable Cryogenics (ECRYO) Pressure Transducer Calibration Test

    NASA Technical Reports Server (NTRS)

    Diaz, Carlos E., Jr.

    2015-01-01

    This paper provides a summary of the findings of recent activities conducted by Marshall Space Flight Center's (MSFC) In-Space Propulsion Branch and MSFC's Metrology and Calibration Lab to assess the performance of current "state of the art" pressure transducers for use in long duration storage and transfer of cryogenic propellants. A brief historical narrative in this paper describes the Evolvable Cryogenics program and the relevance of these activities to the program. This paper also provides a review of three separate test activities performed throughout this effort, including: (1) the calibration of several pressure transducer designs in a liquid nitrogen cryogenic environmental chamber, (2) the calibration of a pressure transducer in a liquid helium Dewar, and (3) the calibration of several pressure transducers at temperatures ranging from 20 to 70 degrees Kelvin (K) using a "cryostat" environmental chamber. These three separate test activities allowed for study of the sensors along a temperature range from 4 to 300 K. The combined data shows that both the slope and intercept of the sensor's calibration curve vary as a function of temperature. This homogeneous function is contrary to the linearly decreasing relationship assumed at the start of this investigation. Consequently, the data demonstrates the need for lookup tables to change the slope and intercept used by any data acquisition system. This ultimately would allow for more accurate pressure measurements at the desired temperature range. This paper concludes with a review of a request for information (RFI) survey conducted amongst different suppliers to determine the availability of current "state of the art" flight-qualified pressure transducers. The survey identifies requirements that are most difficult for the suppliers to meet, most notably the capability to validate the sensor's performance at temperatures below 70 K.

  16. Evolutionary genomics of fast evolving tunicates.

    PubMed

    Berná, Luisa; Alvarez-Valin, Fernando

    2014-07-08

    Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis. These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements. In Ciona, genome reorganization was less severe being more similar to the other chordates in several aspects. Rates and patterns of molecular evolution are also peculiar in tunicates, being Ciona about 50% faster than vertebrates and Oikopleura three times faster. In fact, the latter species is considered as the fastest evolving metazoan recorded so far. Two processes of increase in evolutionary rates have taken place in tunicates. One of them is more extreme, and basically restricted to genes encoding regulatory proteins (transcription regulators, chromatin remodeling proteins, and metabolic regulators), and the other one is less pronounced but affects the whole genome. Very likely adaptive evolution has played a very significant role in the first, whereas the functional and/or evolutionary causes of the second are less clear and the evidence is not conclusive. The evidences supporting the incidence of increased mutation and less efficient negative selection are presented and discussed.

  17. Evolutionary Genomics of Fast Evolving Tunicates

    PubMed Central

    Berná, Luisa; Alvarez-Valin, Fernando

    2014-01-01

    Tunicates have been extensively studied because of their crucial phylogenetic location (the closest living relatives of vertebrates) and particular developmental plan. Recent genome efforts have disclosed that tunicates are also remarkable in their genome organization and molecular evolutionary patterns. Here, we review these latter aspects, comparing the similarities and specificities of two model species of the group: Oikopleura dioica and Ciona intestinalis. These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements. In Ciona, genome reorganization was less severe being more similar to the other chordates in several aspects. Rates and patterns of molecular evolution are also peculiar in tunicates, being Ciona about 50% faster than vertebrates and Oikopleura three times faster. In fact, the latter species is considered as the fastest evolving metazoan recorded so far. Two processes of increase in evolutionary rates have taken place in tunicates. One of them is more extreme, and basically restricted to genes encoding regulatory proteins (transcription regulators, chromatin remodeling proteins, and metabolic regulators), and the other one is less pronounced but affects the whole genome. Very likely adaptive evolution has played a very significant role in the first, whereas the functional and/or evolutionary causes of the second are less clear and the evidence is not conclusive. The evidences supporting the incidence of increased mutation and less efficient negative selection are presented and discussed. PMID:25008364

  18. Semantic Elaboration: ERPs Reveal Rapid Transition from Novel to Known

    ERIC Educational Resources Information Center

    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…

  19. Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae.

    PubMed

    Quarterman, Josh; Skerker, Jeffrey M; Feng, Xueyang; Liu, Ian Y; Zhao, Huimin; Arkin, Adam P; Jin, Yong-Su

    2016-07-10

    In the important industrial yeast Saccharomyces cerevisiae, galactose metabolism requires energy production by respiration; therefore, this yeast cannot metabolize galactose under strict anaerobic conditions. While the respiratory dependence of galactose metabolism provides benefits in terms of cell growth and population stability, it is not advantageous for producing fuels and chemicals since a substantial fraction of consumed galactose is converted to carbon dioxide. In order to force S. cerevisiae to use galactose without respiration, a subunit (COX9) of a respiratory enzyme was deleted, but the resulting deletion mutant (Δcox9) was impaired in terms of galactose assimilation. Interestingly, after serial sub-cultures on galactose, the mutant evolved rapidly and was able to use galactose via fermentation only. The evolved strain (JQ-G1) produced ethanol from galactose with a 94% increase in yield and 6.9-fold improvement in specific productivity as compared to the wild-type strain. (13)C-metabolic flux analysis demonstrated a three-fold reduction in carbon flux through the TCA cycle of the evolved mutant with redirection of flux toward the fermentation pathway. Genome sequencing of the JQ-G1 strain revealed a loss of function mutation in a master negative regulator of the Leloir pathway (Gal80p). The mutation (Glu348*) in Gal80p was found to act synergistically with deletion of COX9 for efficient galactose fermentation, and thus the double deletion mutant Δcox9Δgal80 produced ethanol 2.4 times faster and with 35% higher yield than a single knockout mutant with deletion of GAL80 alone. When we introduced a functional COX9 cassette back into the JQ-G1 strain, the JQ-G1-COX9 strain showed a 33% reduction in specific galactose uptake rate and a 49% reduction in specific ethanol production rate as compared to JQ-G1. The wild-type strain was also subjected to serial sub-cultures on galactose but we failed to isolate a mutant capable of utilizing galactose without

  20. Human language is a culturally evolving system.

    PubMed

    Steels, Luc

    2017-02-01

    It is well accepted that languages change rapidly in a process of cultural evolution. But some animal communication systems, in particular bird song, also exhibit cultural change. So where exactly is the difference? This article argues that the main selectionist pressure on human languages is not biological-that is, related to survival and fecundity-but instead is linked to producing enough expressive power for the needs of the community, maximizing communicative success, and reducing cognitive effort. The key question to be answered by an "evolutionary linguistics" approach to language is, What are the causal mechanisms sustaining an evolutionary dynamic based on these selection criteria? In other words, what cognitive mechanisms and social interaction patterns are needed, and how do they allow a language to emerge and remain shared, despite profound variation and never-ending change?

  1. The evolving role of mammary ductoscopy.

    PubMed

    Mokbel, Kefah; Elkak, Abd Elrafea

    2002-01-01

    Mammary ductoscopy (MD) is an emerging technique that allows direct visualisation of the mammary duct system, and that produces sharp and clear video images and ductal washings for cytological analysis. There is a growing body of evidence that MD may have a role in the management of women with pathological nipple discharge, the guiding of breast conserving surgery for cancer, and the screening of high risk women. Further research is required to confirm these potential applications and the feasibility of its use in the rapid intervention and outpatient setting under local anaesthesia. Furthermore, the addition of molecular and genetic analysis of cells obtained by MD and the emergence of newer generations of microendoscopes are likely to enhance the use of this technique.

  2. The Evolvement of Automobile Steering System Based on TRIZ

    NASA Astrophysics Data System (ADS)

    Zhao, Xinjun; Zhang, Shuang

    Products and techniques pass through a process of birth, growth, maturity, death and quit the stage like biological evolution process. The developments of products and techniques conform to some evolvement rules. If people know and hold these rules, they can design new kind of products and forecast the develop trends of the products. Thereby, enterprises can grasp the future technique directions of products, and make product and technique innovation. Below, based on TRIZ theory, the mechanism evolvement, the function evolvement and the appearance evolvement of automobile steering system had been analyzed and put forward some new ideas about future automobile steering system.

  3. Rapid evolutionary turnover underlies conserved lncRNA–genome interactions

    PubMed Central

    Quinn, Jeffrey J.; Zhang, Qiangfeng C.; Georgiev, Plamen; Ilik, Ibrahim A.; Akhtar, Asifa; Chang, Howard Y.

    2016-01-01

    Many long noncoding RNAs (lncRNAs) can regulate chromatin states, but the evolutionary origin and dynamics driving lncRNA–genome interactions are unclear. We adapted an integrative strategy that identifies lncRNA orthologs in different species despite limited sequence similarity, which is applicable to mammalian and insect lncRNAs. Analysis of the roX lncRNAs, which are essential for dosage compensation of the single X chromosome in Drosophila males, revealed 47 new roX orthologs in diverse Drosophilid species across ∼40 million years of evolution. Genetic rescue by roX orthologs and engineered synthetic lncRNAs showed that altering the number of focal, repetitive RNA structures determines roX ortholog function. Genomic occupancy maps of roX RNAs in four species revealed conserved targeting of X chromosome neighborhoods but rapid turnover of individual binding sites. Many new roX-binding sites evolved from DNA encoding a pre-existing RNA splicing signal, effectively linking dosage compensation to transcribed genes. Thus, dynamic change in lncRNAs and their genomic targets underlies conserved and essential lncRNA–genome interactions. PMID:26773003

  4. Rapid Y degeneration and dosage compensation in plant sex chromosomes.

    PubMed

    Papadopulos, Alexander S T; Chester, Michael; Ridout, Kate; Filatov, Dmitry A

    2015-10-20

    The nonrecombining regions of animal Y chromosomes are known to undergo genetic degeneration, but previous work has failed to reveal large-scale gene degeneration on plant Y chromosomes. Here, we uncover rapid and extensive degeneration of Y-linked genes in a plant species, Silene latifolia, that evolved sex chromosomes de novo in the last 10 million years. Previous transcriptome-based studies of this species missed unexpressed, degenerate Y-linked genes. To identify sex-linked genes, regardless of their expression, we sequenced male and female genomes of S. latifolia and integrated the genomic contigs with a high-density genetic map. This revealed that 45% of Y-linked genes are not expressed, and 23% are interrupted by premature stop codons. This contrasts with X-linked genes, in which only 1.3% of genes contained stop codons and 4.3% of genes were not expressed in males. Loss of functional Y-linked genes is partly compensated for by gene-specific up-regulation of X-linked genes. Our results demonstrate that the rate of genetic degeneration of Y-linked genes in S. latifolia is as fast as in animals, and that the evolutionary trajectories of sex chromosomes are similar in the two kingdoms.

  5. Rapid genetic adaptation during the first four months of survival under resource exhaustion.

    PubMed

    Avrani, Sarit; Bolotin, Evgeni; Katz, Sophia; Hershberg, Ruth

    2017-03-28

    Many bacteria, including the model bacterium Escherichia coli can survive for years within spent media, following resource exhaustion. We carried out evolutionary experiments, followed by full genome sequencing of hundreds of evolved clones to study the dynamics by which E. coli adapts during the first four months of survival under resource exhaustion. Our results reveal that bacteria evolving under resource exhaustion are subject to intense selection, manifesting in rapid mutation accumulation, enrichment in functional mutation categories and extremely convergent adaptation. In the most striking example of convergent adaptation, we found that across five independent populations adaptation to conditions of resource exhaustion occurs through mutations to the three same specific positions of the RNA polymerase core enzyme. Mutations to these three sites are strongly antagonistically pleiotropic, in that they sharply reduce exponential growth rates in fresh media. Such antagonistically pleiotropic mutations, combined with the accumulation of additional mutations, severely reduce the ability of bacteria surviving under resource exhaustion to grow exponentially in fresh media. We further demonstrate that the three positions at which these resource exhaustion mutations occur are conserved for the ancestral E. coli allele, across bacterial phyla, with the exception of non-culturable bacteria that carry the resource exhaustion allele at one of these positions, at very high frequencies. Finally, our results demonstrate that adaptation to resource exhaustion is not limited by mutational input and that bacteria are able to rapidly adapt under resource exhaustion in a temporally precise manner through allele frequency fluctuations.

  6. The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa

    PubMed Central

    Wang, Zheng; Li, Ning; Li, Jigang; Dunlap, Jay C.; Trail, Frances

    2016-01-01

    ABSTRACT Rapid responses to changes in incident light are critical to the guidance of behavior and development in most species. Phytochrome light receptors in particular play key roles in bacterial physiology and plant development, but their functions and regulation are less well understood in fungi. Nevertheless, genome-wide expression measurements provide key information that can guide experiments that reveal how genes respond to environmental signals and clarify their role in development. We performed functional genomic and phenotypic analyses of the two phytochromes in Neurospora crassa, a fungal model adapted to a postfire environment that experiences dramatically variable light conditions. Expression of phy-1 and phy-2 was low in early sexual development and in the case of phy-2 increased in late sexual development. Under light stimulation, strains with the phytochromes deleted exhibited increased expression of sexual development-related genes. Moreover, under red light, the phy-2 knockout strain commenced sexual development early. In the evolution of phytochromes within ascomycetes, at least two duplications have occurred, and the faster-evolving phy-2 gene has frequently been lost. Additionally, the three key cysteine sites that are critical for bacterial and plant phytochrome function are not conserved within fungal phy-2 homologs. Through the action of phytochromes, transitions between asexual and sexual reproduction are modulated by light level and light quality, presumably as an adaptation for fast asexual growth and initiation of sexual reproduction of N. crassa in exposed postfire ecosystems. PMID:26956589

  7. An Evolving Trio of Hybrid Stars: C 111

    NASA Technical Reports Server (NTRS)

    Oliversen, Ronald (Technical Monitor); Dupree, Andrea K.

    2004-01-01

    Our goal is to understand the behavior of the outer atmosphere in this intermediate stage to create a comprehensive picture of atmospheric evolution. In the hybrid phase, the large-scale magnetic dynamo activity decays and hydrodynamic processes assume importance. Some hot plasma is still confined close to the star by magnetic loops, yet the confining field is breaking open, the atmosphere can escape through these open field lines, and the diffuse corona may be warm. There may well be a more extended and variable transition process. It remains for FUSE to identify the controlling parameters of the hybrid stars. It shows the positions of our 3 targets in the color-magnitude diagram where it is seen that they are at the extreme end of the hybrid region. Originally we had been awarded the hybrid star Iota Aur, but due to newly imposed pointing constraints of FUSE, that target was not accessible. And so we substituted Iota Dra, a giant of mass similar to our other targets but less evolved. In addition, Iota Dra was recently found to harbor a sub-stellar objects, possibly a planet, and so it could reveal the stellar environment of the planet. This substitution was accepted.

  8. Complex Formation History of Highly Evolved Basaltic Shergottite, Zagami

    NASA Technical Reports Server (NTRS)

    Niihara, T.; Misawa, K.; Mikouchi, T.; Nyquist, L. E.; Park, J.; Hirata, D.

    2012-01-01

    Zagami, a basaltic shergottite, contains several kinds of lithologies such as Normal Zagami consisting of Fine-grained (FG) and Coarse-grained (CG), Dark Mottled lithology (DML), and Olivine-rich late-stage melt pocket (DN). Treiman and Sutton concluded that Zagami (Normal Zagami) is a fractional crystallization product from a single magma. It has been suggested that there were two igneous stages (deep magma chamber and shallow magma chamber or surface lava flow) on the basis of chemical zoning features of pyroxenes which have homogeneous Mg-rich cores and FeO, CaO zoning at the rims. Nyquist et al. reported that FG has a different initial Sr isotopic ratio than CG and DML, and suggested the possibility of magma mixing on Mars. Here we report new results of petrology and mineralogy for DML and the Olivine-rich lithology (we do not use DN here), the most evolved lithology in this rock, to understand the relationship among lithologies and reveal Zagami s formation history

  9. Infevers: an evolving mutation database for auto-inflammatory syndromes.

    PubMed

    Touitou, Isabelle; Lesage, Suzanne; McDermott, Michael; Cuisset, Laurence; Hoffman, Hal; Dode, Catherine; Shoham, Nitza; Aganna, Ebun; Hugot, Jean-Pierre; Wise, Carol; Waterham, Hans; Pugnere, Denis; Demaille, Jacques; Sarrauste de Menthiere, Cyril

    2004-09-01

    The Infevers database (http://fmf.igh.cnrs.fr/infevers/) was established in 2002 to provide investigators with access to a central source of information about all sequence variants associated with periodic fevers: Familial Mediterranean fever (FMF), TNF Receptor Associated Periodic Syndrome (TRAPS), Hyper IgD Syndrome (HIDS), Familial Cold Autoinflammatory Syndrome/Muckle-Wells Syndrome/Chronic Infantile Neurological Cutaneous and Articular Syndrome (FCAS/MWS/CINCA). The prototype of this group of disorders is FMF, a recessive disease characterized by recurrent bouts of unexplained inflammation. FMF is the pivotal member of an expanding family of autoinflammatory disorders, a new term coined to describe illnesses resulting from a defect of the innate immune response. Therefore, we decided to extend the Infevers database to genes connected with autoinflammatory diseases. We present here the biological content of the Infevers database, including the introduction of two new entries: Crohn/Blau and Pyogenic sterile arthritis, pyoderma gangrenosum and acne (PAPA syndrome). Infevers has a range of query capabilities, allowing for simple or complex interrogation of the database. Currently, the database contains 291 sequence variants in related genes (MEFV, TNFRSF1A, MVK, CARD15, PSTPIP1, and CIAS1), consisting of published data and personal communications, which has revealed or refined the preferential mutational sites for each gene. This database will continue to evolve in its content and to improve in its presentation.

  10. Increased morphological asymmetry, evolvability and plasticity in human brain evolution.

    PubMed

    Gómez-Robles, Aida; Hopkins, William D; Sherwood, Chet C

    2013-06-22

    The study of hominin brain evolution relies mostly on evaluation of the endocranial morphology of fossil skulls. However, only some general features of external brain morphology are evident from endocasts, and many anatomical details can be difficult or impossible to examine. In this study, we use geometric morphometric techniques to evaluate inter- and intraspecific differences in cerebral morphology in a sample of in vivo magnetic resonance imaging scans of chimpanzees and humans, with special emphasis on the study of asymmetric variation. Our study reveals that chimpanzee-human differences in cerebral morphology are mainly symmetric; by contrast, there is continuity in asymmetric variation between species, with humans showing an increased range of variation. Moreover, asymmetric variation does not appear to be the result of allometric scaling at intraspecific levels, whereas symmetric changes exhibit very slight allometric effects within each species. Our results emphasize two key properties of brain evolution in the hominine clade: first, evolution of chimpanzee and human brains (and probably their last common ancestor and related species) is not strongly morphologically constrained, thus making their brains highly evolvable and responsive to selective pressures; second, chimpanzee and, especially, human brains show high levels of fluctuating asymmetry indicative of pronounced developmental plasticity. We infer that these two characteristics can have a role in human cognitive evolution.

  11. Albuminoid Genes: Evolving at the Interface of Dispensability and Selection

    PubMed Central

    Cagliani, Rachele; Pozzoli, Uberto; Vertemara, Jacopo; Bresolin, Nereo; Sironi, Manuela

    2014-01-01

    The albuminoid gene family comprises vitamin D-binding protein (GC), alpha-fetoprotein (AFP), afamin (AFM), and albumin (ALB). Albumin is the most abundant human serum protein, and, as the other family members, acts as a transporter of endogenous and exogenous substances including thyroxine, fatty acids, and drugs. Instead, the major cargo of GC is 25-hydroxyvitamin D. We performed an evolutionary study of albuminoid genes and we show that ALB evolved adaptively in mammals. Most positively selected sites are located within albumin-binding sites for fatty acids and thyroxine, as well as at the contact surface with neonatal Fc receptor. Positive selection was also detected for residues forming the prostaglandin-binding pocket. Adaptation to hibernation/torpor might explain the signatures of episodic positive selection we detected for few mammalian lineages. Application of a population genetics–phylogenetics approach showed that purifying selection represented a major force acting on albuminoid genes in both humans and chimpanzees, with the strongest constraint observed for human GC. Population genetic analysis revealed that GC was also the target of locally exerted selective pressure, which drove the frequency increase of different haplotypes in distinct human populations. A search for known variants that modulate GC and 25-hydroxyvitamin D concentrations revealed linkage disequilibrium with positively selected variants, although European and Asian major GC haplotypes carry alleles with reported opposite effect on GC concentration. Data herein indicate that albumin, an extremely abundant housekeeping protein, was the target of pervasive and episodic selection in mammals, whereas GC represented a selection target during the recent evolution of human populations. PMID:25349266

  12. Functional Models for the Oxygen-Evolving Complex of Photosystem II

    PubMed Central

    Cady, Clyde W.; Crabtree, Robert H.; Brudvig, Gary W.

    2010-01-01

    In the last ten years, a number of advances have been made in the study of the oxygen-evolving complex (OEC) of photosystem II (PSII). Along with this new understanding of the natural system has come rapid advance in chemical models of this system. The advance of PSII model chemistry is seen most strikingly in the area of functional models where the few known systems available when this topic was last reviewed has grown into two families of model systems. In concert with this work, numerous mechanistic proposals for photosynthetic water oxidation have been proposed. Here, we review the recent efforts in functional model chemistry of the oxygen-evolving complex of photosystem II. PMID:21037800

  13. Evolving water science in the Anthropocene

    NASA Astrophysics Data System (ADS)

    Savenije, H. H. G.; Hoekstra, A. Y.; van der Zaag, P.

    2014-01-01

    This paper reviews the changing relation between human beings and water since the Industrial Revolution, a period that has been called the Anthropocene because of the unprecedented scale at which humans have altered the planet during this time. We show how the rapidly changing world urges us to continuously improve our understanding of the complex interactions between humans and the water system. The paper starts by demonstrating that hydrology and the science of managing water resources have played key roles in human and economic development throughout history; yet these roles have often been marginalised or obscured. Knowledge of hydrology and water resources engineering and management helped to transform the landscape, and thus also the very hydrology within catchments itself. It is only fairly recent that water experts have become conscious of such mechanisms, exemplified by several concepts that try to incorporate them - integrated water resources management, eco-hydrology, socio-hydrology. We have reached a stage at which a more systemic understanding of scale interdependencies can inform the sustainable governance of water systems, using new concepts like precipitation sheds, virtual water transfers, water footprints, and water value flow.

  14. Evolving water science in the Anthropocene

    NASA Astrophysics Data System (ADS)

    Savenije, H. H. G.; Hoekstra, A. Y.; van der Zaag, P.

    2013-06-01

    This paper reviews the changing relation between man and water since the industrial revolution, the period that has been called the Anthropocene because of the unprecedented scale at which humans have altered the planet. We show how the rapidly changing reality urges us to continuously improve our understanding of the complex interactions between man and the water system. The paper starts with demonstrating that hydrology and the science of water resources management have played key roles in human and economic development throughout history; yet these roles have often been marginalised or obscured. Knowledge on hydrology and water resources engineering and management helped to transform the landscape, and thus also the very hydrology within catchments itself. It is only fairly recent that water experts have become self-conscious of such mechanisms, exemplified by several concepts that try to internalise them (integrated water resources management, eco-hydrology, socio-hydrology). We have reached a stage where a more systemic understanding of scale interdependencies can inform the sustainable governance of water systems, using new concepts like precipitationsheds, virtual water transfers, water footprint and water value flow.

  15. Evolving Perspectives on Lyme Borreliosis in Canada

    PubMed Central

    Sperling, JLH; Middelveen, MJ; Klein, D; Sperling, FAH

    2012-01-01

    With cases now documented in every province, Lyme borreliosis (LB) is emerging as a serious public health risk in Canada. Controversy over the contribution of LB to the burden of chronic disease is maintained by difficulty in capturing accurate Canadian statistics, especially early clinical cases of LB. The use of dogs as sentinel species demon-strates that potential contact with Borrelia burgdorferi spirochetes, as detected by C6 peptide, extends across the country. Dissemination of infected ticks by migratory birds and rapid establishment of significant levels of infection have been well described. Canadian public health response has focused on identification of established populations of the tick vectors, Ixodes scapularis and I. pacificus, on the assumption that these are the only important vectors of the disease across Canada. Strains of B. burgdorferi circulating in Canada and the full range of their reservoir species and coinfections remain to be explored. Ongoing surveys and historical records demonstrate that Borrelia-positive Ixodes species are regu-larly present in regions of Canada that have previously been considered to be outside of the ranges of these species in re-cent modeling efforts. We present data demonstrating that human cases of LB are found across the nation. Consequently, physician education and better early diagnoses are needed to prevent long term sequelae. An international perspective will be paramount for developing improved Canadian guidelines that recognize the complexity and diversity of Lyme borreliosis. PMID:23091570

  16. Evolving Views on a Dynamic Greenhouse Earth

    NASA Astrophysics Data System (ADS)

    Hollis, Chris; Huber, Matthew

    2009-06-01

    Climatic and Biotic Events of the Paleogene (CBEP 2009) Conference; Wellington, New Zealand, 12-15 January 2009; The Paleogene (65-24 million years ago) was a dynamic period in Earth's history in which major mammal groups became established and diversified, rapid and repeated extreme global warming events occurred, and climate began its stuttering progression from a greenhouse to an icehouse climate state. With atmospheric carbon dioxide concentrations in the range projected to occur over the next several centuries (>1000 parts per million), the Paleogene is also a window into our future (see J. C. Zachos et al., Nature, 451, 279-283, 2008). Long-standing interest in understanding the causes and consequences of global change in the Paleogene and the current timeliness of greenhouse climate research explain why conferences are periodically devoted to the climatic and biotic events of the Paleogene. The 2009 conference, held in New Zealand, attracted 130 participants from 20 countries. Presentations demonstrated substantial progress in new climate proxy development, new multiproxy approaches, and closer integration of paleoclimate records with climate models, consolidating around three main issues.

  17. Static and Evolving Norovirus Genotypes: Implications for Epidemiology and Immunity

    PubMed Central

    Karangwa, Consolee K.; Sosnovtsev, Stanislav V.

    2017-01-01

    Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII.4. The non-GII.4 genotypes were comprised of one or more intra-genotypic variants, with each variant containing strains that differed by only a few residues over several decades (remaining “static”) and that have co-circulated with no clear epidemiologic pattern. In contrast, the GII.4 genotype presented the largest number of variants (>10) that have evolved over time with a clear pattern of periodic variant replacement. To expand our understanding of these two patterns of diversification (“static” versus “evolving”), we analyzed using NGS the nearly full-length norovirus genome in healthy individuals infected with GII.4, GII.6 or GII.17 viruses in different outbreak settings. The GII.4 viruses accumulated mutations rapidly within and between hosts, while the GII.6 and GII.17 viruses remained relatively stable, consistent with their diversification patterns. Further analysis of genetic relationships and natural history patterns identified groupings of certain genotypes into larger related clusters designated here as “immunotypes”. We propose that “immunotypes” and their evolutionary patterns influence the prevalence of a particular norovirus genotype in the human population. PMID:28103318

  18. Novel Drugs of Abuse: A Snapshot of an Evolving Marketplace

    PubMed Central

    Vandrey, Ryan; Johnson, Matthew W.; Johnson, Patrick S.; Khalil, Miral A.

    2014-01-01

    Background & objectives Over the past decade, non-medical use of novel drugs has proliferated worldwide. In most cases these are synthetic drugs first synthesized in academic or pharmaceutical laboratories for research or drug development purposes, but also include naturally occurring substances that do not fit the typical pharmacological or behavioral profile of traditional illicit substances. Perhaps most unique to this generation of new drugs is that they are being sold over the counter and on the Internet as “legal highs” or substitutes for traditional illicit drugs such as cannabis, cocaine, amphetamines, MDMA, and LSD. The purpose of this review is to provide an overview of novel drugs in current use, including the epidemiology of use and toxicologic and pharmacological properties, and to offer some guidelines to clinicians who see patients experiencing adverse effects from these drugs. Method We review the known scientific literature on recently introduced synthetic drug types, synthetic cannabinoids and synthetic cathinones, and the hallucinogen Salvia divinorum. Results These substances comprise part of a rapidly evolving and controversial drug market that has challenged definitions of what is legal and illegal, has benefitted from open commercial sales without regulatory oversight, and is noteworthy for the pace at which new substances are introduced. Conclusions This emerging trend in substance use presents significant and unique public health and criminal justice challenges. At this time, these substances are not detected in routine drug screens and substance-specific treatment for cases of use-related toxicity are not available. Clinicians are encouraged to learn characteristic signs associated with misuse of novel drugs to recognize cases in their practice, and are recommended to use a symptom-specific approach for treatment in each case. PMID:24921061

  19. Vulnerabilities—bibliometric analysis and literature review of evolving concepts

    NASA Astrophysics Data System (ADS)

    Giupponi, Carlo; Biscaro, Claudio

    2015-12-01

    In this work we analyse the evolution of the vulnerability concept in the research streams of climate change adaptation (CCA) and disaster risk reduction (DRR). We combine a traditional literature review with data mining procedures applied to bibliographic databases to reconstruct the history of the concept within various research topics, showing its evolution and convergences over time. To do that, we integrate different methods combining machine learning algorithms with network and cluster analyses to examine a set of 3757 articles, analysing their distinctive features and similarities on the basis of their contents as well as co-authorships. Bibliometric analyses enable the identification of different communities of articles, pinpointing key papers and authors, while literature review makes it possible to assess the concept of vulnerability evolved within and beyond research communities and scientific networks. Moreover, this work examines the role played by documents published by UN institutions (UNDRO, UNISDR, IPCC) in contributing to the evolution of vulnerability and related concepts. Results show that signs of convergence are evident between the two research streams, and that the IPCC reports have played a major role in proposing solutions for unifying definitions of vulnerability. We observe that the phases of preparation of the IPCC reports are very rich in methodological and terminological developments, while after publication, the literature shows evident signs of propagation of the proposed concepts. The DRR research stream developed before the research stream on CCA, but the latter flourished rapidly and became much larger in terms of number of publications. Nevertheless, in terms of contents, adaptation studies and the IPCC have shown increasing adoption of the concepts developed within the disaster research stream, in particular with regard to the interpretation of vulnerability as one of the dimensions of risk.

  20. Adoption of Geospatial Systems towards evolving Sustainable Himalayan Mountain Development

    NASA Astrophysics Data System (ADS)

    Murthy, M. S. R.; Bajracharya, B.; Pradhan, S.; Shestra, B.; Bajracharya, R.; Shakya, K.; Wesselmann, S.; Ali, M.; Bajracharya, S.; Pradhan, S.

    2014-11-01

    Natural resources dependence of mountain communities, rapid social and developmental changes, disaster proneness and climate change are conceived as the critical factors regulating sustainable Himalayan mountain development. The Himalayan region posed by typical geographic settings, diverse physical and cultural diversity present a formidable challenge to collect and manage data, information and understands varied socio-ecological settings. Recent advances in earth observation, near real-time data, in-situ measurements and in combination of information and communication technology have transformed the way we collect, process, and generate information and how we use such information for societal benefits. Glacier dynamics, land cover changes, disaster risk reduction systems, food security and ecosystem conservation are a few thematic areas where geospatial information and knowledge have significantly contributed to informed decision making systems over the region. The emergence and adoption of near-real time systems, unmanned aerial vehicles (UAV), board-scale citizen science (crowd-sourcing), mobile services and mapping, and cloud computing have paved the way towards developing automated environmental monitoring systems, enhanced scientific understanding of geophysical and biophysical processes, coupled management of socio-ecological systems and community based adaptation models tailored to mountain specific environment. There are differentiated capacities among the ICIMOD regional member countries with regard to utilization of earth observation and geospatial technologies. The region can greatly benefit from a coordinated and collaborative approach to capture the opportunities offered by earth observation and geospatial technologies. The regional level data sharing, knowledge exchange, and Himalayan GEO supporting geospatial platforms, spatial data infrastructure, unique region specific satellite systems to address trans-boundary challenges would go a long way in

  1. Search for Close-in Planets around Evolved Stars with Phase-curve variations and Radial Velocity Measurements

    NASA Astrophysics Data System (ADS)

    Hirano, Teruyuki; Sato, Bun'ei; Masuda, Kento; Benomar, Othman Michel; Takeda, Yoichi; Omiya, Masashi; Harakawa, Hiroki

    2016-10-01

    Tidal interactions are a key process to understand the evolution history of close-in exoplanets. But tidals still have a large uncertainty in their prediction for the damping timescales of stellar obliquity and semi-major axis. We have worked on a search for transiting giant planets around evolved stars, for which few close-in planets were discovered. It has been reported that evolved stars lack close-in planets, which is often attributed to the tidal evolution and/or engulfment of close-in planets by the hosts. Meanwhile, Kepler has detected a certain fraction of transiting planet candidates around evolved stars. Confirming the planetary nature for these candidates is especially important since the comparison between the occurrence rates of close-in planets around main sequence stars and evolved stars provides a unique opportunity to discuss the final stage of close-in planets. With the aim of confirming KOI planet candidates around evolved stars, we measured precision radial velocities (RVs) for evolved stars with transiting planet candidates using Subaru/HDS. We also developed a new code which simultaneously models and fits the observed RVs and phase-curve variations in the Kepler data (e.g., transits, stellar ellipsoidal variations, and planet emission/reflected light). As a result of applying the global fit to KOI giants/subgiants, we confirmed two giant planets around evolved stars (Kepler-91 and KOI-1894), as well as revealed that KOI-977 is more likely a false positive.

  2. Hawaii's volcanoes revealed

    USGS Publications Warehouse

    Eakins, Barry W.; Robinson, Joel E.; Kanamatsu, Toshiya; Naka, Jiro; Smith, John R.; Takahashi, Eiichi; Clague, David A.

    2003-01-01

    Hawaiian volcanoes typically evolve in four stages as volcanism waxes and wanes: (1) early alkalic, when volcanism originates on the deep sea floor; (2) shield, when roughly 95 percent of a volcano's volume is emplaced; (3) post-shield alkalic, when small-volume eruptions build scattered cones that thinly cap the shield-stage lavas; and (4) rejuvenated, when lavas of distinct chemistry erupt following a lengthy period of erosion and volcanic quiescence. During the early alkalic and shield stages, two or more elongate rift zones may develop as flanks of the volcano separate. Mantle-derived magma rises through a vertical conduit and is temporarily stored in a shallow summit reservoir from which magma may erupt within the summit region or be injected laterally into the rift zones. The ongoing activity at Kilauea's Pu?u ?O?o cone that began in January 1983 is one such rift-zone eruption. The rift zones commonly extend deep underwater, producing submarine eruptions of bulbous pillow lava. Once a volcano has grown above sea level, subaerial eruptions produce lava flows of jagged, clinkery ?a?a or smooth, ropy pahoehoe. If the flows reach the ocean they are rapidly quenched by seawater and shatter, producing a steep blanket of unstable volcanic sediment that mantles the upper submarine slopes. Above sea level then, the volcanoes develop the classic shield profile of gentle lava-flow slopes, whereas below sea level slopes are substantially steeper. While the volcanoes grow rapidly during the shield stage, they may also collapse catastrophically, generating giant landslides and tsunami, or fail more gradually, forming slumps. Deformation and seismicity along Kilauea's south flank indicate that slumping is occurring there today. Loading of the underlying Pacific Plate by the growing volcanic edifices causes subsidence, forming deep basins at the base of the volcanoes. Once volcanism wanes and lava flows no longer reach the ocean, the volcano continues to submerge, while

  3. The remarkable outburst of the highly-evolved post period-minimum dwarf nova SSS J122221.7-311525

    NASA Astrophysics Data System (ADS)

    Neustroev, V. V.; Marsh, T. R.; Zharikov, S. V.; Knigge, C.; Kuulkers, E.; Osborne, J. P.; Page, K. L.; Steeghs, D.; Suleimanov, V. F.; Tovmassian, G.; Breedt, E.; Frebel, A.; García-Díaz, Ma. T.; Hambsch, F.-J.; Jacobson, H.; Parsons, S. G.; Ryu, T.; Sabin, L.; Sjoberg, G.; Miroshnichenko, A. S.; Reichart, D. E.; Haislip, J. B.; Ivarsen, K. M.; LaCluyze, A. P.; Moore, J. P.

    2017-01-01

    We report extensive 3-yr multiwavelength observations of the WZ Sge-type dwarf nova SSS J122221.7-311525 during its unusual double superoutburst, the following decline and in quiescence. The second segment of the superoutburst had a long duration of 33 days and a very gentle decline with a rate of 0.02 mag d-1, and it displayed an extended post-outburst decline lasting at least 500 days. Simultaneously with the start of the rapid fading from the superoutburst plateau, the system showed the appearance of a strong NIR excess resulting in very red colours, which reached extreme values (B-I≃1.4) about 20 days later. The colours then became bluer again, but it took at least 250 days to acquire a stable level. Superhumps were clearly visible in the light curve from our very first time-resolved observations until at least 420 days after the rapid fading from the superoutburst. The spectroscopic and photometric data revealed an orbital period of 109.80 min and a fractional superhump period excess ≲0.8%, indicating a very low mass ratio q ≲0.045. With such a small mass ratio the donor mass should be below the hydrogen-burning minimum mass limit. The observed IR flux in quiescence is indeed much lower than is expected from a CV with a near-main sequence donor star. This strongly suggests a brown-dwarf-like nature for the donor and that SSS J122221.7-311525 has already evolved away from the period minimum towards longer periods, with the donor now extremely dim.

  4. PUBLISHER'S NOTE: Rapid Communications Rapid Communications

    NASA Astrophysics Data System (ADS)

    Miller, Tom

    2009-09-01

    As part of a general review of Superconductor Science and Technology, we have been examining the scope for Rapid Communications (RAPs). We recognize these articles make up an important part of the journal representing the latest state-of-the-art research in superconductivity. To reflect this, we have devised a new scope for this article type: 'Rapid Communications. The journal offers open access to outstanding short articles (no longer than 5 journal pages or 4500 words including figures) reporting new and timely developments in superconductivity and its applications. These articles should report very substantial new advances in superconductivity to the readers of Superconductor Science and Technology, but are not expected to meet any requirement of 'general interest'. RAPs will be processed quickly (average receipt to online publication for RAPs is around 60 days) and are permanently free to read in the electronic journal. Authors submitting a RAP should provide reasons why the work is urgent and requires rapid publication. Each RAP will be assessed for suitability by our Reviews and Rapid Communications Editor before full peer review takes place.' The essential points are: They should report very substantial new advances in superconductivity and its application; They must be no longer than 5 journal pages long (approx. 4500 words); Average publication time for a Rapid Communication is 60 days; They are free to read. As mentioned in the previous publisher's announcement (2009 Supercond. Sci. Technol. 22 010101), each submitted Rapid Communication must come with a letter justifying why it should be prioritized over regular papers and will be pre-assessed by our Reviews and Rapid Communications Editor. In addition, we will work with the authors of any Rapid Communication to promote and raise the visibility of the work presented in it. We will be making further changes to the journal in the near future and we write to you accordingly. Thank you for your kind

  5. Evolving role of mitomycin-C laryngology

    NASA Astrophysics Data System (ADS)

    Richards, Steven V.; Garrett, C. Gaelyn

    2001-05-01

    Topical mitomycin-C, a chemotherapeutic agent and a fibroblast inhibitor, has been successfully used in larynx, primarily to treat stenosis. Subglottic, tracheal, and anterior glottic stenosis have all shown promising results in a canine model. Less favorable results have been obtained when topical mitomycin-C is used on the vocal folds following surgical excision of mucosa. In the vocal fold studies, laryngeal videostroboscopy revealed diminished mucosal wave vibration in the vocal folds treated with mitomycin-C as well as a more atrophic appearance to the vibratory surface. The tissue treated with mitomycin-C showed fewer fibroblasts and less collagen. However, inflammatory infiltrate was not significantly different between the treated and untreated tissue. These results are consistent with the known suppression of fibroblast proliferation by mitomycin-C. In contrast to the positive effects of mitomycin-C on stenosis, the observed decrease in the healing response in the vocal fold had negative consequences on vocal fold vibratory pattern.

  6. Homogeneously dispersed, multimetal oxygen-evolving catalysts

    SciTech Connect

    Zhang, Bo; Zheng, Xueli; Voznyy, Oleksandr; Comin, Riccardo; Bajdich, Michal; Garcia-Melchor, Max; Han, Lili; Xu, Jixian; Liu, Min; Zheng, Lirong; F. Pelayo Garcia de Arquer; Dinh, Cao Thang; Fan, Fengjia; Yuan, Mingjian; Yassitepe, Emre; Chen, Ning; Regier, Tom; Liu, Pengfei; Li, Yuhang; De Luna, Phil; Janmohamed, Alyf; Xin, Huolin L.; Yang, Huagui; Vojvodic, Aleksandra; Sargent, Edward H.

    2016-03-24

    Earth-abundant first-row (3d) transition-metal-based catalysts have been developed for the oxygen-evolution reaction (OER); however, they operate at overpotentials significantly above thermodynamic requirements. Density functional theory suggested that non-3d high-valency metals such as tungsten can modulate 3d metal oxides, providing near-optimal adsorption energies for OER intermediates. We developed a room-temperature synthesis to produce gelled oxy-hydroxide materials with an atomically homogeneous metal distribution. These gelled FeCoW oxy-hydroxide exhibits the lowest overpotential (191 mV) reported at 10 mA per square centimeter in alkaline electrolyte. Here, the catalyst shows no evidence of degradation following more than 500 hours of operation. X-ray absorption and computational studies reveal a synergistic interplay between W, Fe and Co in producing a favorable local coordination environment and electronic structure that enhance the energetics for OER.

  7. Unconventional protein secretion: an evolving mechanism

    PubMed Central

    Malhotra, Vivek

    2013-01-01

    The process by which proteins are secreted without entering the classical endoplasmic reticulum (ER)–Golgi complex pathway, in eukaryotic cells, is conveniently called unconventional protein secretion. Recent studies on one such protein called Acb1 have revealed a number of components involved in its secretion. Interestingly, conditions that promote the secretion of Acb1 trigger the biogenesis of a new compartment called CUPS (Compartment for Unconventional Protein Secretion). CUPS form near the ER exit site but lack ER-specific proteins. Other proteins that share some of the features common with the secretion of Acb1 are interleukin-1β and tissue transglutaminase. Here I will review recent advances made in the field and propose a new model for unconventional protein secretion. PMID:23665917

  8. Adaptation of Escherichia coli to glucose promotes evolvability in lactose.

    PubMed

    Phillips, Kelly N; Castillo, Gerardo; Wünsche, Andrea; Cooper, Tim F

    2016-02-01

    The selective history of a population can influence its subsequent evolution, an effect known as historical contingency. We previously observed that five of six replicate populations that were evolved in a glucose-limited environment for 2000 generations, then switched to lactose for 1000 generations, had higher fitness increases in lactose than populations started directly from the ancestor. To test if selection in glucose systematically increased lactose evolvability, we started 12 replay populations--six from a population subsample and six from a single randomly selected clone--from each of the six glucose-evolved founder populations. These replay populations and 18 ancestral populations were evolved for 1000 generations in a lactose-limited environment. We found that replay populations were initially slightly less fit in lactose than the ancestor, but were more evolvable, in that they increased in fitness at a faster rate and to higher levels. This result indicates that evolution in the glucose environment resulted in genetic changes that increased the potential of genotypes to adapt to lactose. Genome sequencing identified four genes--iclR, nadR, spoT, and rbs--that were mutated in most glucose-evolved clones and are candidates for mediating increased evolvability. Our results demonstrate that short-term selective costs during selection in one environment can lead to changes in evolvability that confer longer term benefits.

  9. The genotype-phenotype map of an evolving digital organism.

    PubMed

    Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

    2017-02-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

  10. Loops and autonomy promote evolvability of ecosystem networks.

    PubMed

    Luo, Jianxi

    2014-09-29

    The structure of ecological networks, in particular food webs, determines their ability to evolve further, i.e. evolvability. The knowledge about how food web evolvability is determined by the structures of diverse ecological networks can guide human interventions purposefully to either promote or limit evolvability of ecosystems. However, the focus of prior food web studies was on stability and robustness; little is known regarding the impact of ecological network structures on their evolvability. To correlate ecosystem structure and evolvability, we adopt the NK model originally from evolutionary biology to generate and assess the ruggedness of fitness landscapes of a wide spectrum of model food webs with gradual variation in the amount of feeding loops and link density. The variation in network structures is controlled by linkage rewiring. Our results show that more feeding loops and lower trophic link density, i.e. higher autonomy of species, of food webs increase the potential for the ecosystem to generate heritable variations with improved fitness. Our findings allow the prediction of the evolvability of actual food webs according to their network structures, and provide guidance to enhancing or controlling the evolvability of specific ecosystems.

  11. The genotype-phenotype map of an evolving digital organism

    PubMed Central

    Zaman, Luis; Wagner, Andreas

    2017-01-01

    To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable. PMID:28241039

  12. Osmoregulatory physiology and rapid evolution of salinity tolerance in threespine stickleback recently introduced to fresh water

    USGS Publications Warehouse

    Divino, Jeffrey N; Monette, Michelle Y.; McCormick, Stephen; Yancey, Paul H.; Flannery, Kyle G.; Bell, Michael A.; Rollins, Jennifer L.; von Hippel, Frank A.; Schultz, Eric T.

    2016-01-01

    Conclusion: Enhanced freshwater tolerance has evolved rapidly in recently landlocked stickleback compared with their anadromous ancestors (0.569 haldanes), but the former have retained ancestral seawater-osmoregulatory function.

  13. Gene Essentiality Is a Quantitative Property Linked to Cellular Evolvability.

    PubMed

    Liu, Gaowen; Yong, Mei Yun Jacy; Yurieva, Marina; Srinivasan, Kandhadayar Gopalan; Liu, Jaron; Lim, John Soon Yew; Poidinger, Michael; Wright, Graham Daniel; Zolezzi, Francesca; Choi, Hyungwon; Pavelka, Norman; Rancati, Giulia

    2015-12-03

    Gene essentiality is typically determined by assessing the viability of the corresponding mutant cells, but this definition fails to account for the ability of cells to adaptively evolve to genetic perturbations. Here, we performed a stringent screen to assess the degree to which Saccharomyces cerevisiae cells can survive the deletion of ~1,000 individual "essential" genes and found that ~9% of these genetic perturbations could in fact be overcome by adaptive evolution. Our analyses uncovered a genome-wide gradient of gene essentiality, with certain essential cellular functions being more "evolvable" than others. Ploidy changes were prevalent among the evolved mutant strains, and aneuploidy of a specific chromosome was adaptive for a class of evolvable nucleoporin mutants. These data justify a quantitative redefinition of gene essentiality that incorporates both viability and evolvability of the corresponding mutant cells and will enable selection of therapeutic targets associated with lower risk of emergence of drug resistance.

  14. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.

    PubMed

    Zhou, Aifen; Hillesland, Kristina L; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M; Ma, Qiao; Qu, Yuanyuan; Stahl, David A; Wall, Judy D; Hazen, Terry C; Fields, Matthew W; Arkin, Adam P; Zhou, Jizhong

    2015-11-01

    To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.

  15. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

    PubMed Central

    Zhou, Aifen; Hillesland, Kristina L; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M; Ma, Qiao; Qu, Yuanyuan; Stahl, David A; Wall, Judy D; Hazen, Terry C; Fields, Matthew W; Arkin, Adam P; Zhou, Jizhong

    2015-01-01

    To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance. PMID:25848870

  16. The stratospheric polar vortex: evolving perspectives

    NASA Astrophysics Data System (ADS)

    Plumb, R. A.

    2005-12-01

    The discovery of dramatic Antarctic ozone depletion occurred at a time of rapid change in our understanding of stratospheric dynamics. The existence of the polar vortex, encircled by the polar night jet, had been well known for some time, as had the planetary scale Rossby waves that so dominate stratospheric meteorology. But, 25 years ago, the concepts of Rossby wave breaking, and of the "surf zone" and the sharpness of its boundaries at the vortex edge and in the subtropics, were relatively new, and the role of these waves in the driving of the mean diabatic circulation was not fully appreciated. While the local importance of gravity wave drag in the mesosphere was recognized by that time, its impact in the stratosphere was by no means clear. For a time, it was thought by many that the "ozone hole" was produced by anomalous polar upwelling, whose existence seemed to be demanded by observations of widespread, anomalously low temperatures in high southern latitudes in spring, which (at first) did not appear to be a consequence of depleted ozone. In the event, of course, chemical observations provided overwhelming support for the chemical depletion theory, while tracer observations, as well as revised radiative calculations, undermined the case for polar upwelling. The demands of stratospheric chemistry have always required that dynamical understanding of the stratosphere should extend beyond traditional meteorology to include questions of the transport of chemical species. Stratospheric transport has many facets, of which one - the impermeability of the vortex edge - was brought into focus by the appearance of the ozone hole and the need to understand the degree to which vortex air is isolated from its environment. The issue was controversial for a time, but analyses of tracer observations have confirmed expectations based on dynamical theory and on modeling studies that the isolation is strong, except during major vortex disturbances. Interest in polar vortex

  17. Detection of timescales in evolving complex systems

    PubMed Central

    Darst, Richard K.; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

    2016-01-01

    Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system’s configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system. PMID:28004820

  18. Detection of timescales in evolving complex systems

    NASA Astrophysics Data System (ADS)

    Darst, Richard K.; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

    2016-12-01

    Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system’s configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system.

  19. Emergency room coverage: an evolving crisis.

    PubMed

    Davison, Steven P

    2004-08-01

    Historically, a newly graduated plastic surgeon in the United States could build a practice from his or her emergency room coverage. The historical cliche was for the surgeon to be affable, able, and available, and from that basis one's practice would grow. Emergency room exposure was an avenue for starting a practice, developing recognition, and, after that, building a referral pattern. Recently, the cross-shifting influence of management care, rising malpractice insurance costs, and risk ratio are changing this cliche to a crisis. An evaluation of a 2 1/2-year exposure to emergency room coverage has revealed a completely different profile. A total of 300 patient visits resulting in 69 surgical operations were evaluated for insurance and remuneration history. The findings indicated a significant remuneration dilemma for emergency room coverage. Interestingly, a remuneration problem exists in a market different from what one would expect. In this study, a sample from a suburban hospital, rather than an inner-city university hospital, is the greater problem.

  20. Homogeneously dispersed, multimetal oxygen-evolving catalysts

    DOE PAGES

    Zhang, Bo; Zheng, Xueli; Voznyy, Oleksandr; ...

    2016-03-24

    Earth-abundant first-row (3d) transition-metal-based catalysts have been developed for the oxygen-evolution reaction (OER); however, they operate at overpotentials significantly above thermodynamic requirements. Density functional theory suggested that non-3d high-valency metals such as tungsten can modulate 3d metal oxides, providing near-optimal adsorption energies for OER intermediates. We developed a room-temperature synthesis to produce gelled oxy-hydroxide materials with an atomically homogeneous metal distribution. These gelled FeCoW oxy-hydroxide exhibits the lowest overpotential (191 mV) reported at 10 mA per square centimeter in alkaline electrolyte. Here, the catalyst shows no evidence of degradation following more than 500 hours of operation. X-ray absorption and computationalmore » studies reveal a synergistic interplay between W, Fe and Co in producing a favorable local coordination environment and electronic structure that enhance the energetics for OER.« less

  1. Proteomics Reveals Novel Drosophila Seminal Fluid Proteins Transferred at Mating

    PubMed Central

    Findlay, Geoffrey D; Yi, Xianhua; MacCoss, Michael J; Swanson, Willie J

    2008-01-01

    Across diverse taxa, seminal fluid proteins (Sfps) transferred at mating affect the reproductive success of both sexes. Such reproductive proteins often evolve under positive selection between species; because of this rapid divergence, Sfps are hypothesized to play a role in speciation by contributing to reproductive isolation between populations. In Drosophila, individual Sfps have been characterized and are known to alter male sperm competitive ability and female post-mating behavior, but a proteomic-scale view of the transferred Sfps has been missing. Here we describe a novel proteomic method that uses whole-organism isotopic labeling to detect transferred Sfps in mated female D. melanogaster. We identified 63 proteins, which were previously unknown to function in reproduction, and confirmed the transfer of dozens of predicted Sfps. Relative quantification of protein abundance revealed that several of these novel Sfps are abundant in seminal fluid. Positive selection and tandem gene duplication are the prevailing forces of Sfp evolution, and comparative proteomics with additional species revealed lineage-specific changes in seminal fluid content. We also report a proteomic-based gene discovery method that uncovered 19 previously unannotated genes in D. melanogaster. Our results demonstrate an experimental method to identify transferred proteins in any system that is amenable to isotopic labeling, and they underscore the power of combining proteomic and evolutionary analyses to shed light on the complex process of Drosophila reproduction. PMID:18666829

  2. Heritability, evolvability, phenotypic plasticity and temporal variation in sperm-competition success of Drosophila melanogaster.

    PubMed

    Dobler, R; Reinhardt, K

    2016-05-01

    Sperm-competition success (SCS) is seen as centrally important for evolutionary change: superior fathers sire superior sons and thereby inherit the traits that make them superior. Additional hypotheses, that phenotypic plasticity in SCS and sperm ageing explain variation in paternity, are less considered. Even though various alleles have individually been shown to be correlated with variation in SCS, few studies have addressed the heritability, or evolvability, of overall SCS. Those studies that have addressed found low or no heritability and have not examined evolvability. They have further not excluded phenotypic plasticity, and temporal effects on SCS, despite their known dramatic effects on sperm function. In Drosophila melanogaster, we found that both standard components of sperm competition, sperm defence and sperm offence, showed nonsignificant heritability across several offspring cohorts. Instead, our analysis revealed, for the first time, the existence of phenotypic plasticity in SCS across an extreme environment (5% CO2 ), and an influence of sperm ageing. Evolvability of SCS was substantial for sperm defence but weak for sperm offence. Our results suggest that the paradigm of explaining evolution by sperm competition is more complex and will benefit from further experimental work on the heritability or evolvability of SCS, measuring phenotypic plasticity, and separating the effects of sperm competition and sperm ageing.

  3. Rapid radiation in bacteria leads to a division of labour

    PubMed Central

    Kim, Wook; Levy, Stuart B.; Foster, Kevin R.

    2016-01-01

    The division of labour is a central feature of the most sophisticated biological systems, including genomes, multicellular organisms and societies, which took millions of years to evolve. Here we show that a well-organized and robust division of labour can evolve in a matter of days. Mutants emerge within bacterial colonies and work with the parent strain to gain new territory. The two strains self-organize in space: one provides a wetting polymer at the colony edge, whereas the other sits behind and pushes them both along. The emergence of the interaction is repeatable, bidirectional and only requires a single mutation to alter production of the intracellular messenger, cyclic-di-GMP. Our work demonstrates the power of the division of labour to rapidly solve biological problems without the need for long-term evolution or derived sociality. We predict that the division of labour will evolve frequently in microbial populations, where rapid genetic diversification is common. PMID:26852925

  4. Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae.

    PubMed

    Kim, Soo Rin; Skerker, Jeffrey M; Kang, Wei; Lesmana, Anastashia; Wei, Na; Arkin, Adam P; Jin, Yong-Su

    2013-01-01

    Economic bioconversion of plant cell wall hydrolysates into fuels and chemicals has been hampered mainly due to the inability of microorganisms to efficiently co-ferment pentose and hexose sugars, especially glucose and xylose, which are the most abundant sugars in cellulosic hydrolysates. Saccharomyces cerevisiae cannot metabolize xylose due to a lack of xylose-metabolizing enzymes. We developed a rapid and efficient xylose-fermenting S. cerevisiae through rational and inverse metabolic engineering strategies, comprising the optimization of a heterologous xylose-assimilating pathway and evolutionary engineering. Strong and balanced expression levels of the XYL1, XYL2, and XYL3 genes constituting the xylose-assimilating pathway increased ethanol yields and the xylose consumption rates from a mixture of glucose and xylose with little xylitol accumulation. The engineered strain, however, still exhibited a long lag time when metabolizing xylose above 10 g/l as a sole carbon source, defined here as xylose toxicity. Through serial-subcultures on xylose, we isolated evolved strains which exhibited a shorter lag time and improved xylose-fermenting capabilities than the parental strain. Genome sequencing of the evolved strains revealed that mutations in PHO13 causing loss of the Pho13p function are associated with the improved phenotypes of the evolved strains. Crude extracts of a PHO13-overexpressing strain showed a higher phosphatase activity on xylulose-5-phosphate (X-5-P), suggesting that the dephosphorylation of X-5-P by Pho13p might generate a futile cycle with xylulokinase overexpression. While xylose consumption rates by the evolved strains improved substantially as compared to the parental strain, xylose metabolism was interrupted by accumulated acetate. Deletion of ALD6 coding for acetaldehyde dehydrogenase not only prevented acetate accumulation, but also enabled complete and efficient fermentation of xylose as well as a mixture of glucose and xylose by the

  5. The Evolving Context for Science and Society

    NASA Astrophysics Data System (ADS)

    Leshner, Alan I.

    2012-01-01

    The relationship between science and the rest of society is critical both to the support it receives from the public and to the receptivity of the broader citizenry to science's explanations of the nature of the world and to its other outputs. Science's ultimate usefulness depends on a receptive public. For example, given that science and technology are imbedded in virtually every issue of modern life, either as a cause or a cure, it is critical that the relationship be strong and that the role of science is well appreciated by society, or the impacts of scientific advances will fall short of their great potential. Unfortunately, a variety of problems have been undermining the science-society relationship for over a decade. Some problems emerge from within the scientific enterprise - like scientific misconduct or conflicts of interest - and tarnish or weaken its image and credibility. Other problems and stresses come from outside the enterprise. The most obvious external pressure is that the world economic situation is undermining the financial support of both the conduct and infrastructure of science. Other examples of external pressures include conflicts between what science is revealing and political or economic expediency - e.g., global climate change - or instances where scientific advances encroach upon core human values or beliefs - e.g., scientific understanding of the origins and evolution of the universe as compared to biblical accounts of creation. Significant efforts - some dramatically non-traditional for many in the scientific community - are needed to restore balance to the science-society relationship.

  6. Evolving role of pharmaceutical physicians in the industry: Indian perspective.

    PubMed

    Patil, Anant; Rajadhyaksha, Viraj

    2012-01-01

    The Indian pharmaceutical industry, like any other industry, has undergone significant change in the last decade. The role of a Medical advisor has always been of paramount importance in the pharmaceutical companies in India. On account of the evolving medical science and the competitive environment, the medical advisor's role is also increasingly becoming critical. In India, with changes in regulatory rules, safety surveillance, and concept of medical liaisons, the role of the medical advisor is evolving continuously and is further likely to evolve in the coming years in important areas like health economics, public private partnerships, and strategic planning.

  7. Heterogeneous edge weights promote epidemic diffusion in weighted evolving networks

    NASA Astrophysics Data System (ADS)

    Duan, Wei; Song, Zhichao; Qiu, Xiaogang

    2016-08-01

    The impact that the heterogeneities of links’ weights have on epidemic diffusion in weighted networks has received much attention. Investigating how heterogeneous edge weights affect epidemic spread is helpful for disease control. In this paper, we study a Reed-Frost epidemic model in weighted evolving networks. Our results indicate that a higher heterogeneity of edge weights leads to higher epidemic prevalence and epidemic incidence at earlier stage of epidemic diffusion in weighted evolving networks. In addition, weighted evolving scale-free networks come with a higher epidemic prevalence and epidemic incidence than unweighted scale-free networks.

  8. Evolving role of pharmaceutical physicians in the industry: Indian perspective

    PubMed Central

    Patil, Anant; Rajadhyaksha, Viraj

    2012-01-01

    The Indian pharmaceutical industry, like any other industry, has undergone significant change in the last decade. The role of a Medical advisor has always been of paramount importance in the pharmaceutical companies in India. On account of the evolving medical science and the competitive environment, the medical advisor's role is also increasingly becoming critical. In India, with changes in regulatory rules, safety surveillance, and concept of medical liaisons, the role of the medical advisor is evolving continuously and is further likely to evolve in the coming years in important areas like health economics, public private partnerships, and strategic planning. PMID:22347701

  9. Rapid Evolution of Phenotypic Plasticity and Shifting Thresholds of Genetic Assimilation in the Nematode Caenorhabditis remanei

    PubMed Central

    Sikkink, Kristin L.; Reynolds, Rose M.; Ituarte, Catherine M.; Cresko, William A.; Phillips, Patrick C.

    2014-01-01

    Many organisms can acclimate to new environments through phenotypic plasticity, a complex trait that can be heritable, subject to selection, and evolve. However, the rate and genetic basis of plasticity evolution remain largely unknown. We experimentally evolved outbred populations of the nematode Caenorhabditis remanei under an acute heat shock during early larval development. When raised in a nonstressful environment, ancestral populations were highly sensitive to a 36.8° heat shock and exhibited high mortality. However, initial exposure to a nonlethal high temperature environment resulted in significantly reduced mortality during heat shock (hormesis). Lines selected for heat shock resistance rapidly evolved the capacity to withstand heat shock in the native environment without any initial exposure to high temperatures, and early exposure to high temperatures did not lead to further increases in heat resistance. This loss of plasticity would appear to have resulted from the genetic assimilation of the heat induction response in the noninducing environment. However, analyses of transcriptional variation via RNA-sequencing from the selected populations revealed no global changes in gene regulation correlated with the observed changes in heat stress resistance. Instead, assays of the phenotypic response across a broader range of temperatures revealed that the induced plasticity was not fixed across environments, but rather the threshold for the response was shifted to higher temperatures over evolutionary time. These results demonstrate that apparent genetic assimilation can result from shifting thresholds of induction across environments and that analysis of the broader environmental context is critically important for understanding the evolution of phenotypic plasticity. PMID:24727288

  10. Diversity Against Adversity: How Adaptive Immune System Evolves Potent Antibodies

    NASA Astrophysics Data System (ADS)

    Heo, Muyoung; Zeldovich, Konstantin B.; Shakhnovich, Eugene I.

    2011-07-01

    Adaptive immunity is an amazing mechanism, whereby new protein functions—affinity of antibodies (Immunoglobulins) to new antigens—evolve through mutation and selection in a matter of a few days. Despite numerous experimental studies, the fundamental physical principles underlying immune response are still poorly understood. In considerable departure from past approaches, here, we propose a microscopic multiscale model of adaptive immune response, which consists of three essential players: The host cells, viruses, and B-cells in Germinal Centers (GC). Each moiety carries a genome, which encodes proteins whose stability and interactions are determined from their sequences using laws of Statistical Mechanics, providing an exact relationship between genomic sequences and strength of interactions between pathogens and antibodies and antibodies and host proteins (autoimmunity). We find that evolution of potent antibodies (the process known as Affinity Maturation (AM)) is a delicate balancing act, which has to reconcile the conflicting requirements of protein stability, lack of autoimmunity, and high affinity of antibodies to incoming antigens. This becomes possible only when antibody producing B cells elevate their mutation rates (process known as Somatic Hypermutation (SHM)) to fall into a certain range—not too low to find potency increasing mutations but not too high to destroy stable Immunoglobulins and/or already achieved affinity. Potent antibodies develop through clonal expansion of initial B cells expressing marginally potent antibodies followed by their subsequent affinity maturation through mutation and selection. As a result, in each GC the population of mature potent Immunoglobulins is monoclonal being ancestors of a single cell from initial (germline) pool. We developed a simple analytical theory, which provides further rationale to our findings. The model and theory reveal the molecular factors that determine the efficiency of affinity maturation

  11. Nutritional immunity. Escape from bacterial iron piracy through rapid evolution of transferrin.

    PubMed

    Barber, Matthew F; Elde, Nels C

    2014-12-12

    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.

  12. Evolving food retail environments in Thailand and implications for the health and nutrition transition

    PubMed Central

    Banwell, Cathy; Dixon, Jane; Seubsman, Sam-ang; Pangsap, Suttinan; Kelly, Matthew; Sleigh, Adrian

    2013-01-01

    Objective An investigation into evolving food retail systems in Thailand Design Rapid assessment procedures based on qualitative research methods such as interviews, focus groups discussions and site visits Setting Seven freshmarkets located in the four main regions of Thailand Subjects Managers, food specialists, vendors and shoppers from seven freshmarkets who participated in interviews and focus group discussions. Results Freshmarkets are under economic pressure and are declining in number. They are attempting to resist the competition from supermarkets by improving convenience, food diversity, quality and safety. Conclusions Obesity has increased in Thailand at the same time as rapid growth of modern food retail formats has occurred. As freshmarkets are overtaken by supermarkets there is a likely loss of fresh, healthy, affordable food for poorer Thais, and a diminution of regional culinary culture, women’s jobs and social capital with implications for the health and nutrition transition in Thailand. PMID:23021291

  13. Anabolic androgenic steroid induced myocardial toxicity: an evolving problem in an ageing population

    PubMed Central

    Rothman, Richard D; Weiner, Rory B; Pope, Harrison; Kanayama, Gen; Hutter, Adolph M; Fifer, Michael A; Dec, G William; Baggish, Aaron L

    2011-01-01

    Widespread use of anabolic androgenic steroid (AAS) abuse is a rapidly increasing public health concern with an expanding demographic. Previous studies and reports have been exclusive to young individuals at low risk for traditional, non-AAS associated, cardiovascular disease. To date, the impact of AAS use on older patients has not been well characterised. The patient herein presented documents a dramatic case of an older individual who developed decompensated heart failure secondary to illicit use of AAS, highlighting an evolving problem among a rapidly expanding demographic and illustrating that a) AAS, used to alter appearance or augment performance, is no longer an issue confined to young adults; b) older individuals with ageing myocardium may be particularly susceptible to AAS toxicity and may present with fulminate congestive heart failure; and that c) AAS abstinence coupled with traditional heart failure pharmacotherapy may be an effective treatment for this condition. PMID:22688938

  14. In situ regeneration of bioactive coatings enabled by an evolved Staphylococcus aureus sortase A

    NASA Astrophysics Data System (ADS)

    Ham, Hyun Ok; Qu, Zheng; Haller, Carolyn A.; Dorr, Brent M.; Dai, Erbin; Kim, Wookhyun; Liu, David R.; Chaikof, Elliot L.

    2016-04-01

    Surface immobilization of bioactive molecules is a central paradigm in the design of implantable devices and biosensors with improved clinical performance capabilities. However, in vivo degradation or denaturation of surface constituents often limits the long-term performance of bioactive films. Here we demonstrate the capacity to repeatedly regenerate a covalently immobilized monomolecular thin film of bioactive molecules through a two-step stripping and recharging cycle. Reversible transpeptidation by a laboratory evolved Staphylococcus aureus sortase A (eSrtA) enabled the rapid immobilization of an anti-thrombogenic film in the presence of whole blood and permitted multiple cycles of film regeneration in vitro that preserved its biological activity. Moreover, eSrtA transpeptidation facilitated surface re-engineering of medical devices in situ after in vivo implantation through removal and restoration film constituents. These studies establish a rapid, orthogonal and reversible biochemical scheme to regenerate selective molecular constituents with the potential to extend the lifetime of bioactive films.

  15. Evolutionary genetics: you are what you evolve to eat.

    PubMed

    Dworkin, Ian; Jones, Corbin D

    2015-04-20

    The evolution of host specialization can potentially limit future evolutionary opportunities. A new study now shows how Drosophila sechellia, specialized on the toxic Morinda fruit, has evolved new nutritional needs influencing its reproduction.

  16. Evolving Darwin's 'most wonderful' plant: ecological steps to a snap-trap.

    PubMed

    Gibson, Thomas C; Waller, Donald M

    2009-08-01

    Among carnivorous plants, Darwin was particularly fascinated by the speed and sensitivity of snap-traps in Dionaea and Aldrovanda. Recent molecular work confirms Darwin's conjecture that these monotypic taxa are sister to Drosera, meaning that snap-traps evolved from a 'flypaper' trap. Transitions include tentacles being modified into trigger hairs and marginal 'teeth', the loss of sticky tentacles, depressed digestive glands, and rapid leaf movement. Pre-adaptations are known for all these traits in Drosera yet snap-traps only evolved once. We hypothesize that selection to catch and retain large insects favored the evolution of elongate leaves and snap-tentacles in Drosera and snap-traps. Although sticky traps efficiently capture small prey, they allow larger prey to escape and may lose nutrients. Dionaea's snap-trap efficiently captures and processes larger prey providing higher, but variable, rewards. We develop a size-selective model and parametrize it with field data to demonstrate how selection to capture larger prey strongly favors snap-traps. As prey become larger, they also become rarer and gain the power to rip leaves, causing returns to larger snap-traps to plateau. We propose testing these hypotheses with specific field data and Darwin-like experiments. The complexity of snap-traps, competition with pitfall traps, and their association with ephemeral habitats all help to explain why this curious adaptation only evolved once.

  17. Evolvable hardware: genetic search in a physical realm

    NASA Astrophysics Data System (ADS)

    Raichman, Nadav; Segev, Ronen; Ben-Jacob, Eshel

    2003-08-01

    The application of evolution-inspired strategies to hardware design and circuit self-configuration leads to the concept of evolvable hardware (EHW). EHW refers to self-configuration of electronic hardware by evolutionary/genetic algorithms (EA and GA, respectively). Unconventional circuits, for which there are no textbook design guidelines, are particularly appealing for EHW. Here we applied an evolutionary algorithm on a configurable digital FPGA chip in order to evolve analog-behavior circuits. Though the configurable chip is explicitly built for digital designs, analog circuits were successfully evolved by allowing feedback routings and by disabling the general clock. The results were unconventional circuits that were well fitted both to the task for which the circuits were evolved, and to the environment in which the evolution took place. We analyzed the morphotype (configuration) changes in circuit size and circuit operation through evolutionary time. The results showed that the evolved circuit structure had two distinct areas: an active area in which signal processing took place and a surrounding neutral area. The active area of the evolved circuits was small in size, but complex in structure. Results showed that the active area may grow during evolution, indicating that progress is achieved through the addition of units taken from the neutral area. Monitor views of the circuit outputs through evolution indicate that several distinct stages occurred in which evolution evolved. This is in accordance with the plots of fitness that show a progressive climb in a stair-like manner. Competitive studies were also performed of evolutions with various population sizes. Results showed that the smaller the size of the evolved population, the faster was the evolutionary process. This was attributed to the high degeneracy in gene variance within the large population, resulting in a futile search.

  18. Mass Loss and Dust Injection rates from Evolved Stars

    NASA Astrophysics Data System (ADS)

    Sargent, Benjamin A.

    2010-01-01

    The Spitzer Space Telescope is continuing to contribute greatly to our understanding of the mass return from evolved stars in the Magellanic Clouds (MCs). I first review a number of smaller early Spitzer studies of evolved stars in the Large Magellanic Cloud (LMC) and Small Magellanic Cloud (SMC). These studies often built upon earlier such studies using data from prior missions, like the Midcourse Space Experiment. I discuss various Spitzer spectroscopic studies that have investigated the dust compositions of evolved stars in the lower metallicity environments of the MCs. Also, I review studies of the MCs' massive evolved stars, which have been given somewhat less attention than other populations. Excitingly, using Spitzer data, for the first time the mass-loss from the diverse evolved star MC populations is being quantified. With the advent of the Surveying the Agents of a Galaxy's Evolution (SAGE; PI: M. Meixner) Spitzer Legacy program, tens of thousands of stars in the LMC have been classified as evolved stars using SAGE Spitzer data. I briefly review how evolved stars are classified (e.g., by using color-magnitude and color-color diagrams) using data from the SAGE surveys. Finally, I discuss work on radiative transfer (RT) modeling of evolved stars, which follows earlier work estimating their mass-loss using colors or emission in excess of stellar photosphere emission. This RT work starts by seeking acceptable dust properties for RT models of both SAGE Spectral Energy Distributions (SEDs) and SAGE-Spectroscopy (Spitzer Legacy program; PI: F. Kemper) spectra of asymptotic giant branch (AGB) stars. Afterwards, large grids of RT models are constructed to determine mass-loss rates for AGB stars and red supergiants in the SAGE samples of the LMC and, eventually, the SMC.

  19. Ammonia Binds to the Dangler Manganese of the Photosystem II Oxygen-Evolving Complex.

    PubMed

    Oyala, Paul H; Stich, Troy A; Debus, Richard J; Britt, R David

    2015-07-15

    High-resolution X-ray structures of photosystem II reveal several potential substrate binding sites at the water-oxidizing/oxygen-evolving 4MnCa cluster. Aspartate-61 of the D1 protein hydrogen bonds with one such water (W1), which is bound to the dangler Mn4A of the oxygen-evolving complex. Comparison of pulse EPR spectra of (14)NH3 and (15)NH3 bound to wild-type Synechocystis PSII and a D1-D61A mutant lacking this hydrogen-bonding interaction demonstrates that ammonia binds as a terminal NH3 at this dangler Mn4A site and not as a partially deprotonated bridge between two metal centers. The implications of this finding on identifying the binding sites of the substrate and the subsequent mechanism of dioxygen formation are discussed.

  20. Modular Orbital Demonstration of an Evolvable Space Telescope (MODEST)

    NASA Astrophysics Data System (ADS)

    Baldauf, Brian; Conti, Alberto

    2016-01-01

    The "Search for Life" via imaging of exoplanets is a mission that requires extremely stable telescopes with apertures in the 10 m to 20 m range. The High Definition Space Telescope (HDST) envisioned for this mission would have an aperture >10 m, which is a larger payload than what can be delivered to space using a single launch vehicle. Building and assembling the mirror segments enabling large telescopes will likely require multiple launches and assembly in space. Space-based telescopes with large apertures will require major changes to system architectures.The Optical Telescope Assembly (OTA) for HDST is a primary mission cost driver. Enabling and affordable solutions for this next generation of large aperture space-based telescope are needed.This paper reports on the concept for the Modular Orbital Demonstration of an Evolvable Space Telescope (MODEST), which demonstrates on-orbit robotic and/or astronaut assembly of a precision optical telescope in space. It will also facilitate demonstration of active correction of phase and mirror shape. MODEST is proposed to be delivered to the ISS using standard Express Logistics Carriers (ELCs) and can mounted to one of a variety of ISS pallets. Post-assembly value includes space, ground, and environmental studies, and a testbed for new instruments. This demonstration program for next generation mirror technology provides significant risk reduction and demonstrates the technology in a six-mirror phased telescope. Other key features of the demonstration include the use of an active primary optical surface with wavefront feedback control that allows on-orbit optimization and demonstration of precise surface control to meet optical system wavefront and stability requirements.MODEST will also be used to evaluate advances in lightweight mirror and metering structure materials such as SiC or Carbon Fiber Reinforced Polymer that have excellent mechanical and thermal properties, e.g. high stiffness, high modulus, high thermal

  1. An Evolving Perspective on the Atmosphere and Surface of Mars

    NASA Astrophysics Data System (ADS)

    Leovy, C. B.

    2000-10-01

    Three issues drive our evolving effort to understand the evolution of the atmosphere and surface of Mars: the origin of outflow channels and valley networks, the hemispheric dichotomy, and most recently, evidence from the Mars Global Surveyor pointing toward running water and possibly to standing bodies of water in the recent past. Outflow channels are widely assumed to have been formed by massive liquid water floods during the Hesperian to early Amazonian periods, while the valley network features are generally believed to have been formed by widespread and repeated surface water flows or groundwater sapping events during the Noachian period. Despite morphologies that strikingly implicate fluvial processes, unresolved difficulties with the flowing water interpretation of these features remain. These include adequate explanations for the fate of the large volume of water required to produce outflow channels and of the mechanisms needed to maintain the warm surface temperatures that would have allowed widespread formation of valley networks by surface erosion or sapping. Thus alternatives to the flowing water hypothesis must still be considered. Recently N. Hoffman (2000, Icarus, p. 126) has proposed that release of carbon dioxide from subsurface clathrate deposits or pressurized liquid carbon dioxide reservoirs could have formed these features by fueling powerful turbidity currents. Even without buried carbon dioxide reservoirs, turbidity currents associated with dust storms are prominent on Mars today, are responsible for widespread erosion and deposition of fine materials, and may have substantially contributed to both outflow channel and valley network features. Fine particle erosion and transport by wind is highly sensitive to both surface pressure and surface roughness. As a consequence, a deep regolith consisting of a mixture of cobbles, boulders, and fine particles may be unstable with respect to wind erosion. As wind removes fine materials locally, the

  2. Climate in Context - How partnerships evolve in regions

    NASA Astrophysics Data System (ADS)

    Parris, A. S.

    2014-12-01

    In 2015, NOAA's RISA program will celebrate its 20th year of exploration in the development of usable climate information. In the mid-1990s, a vision emerged to develop interdisciplinary research efforts at the regional scale for several important reasons. Recognizable climate patterns, such as the El Nino Southern Oscillation (ENSO), emerge at the regional level where our understanding of observations and models coalesce. Critical resources for society are managed in a context of regional systems, such as water supply and human populations. Multiple scales of governance (local, state, and federal) with complex institutional relationships can be examined across a region. Climate information (i.e. data, science, research etc) developed within these contexts has greater potential for use. All of this work rests on a foundation of iterative engagement between scientists and decision makers. Throughout these interactions, RISAs have navigated diverse politics, extreme events and disasters, socio-economic and ecological disruptions, and advances in both science and technology. Our understanding of information needs is evolving into a richer understanding of complex institutional, legal, political, and cultural contexts within which people can use science to make informed decisions. The outcome of RISA work includes both cases where climate information was used in decisions and cases where capacity for using climate information and making climate resilient decisions has increased over time. In addition to balancing supply and demand of scientific information, RISAs are engaged in a social process of reconciling climate information use with important drivers of society. Because partnerships are critical for sustained engagement, and because engagement is critically important to the use of science, the rapid development of new capacity in regionally-based science programs focused on providing climate decision support is both needed and challenging. New actors can bolster

  3. A Modular Orbital Demonstration of an Evolvable Space Telescope (MODEST)

    NASA Astrophysics Data System (ADS)

    Conti, Alberto; Arenberg, Jonathan; Baldauf, Brian

    2017-01-01

    The “Search for Life” (direct imaging of earth-like planets) will require extremely stable telescopes with apertures in the 10 m to 20 m range. Such apertures are larger than what can be delivered to space using current or planned future launch vehicles. Building and assembling large telescopes in space is therefore likely to require not only multiple launches but importantly assembly in spce. As a result, space-based telescopes with large apertures will require major changes to our conventional telescope design and architecture.Here we report on the concept for the Modular Orbital Demonstration of an Evolvable Space Telescope (MODEST) to demonstrates the on-orbit robotic and/or astronaut assembly of an optical telescope in space. MODEST is a proposed International Space Station (ISS demonstration that will make use of the standard Express Logistics Carriers (ELCs) and can mounted to one of a variety of ISS pallets.MODEST will provides significant risk reduction for the next generation of space observatories, and demonstrates the technology needed to assemble a six-mirror phased telescope. Key modest features include the use of an active primary optical surface with wavefront feedback control to allow on-orbit optimization, and the precise surface control to meet optical system wavefront and stability requirements.MODEST will also be used to evaluate advances in lightweight mirror and metering structure materials such as SiC or Carbon Fiber Reinforced Polymer (CFRP) that have excellent mechanical and thermal properties, e.g. high stiffness, high modulus, high thermal conductivity, and low thermal expansion. Mirrors built from these materials can be rapidly replicated in a highly cost effective manner, making them an excellent candidate for a low cost, high performance Optical Telescope Assembly paving the way for enabling affordable solutions for the next generation of large aperture space-based telescope.MODEST post-assembly value includes space, ground, and

  4. Comparison of laser-based rapid prototyping techniques

    NASA Astrophysics Data System (ADS)

    Humphreys, Hugh; Wimpenny, David

    2002-04-01

    A diverse range of Rapid Prototyping, or layer manufacturing techniques have evolved since the introduction of the first process in the late 1980s. Many, although not all, rapid prototyping processes rely on lasers to provide a localised and controllable source of light for curing a liquid photopolymer or heat to fuse thermoplastic powders to form objects. This paper will provide an overview of laser based rapid prototyping methods and discuss the future direction of this technology in light of the threats posed by low cost 3D printing techniques and the opportunity for the direct manufacture of metal components.

  5. Did life history evolve in response to parasites in invasive populations of Melanoides tuberculata?

    NASA Astrophysics Data System (ADS)

    Escobar, Juan Sebastián; Correa, Ana Cristina; David, Patrice

    2009-09-01

    Enemy release and rapid evolution are often assumed to promote biological invasions. In the parthenogenetic snail Melanoides tuberculata, one invasive strain (MAD) was assumed to benefit from enemy release until a heavily parasitized population was found in Colombia (in the area of introduction). This population is prosperous despite important losses in the reproductive potential due to a high prevalence of a trematode that castrates snails. We studied genetic variation in life-history traits among five populations from the invaded area to test whether life histories had recently evolved in the parasitized population in such a way that snails have more chance to reproduce before being parasitized. We find significant genetic differences among populations, though they are not in the expected direction. Individuals from the parasitized population were smaller at birth, grew slower, and reproduced later and at a bigger size than individuals from the non-parasitized populations. We conclude that the life-history traits of this snail strain did not need to evolve in order to allow population renewal in the invaded area, even in the presence of parasites. This implies that enemy release and/or rapid evolution were not necessary for this strain to invade.

  6. Select forelimb muscles have evolved superfast contractile speed to support acrobatic social displays

    PubMed Central

    Fuxjager, Matthew J; Goller, Franz; Dirkse, Annika; Sanin, Gloria D; Garcia, Sarah

    2016-01-01

    Many species perform rapid limb movements as part of their elaborate courtship displays. However, because muscle performance is constrained by trade-offs between contraction speed and force, it is unclear how animals evolve the ability to produce both unusually fast appendage movement and limb force needed for locomotion. To address this issue, we compare the twitch speeds of forelimb muscles in a group of volant passerine birds, which produce different courtship displays. Our results show that the two taxa that perform exceptionally fast wing displays have evolved 'superfast' contractile kinetics in their main humeral retractor muscle. By contrast, the two muscles that generate the majority of aerodynamic force for flight show unmodified contractile kinetics. Altogether, these results suggest that muscle-specific adaptations in contractile speed allow certain birds to circumvent the intrinsic trade-off between muscular speed and force, and thereby use their forelimbs for both rapid gestural displays and powered locomotion. DOI: http://dx.doi.org/10.7554/eLife.13544.001 PMID:27067379

  7. Páramo is the world's fastest evolving and coolest biodiversity hotspot.

    PubMed

    Madriñán, Santiago; Cortés, Andrés J; Richardson, James E

    2013-10-09

    Understanding the processes that cause speciation is a key aim of evolutionary biology. Lineages or biomes that exhibit recent and rapid diversification are ideal model systems for determining these processes. Species rich biomes reported to be of relatively recent origin, i.e., since the beginning of the Miocene, include Mediterranean ecosystems such as the California Floristic Province, oceanic islands such as the Hawaiian archipelago and the Neotropical high elevation ecosystem of the Páramos. Páramos constitute grasslands above the forest tree-line (at elevations of c. 2800-4700 m) with high species endemism. Organisms that occupy this ecosystem are a likely product of unique adaptations to an extreme environment that evolved during the last three to five million years when the Andes reached an altitude that was capable of sustaining this type of vegetation. We compared net diversification rates of lineages in fast evolving biomes using 73 dated molecular phylogenies. Based on our sample, we demonstrate that average net diversification rates of Páramo plant lineages are faster than those of other reportedly fast evolving hotspots and that the faster evolving lineages are more likely to be found in Páramos than the other hotspots. Páramos therefore represent the ideal model system for studying diversification processes. Most of the speciation events that we observed in the Páramos (144 out of 177) occurred during the Pleistocene possibly due to the effects of species range contraction and expansion that may have resulted from the well-documented climatic changes during that period. Understanding these effects will assist with efforts to determine how future climatic changes will impact plant populations.

  8. Páramo is the world's fastest evolving and coolest biodiversity hotspot

    PubMed Central

    Madriñán, Santiago; Cortés, Andrés J.; Richardson, James E.

    2013-01-01

    Understanding the processes that cause speciation is a key aim of evolutionary biology. Lineages or biomes that exhibit recent and rapid diversification are ideal model systems for determining these processes. Species rich biomes reported to be of relatively recent origin, i.e., since the beginning of the Miocene, include Mediterranean ecosystems such as the California Floristic Province, oceanic islands such as the Hawaiian archipelago and the Neotropical high elevation ecosystem of the Páramos. Páramos constitute grasslands above the forest tree-line (at elevations of c. 2800–4700 m) with high species endemism. Organisms that occupy this ecosystem are a likely product of unique adaptations to an extreme environment that evolved during the last three to five million years when the Andes reached an altitude that was capable of sustaining this type of vegetation. We compared net diversification rates of lineages in fast evolving biomes using 73 dated molecular phylogenies. Based on our sample, we demonstrate that average net diversification rates of Páramo plant lineages are faster than those of other reportedly fast evolving hotspots and that the faster evolving lineages are more likely to be found in Páramos than the other hotspots. Páramos therefore represent the ideal model system for studying diversification processes. Most of the speciation events that we observed in the Páramos (144 out of 177) occurred during the Pleistocene possibly due to the effects of species range contraction and expansion that may have resulted from the well-documented climatic changes during that period. Understanding these effects will assist with efforts to determine how future climatic changes will impact plant populations. PMID:24130570

  9. Rapid evolution of dispersal ability makes biological invasions faster and more variable

    PubMed Central

    Ochocki, Brad M.; Miller, Tom E. X.

    2017-01-01

    Genetic variation in dispersal ability may result in the spatial sorting of alleles during range expansion. Recent theory suggests that spatial sorting can favour the rapid evolution of life history traits at expanding fronts, and therefore modify the ecological dynamics of range expansion. Here we test this prediction by disrupting spatial sorting in replicated invasions of the bean beetle Callosobruchus maculatus across homogeneous experimental landscapes. We show that spatial sorting promotes rapid evolution of dispersal distance, which increases the speed and variability of replicated invasions: after 10 generations of range expansion, invasions subject to spatial sorting spread 8.9% farther and exhibit 41-fold more variable spread dynamics relative to invasions in which spatial sorting is suppressed. Correspondingly, descendants from spatially evolving invasions exhibit greater mean and variance in dispersal distance. Our results reveal an important role for rapid evolution during invasion, even in the absence of environmental filters, and argue for evolutionarily informed forecasts of invasive spread by exotic species or climate change migration by native species. PMID:28128215

  10. Rapid evolution of dispersal ability makes biological invasions faster and more variable.

    PubMed

    Ochocki, Brad M; Miller, Tom E X

    2017-01-27

    Genetic variation in dispersal ability may result in the spatial sorting of alleles during range expansion. Recent theory suggests that spatial sorting can favour the rapid evolution of life history traits at expanding fronts, and therefore modify the ecological dynamics of range expansion. Here we test this prediction by disrupting spatial sorting in replicated invasions of the bean beetle Callosobruchus maculatus across homogeneous experimental landscapes. We show that spatial sorting promotes rapid evolution of dispersal distance, which increases the speed and variability of replicated invasions: after 10 generations of range expansion, invasions subject to spatial sorting spread 8.9% farther and exhibit 41-fold more variable spread dynamics relative to invasions in which spatial sorting is suppressed. Correspondingly, descendants from spatially evolving invasions exhibit greater mean and variance in dispersal distance. Our results reveal an important role for rapid evolution during invasion, even in the absence of environmental filters, and argue for evolutionarily informed forecasts of invasive spread by exotic species or climate change migration by native species.

  11. Monotremes and the evolution of rapid eye movement sleep.

    PubMed

    Siegel, J M; Manger, P R; Nienhuis, R; Fahringer, H M; Pettigrew, J D

    1998-07-29

    Early studies of the echidna led to the conclusion that this monotreme did not have rapid eye movement (REM) sleep. Because the monotremes had diverged from the placental and marsupial lines very early in mammalian evolution, this finding was used to support the hypothesis that REM sleep evolved after the start of the mammalian line. The current paper summarizes our recent work on sleep in the echidna and platypus and leads to a very different interpretation. By using neuronal recording from mesopontine regions in the echidna, we found that despite the presence of a high-voltage cortical electroencephalogram (EEG), brainstem units fire in irregular bursts intermediate in intensity between the regular non-REM sleep pattern and the highly irregular REM sleep pattern seen in placentals. Thus the echidna displays brainstem activation during sleep with high-voltage cortical EEG. This work encouraged us to do the first study of sleep, to our knowledge, in the platypus. In the platypus we saw sleep with vigorous rapid eye, bill and head twitching, identical in behaviour to that which defines REM sleep in placental mammals. Recording of the EEG in the platypus during natural sleep and waking states revealed that it had moderate and high-voltage cortical EEGs during this REM sleep state. The platypus not only has REM sleep, but it had more of it than any other animal. The lack of EEG voltage reduction during REM sleep in the platypus, and during the REM sleep-like state of the echidna, has some similarity to the sleep seen in neonatal sleep in placentals. The very high amounts of REM sleep seen in the platypus also fit with the increased REM sleep duration seen in altricial mammals. Our findings suggest that REM sleep originated earlier in mammalian evolution than had previously been thought and is consistent with the hypothesis that REM sleep, or a precursor state with aspects of REM sleep, may have had its origin in reptilian species.

  12. On the spectroscopic nature of the cool evolved Am star HD151878

    NASA Astrophysics Data System (ADS)

    Freyhammer, L. M.; Elkin, V. G.; Kurtz, D. W.

    2008-10-01

    Recently, Tiwari, Chaubey & Pandey detected the bright component of the visual binary HD151878 to exhibit rapid photometric oscillations through a Johnson B filter with a period of 6min (2.78mHz) and a high, modulated amplitude up to 22mmag peak-to-peak, making this star by far the highest amplitude rapidly oscillating Ap (roAp) star known. As a new roAp star, HD151878 is of additional particular interest as a scarce example of the class in the northern sky, and only the second known case of an evolved roAp star - the other being HD116114. We used the FIbre-fed Echelle Spectrograph at the Nordic Optical Telescope to obtain high time-resolution spectra at high dispersion to attempt to verify the rapid oscillations. We show here that the star at this epoch is spectroscopically stable to rapid oscillations of no more than a few tens of ms-1. The high-resolution spectra furthermore show the star to be of type Am rather than Ap and we show the star lacks most of the known characteristics for roAp stars. We conclude that this is an Am star that does not pulsate with a 6-min period. The original discovery of pulsation is likely to be an instrumental artefact. Based on observations collected at the Nordic Optical Telescope as part of programme 36-418. E-mail: lfreyham@gmail.com

  13. How Hierarchical Topics Evolve in Large Text Corpora.

    PubMed

    Cui, Weiwei; Liu, Shixia; Wu, Zhuofeng; Wei, Hao

    2014-12-01

    Using a sequence of topic trees to organize documents is a popular way to represent hierarchical and evolving topics in text corpora. However, following evolving topics in the context of topic trees remains difficult for users. To address this issue, we present an interactive visual text analysis approach to allow users to progressively explore and analyze the complex evolutionary patterns of hierarchical topics. The key idea behind our approach is to exploit a tree cut to approximate each tree and allow users to interactively modify the tree cuts based on their interests. In particular, we propose an incremental evolutionary tree cut algorithm with the goal of balancing 1) the fitness of each tree cut and the smoothness between adjacent tree cuts; 2) the historical and new information related to user interests. A time-based visualization is designed to illustrate the evolving topics over time. To preserve the mental map, we develop a stable layout algorithm. As a result, our approach can quickly guide users to progressively gain profound insights into evolving hierarchical topics. We evaluate the effectiveness of the proposed method on Amazon's Mechanical Turk and real-world news data. The results show that users are able to successfully analyze evolving topics in text data.

  14. Attack resilience of the evolving scientific collaboration network.

    PubMed

    Liu, Xiao Fan; Xu, Xiao-Ke; Small, Michael; Tse, Chi K

    2011-01-01

    Stationary complex networks have been extensively studied in the last ten years. However, many natural systems are known to be continuously evolving at the local ("microscopic") level. Understanding the response to targeted attacks of an evolving network may shed light on both how to design robust systems and finding effective attack strategies. In this paper we study empirically the response to targeted attacks of the scientific collaboration networks. First we show that scientific collaboration network is a complex system which evolves intensively at the local level--fewer than 20% of scientific collaborations last more than one year. Then, we investigate the impact of the sudden death of eminent scientists on the evolution of the collaboration networks of their former collaborators. We observe in particular that the sudden death, which is equivalent to the removal of the center of the egocentric network of the eminent scientist, does not affect the topological evolution of the residual network. Nonetheless, removal of the eminent hub node is exactly the strategy one would adopt for an effective targeted attack on a stationary network. Hence, we use this evolving collaboration network as an experimental model for attack on an evolving complex network. We find that such attacks are ineffectual, and infer that the scientific collaboration network is the trace of knowledge propagation on a larger underlying social network. The redundancy of the underlying structure in fact acts as a protection mechanism against such network attacks.

  15. A slowly evolving host moves first in symbiotic interactions

    NASA Astrophysics Data System (ADS)

    Damore, James; Gore, Jeff

    2011-03-01

    Symbiotic relationships, both parasitic and mutualistic, are ubiquitous in nature. Understanding how these symbioses evolve, from bacteria and their phages to humans and our gut microflora, is crucial in understanding how life operates. Often, symbioses consist of a slowly evolving host species with each host only interacting with its own sub-population of symbionts. The Red Queen hypothesis describes coevolutionary relationships as constant arms races with each species rushing to evolve an advantage over the other, suggesting that faster evolution is favored. Here, we use a simple game theoretic model of host- symbiont coevolution that includes population structure to show that if the symbionts evolve much faster than the host, the equilibrium distribution is the same as it would be if it were a sequential game where the host moves first against its symbionts. For the slowly evolving host, this will prove to be advantageous in mutualisms and a handicap in antagonisms. The model allows for symbiont adaptation to its host, a result that is robust to changes in the parameters and generalizes to continuous and multiplayer games. Our findings provide insight into a wide range of symbiotic phenomena and help to unify the field of coevolutionary theory.

  16. Phenotypic effect of mutations in evolving populations of RNA molecules

    PubMed Central

    2010-01-01

    Background The secondary structure of folded RNA sequences is a good model to map phenotype onto genotype, as represented by the RNA sequence. Computational studies of the evolution of ensembles of RNA molecules towards target secondary structures yield valuable clues to the mechanisms behind adaptation of complex populations. The relationship between the space of sequences and structures, the organization of RNA ensembles at mutation-selection equilibrium, the time of adaptation as a function of the population parameters, the presence of collective effects in quasispecies, or the optimal mutation rates to promote adaptation all are issues that can be explored within this framework. Results We investigate the effect of microscopic mutations on the phenotype of RNA molecules during their in silico evolution and adaptation. We calculate the distribution of the effects of mutations on fitness, the relative fractions of beneficial and deleterious mutations and the corresponding selection coefficients for populations evolving under different mutation rates. Three different situations are explored: the mutation-selection equilibrium (optimized population) in three different fitness landscapes, the dynamics during adaptation towards a goal structure (adapting population), and the behavior under periodic population bottlenecks (perturbed population). Conclusions The ratio between the number of beneficial and deleterious mutations experienced by a population of RNA sequences increases with the value of the mutation rate μ at which evolution proceeds. In contrast, the selective value of mutations remains almost constant, independent of μ, indicating that adaptation occurs through an increase in the amount of beneficial mutations, with little variations in the average effect they have on fitness. Statistical analyses of the distribution of fitness effects reveal that small effects, either beneficial or deleterious, are well described by a Pareto distribution. These results

  17. Educational Psychology as an Evolving Discipline: Trends and Synthesis in Asia Pacific Education Review

    ERIC Educational Resources Information Center

    Kim, Dong-il; Koh, Hye-jung; Jo, Su-yeon; Nam, JeeEun Karin; Kim, Myeung-chan

    2014-01-01

    Educational psychology has seen rapid growth as an academic discipline in recent years. The current study reviewed research articles published in "Asia Pacific Education Review" ("APER"), a journal that has been gaining greater international recognition, to reveal recent trends in educational psychology research in Asia…

  18. Numerical simulation of spatially-evolving instability control in plane channel flow

    NASA Technical Reports Server (NTRS)

    Danabasoglu, G.; Biringen, S.; Streett, C. L.

    1990-01-01

    The applicability of active control by periodic suction-blowing in spatially evolving plane Poiseuille flow is investigated by the direct simulations of the two-dimensional, incompressible Navier-Stokes equations. All the computations were performed for Reynolds number (Re = 7500) which is linearly unstable for this flow. The result reveal that significant reductions in perturbation amplitudes can be obtained by a proper choice of the control wave amplitude and phase even for large disturbance amplitudes. The upstream influence of the control wave is also investigated.

  19. Evolving Systems: An Outcome of Fondest Hopes and Wildest Dreams

    NASA Technical Reports Server (NTRS)

    Frost, Susan A.; Balas, Mark J.

    2012-01-01

    New theory is presented for evolving systems, which are autonomously controlled subsystems that self-assemble into a new evolved system with a higher purpose. Evolving systems of aerospace structures often require additional control when assembling to maintain stability during the entire evolution process. This is the concept of Adaptive Key Component Control that operates through one specific component to maintain stability during the evolution. In addition, this control must often overcome persistent disturbances that occur while the evolution is in progress. Theoretical results will be presented for Adaptive Key Component control for persistent disturbance rejection. An illustrative example will demonstrate the Adaptive Key Component controller on a system composed of rigid body and flexible body modes.

  20. Synthesis of Evolving Cells for Reconfigurable Manufacturing Systems

    NASA Astrophysics Data System (ADS)

    Padayachee, J.; Bright, G.

    2014-07-01

    The concept of Reconfigurable Manufacturing Systems (RMSs) was formulated due to the global necessity for production systems that are able to economically evolve according to changes in markets and products. Technologies and design methods are under development to enable RMSs to exhibit transformable system layouts, reconfigurable processes, cells and machines. Existing factory design methods and software have not yet advanced to include reconfigurable manufacturing concepts. This paper presents the underlying group technology framework for the design of manufacturing cells that are able to evolve according to a changing product mix by mechanisms of reconfiguration. The framework is based on a Norton- Bass forecast and time variant BOM models. An adaptation of legacy group technology methods is presented for the synthesis of evolving cells and two optimization problems are presented within this context.

  1. Cooperative coevolution: an architecture for evolving coadapted subcomponents.

    PubMed

    Potter, M A; De Jong, K A

    2000-01-01

    To successfully apply evolutionary algorithms to the solution of increasingly complex problems, we must develop effective techniques for evolving solutions in the form of interacting coadapted subcomponents. One of the major di