Sample records for classical biological control

  1. Current levels of suppression of waterhyacinth in Florida by classical biological control agents

    USDA-ARS?s Scientific Manuscript database

    Waterhyacinth, Eichhornia crassipes, has been a global target for classical biological control efforts for decades. In Florida, herbicides are the primary tactic employed, usually without regard for the activities of the three biological control agents introduced intentionally during the 1970's, na...

  2. Understanding the side effects of classical biological control

    Treesearch

    Dean Pearson

    2008-01-01

    Classical biological control involves the use of imported natural enemies to suppress or control populations of the target pest species below an economically or ecologically relevant threshold. Biological control is a useful tool for mitigating the impacts of exotic invasive plants; however, its application is not without risk (see Carruthers and D’Antonio...

  3. A Review of the Integration of Classical Biological Control with other Management Techniques to Manage Invasive Weeds in Natural Areas and Rangelands

    USDA-ARS?s Scientific Manuscript database

    Integrating classical biological control with other management techniques such as herbicide, fire, mechanical control, grazing, or plant competition, can be the most effective way to manage invasive weeds in natural areas and rangelands. Biological control agents can be protected from potential nega...

  4. Rationale for classical biological control of cattle fever ticks and proposed methods for field collection of natural enemies

    USDA-ARS?s Scientific Manuscript database

    Classical biological control using specialist parasitoids, predators and/or nematodes from the native ranges of cattle fever ticks Rhipicephalus microplus and Rhipicephalus annulatus could complement existing control strategies for this livestock pest in the transboundary region between Mexico and T...

  5. Retrospective Analysis of a Classical Biological Control Programme

    USDA-ARS?s Scientific Manuscript database

    1. Classical biological control has been a key technology in the management of invasive arthropod pests globally for over 120 years, yet rigorous quantitative evaluations of programme success or failure are rare. Here, I used life table and matrix model analyses, and life table response experiments ...

  6. Molecular comparison of cattle fever ticks from native and introduced ranges with insights into optimal search areas for classical biological control agents

    USDA-ARS?s Scientific Manuscript database

    Classical biological control using specialist parasitoids, predators and/or nematodes from the native ranges of cattle fever ticks could complement existing control strategies for this livestock pest in the transboundary region between Mexico and Texas. DNA fingerprinting tools were used to compare ...

  7. A review of introductions of pathogens and nematodes for classical biological control of insects and mites

    Treesearch

    Ann E. Hajek; Michael L. McManus; Italo Delalibera Junior

    2007-01-01

    Compared with parasitoids and predators, classical biological control programs targeting arthropod pests have used pathogens and nematodes very little. However, some pathogens and nematodes that have been introduced have become established and provided excellent control and have been introduced in increasing numbers of areas over decades, often after distributions of...

  8. Data from: Retrospective analysis of a classical biological control programme

    USDA-ARS?s Scientific Manuscript database

    This database contains the raw data for the publication entitled Naranjo, S.E. 2018. Retrospective analysis of a classical biological control programme. Journal of Applied Ecology https://doi.org/10.1111/1365-2664.13163. Specific data include field-based, partial life table data for immature stage...

  9. Genetic characterization for intraspecific hybridization of an exotic parasitoid prior its introduction for classical biological control

    USDA-ARS?s Scientific Manuscript database

    The successful establishment of an exotic parasitoid in the context of classical biological control of insect pests depends upon its adaptability to the new environment. In theory, intraspecific hybridization may improve the success of the establishment as a result of an increase in the available ge...

  10. Landscape simplification reduces classical biological control and crop yield.

    PubMed

    Grab, Heather; Danforth, Bryan; Poveda, Katja; Loeb, Greg

    2018-03-01

    Agricultural intensification resulting in the simplification of agricultural landscapes is known to negatively impact the delivery of key ecosystem services such as the biological control of crop pests. Both conservation and classical biological control may be influenced by the landscape context in which they are deployed; yet studies examining the role of landscape structure in the establishment and success of introduced natural enemies and their interactions with native communities are lacking. In this study, we investigated the relationship between landscape simplification, classical and conservation biological control services and importantly, the outcome of these interactions for crop yield. We showed that agricultural simplification at the landscape scale is associated with an overall reduction in parasitism rates of crop pests. Additionally, only introduced parasitoids were identified, and no native parasitoids were found in crop habitat, irrespective of agricultural landscape simplification. Pest densities in the crop were lower in landscapes with greater proportions of semi-natural habitats. Furthermore, farms with less semi-natural cover in the landscape and consequently, higher pest numbers, had lower yields than farms in less agriculturally dominated landscapes. Our study demonstrates the importance of landscape scale agricultural simplification in mediating the success of biological control programs and highlights the potential risks to native natural enemies in classical biological control programs against native insects. Our results represent an important contribution to an understanding of the landscape-mediated impacts on crop yield that will be essential to implementing effective policies that simultaneously conserve biodiversity and ecosystem services. © 2018 by the Ecological Society of America.

  11. Indirect nontarget effects of host-specific biological control agents: Implications for biological control

    Treesearch

    Dean E. Pearson; Ragan M. Callaway

    2005-01-01

    Classical biological control of weeds currently operates under the assumption that biological control agents are safe (i.e., low risk) if they do not directly attack nontarget species. However, recent studies indicate that even highly host-specific biological control agents can impact nontarget species through indirect effects. This finding has profound...

  12. Classical Biological Control of Invasive Legacy Crop Pests: New Technologies Offer Opportunities to Revisit Old Pest Problems in Perennial Tree Crops

    PubMed Central

    Hoddle, Mark S.; Warner, Keith; Steggall, John; Jetter, Karen M.

    2014-01-01

    Advances in scientific disciplines that support classical biological control have provided “new tools” that could have important applications for biocontrol programs for some long-established invasive arthropod pests. We suggest that these previously unavailable tools should be used in biological control programs targeting “legacy pests”, even if they have been targets of previously unsuccessful biocontrol projects. Examples of “new tools” include molecular analyses to verify species identities and likely geographic area of origin, climate matching and ecological niche modeling, preservation of natural enemy genetic diversity in quarantine, the use of theory from invasion biology to maximize establishment likelihoods for natural enemies, and improved understanding of the interactions between natural enemy and target pest microbiomes. This review suggests that opportunities exist for revisiting old pest problems and funding research programs using “new tools” for developing biological control programs for “legacy pests” could provide permanent suppression of some seemingly intractable pest problems. As a case study, we use citricola scale, Coccus pseudomagnoliarum, an invasive legacy pest of California citrus, to demonstrate the potential of new tools to support a new classical biological control program targeting this insect. PMID:26463063

  13. Climate matching: implications for the biological control of hemlock woolly adelgid

    Treesearch

    R. Talbot III Trotter

    2008-01-01

    Classical biological control programs are faced with a daunting challenge: inserting a new species into an existing ecological system. In order for the newly introduced biological control species to survive and reproduce, the recipient ecosystem must provide the required biotic and abiotic requirements. The Adelgid Biological Control simulator (ABCs), a simulation...

  14. Classical biological control of an invasive forest pest: a world perspective of the management of Sirex noctilio using the parasitoid Ibalia leucospoides (Hymenoptera: Ibaliidae).

    PubMed

    Fischbein, D; Corley, J C

    2015-02-01

    Classical biological control is a key method for managing populations of pests in long-lived crops such as plantation forestry. The execution of biological control programmes in general, as the evaluation of potential natural enemies remains, to a large extent, an empirical endeavour. Thus, characterizing specific cases to determine patterns that may lead to more accurate predictions of success is an important goal of the much applied ecological research. We review the history of introduction, ecology and behaviour of the parasitoid Ibalia leucospoides. The species is a natural enemy of Sirex noctilio, one of the most important pests of pine afforestation worldwide. We use an invasion ecology perspective given the analogy between the main stages involved in classical biological control and the biological invasion processes. We conclude that success in the establishment, a common reason of failure in biocontrol, is not a limiting factor of success by I. leucospoides. A mismatch between the spread capacity of the parasitoid and that of its host could nevertheless affect control at a regional scale. In addition, we suggest that given its known life history traits, this natural enemy may be a better regulator than suppressor of the host population. Moreover, spatial and temporal refuges of the host population that may favour the local persistence of the interaction probably reduce the degree to which S. noctilio population is suppressed by the parasitoid. We emphasize the fact that some of the biological attributes that promote establishment may negatively affect suppression levels achieved. Studies on established non-native pest-parasitoid interactions may contribute to defining selection criteria for classical biological control which may prove especially useful in integrated pest management IPM programmes of invasive forest insects.

  15. Pre-release host range assessment for classical biological controls: experience with predators for the hemlock woolly adelgid

    Treesearch

    Elizabeth Butin; Montgomery Montgomery; Nathan Havill; Joseph Elkinton

    2002-01-01

    There are few regulations for the release of parasitoids and predators, compared to herbivorous arthropods and pathogens, used as classical biological control agents in the United States. The types of tests conducted prior to release of the predator or parasitoid into the environment are often up to the individual wishing to introduce the new agent. Ethical researchers...

  16. Biological Control of Southern Pine Beetle

    Treesearch

    Fred M. Stephen; C. Wayne Berisford

    2011-01-01

    Exotic invasive forest insects are frequently managed through classical biological control, which involves searching for, introducing, and establishing their exotic natural enemies. Biological control of native bark beetles, including the southern pine beetle (SPB), has been primarily attempted by conserving and manipulating their natural enemies. Knowledge of the role...

  17. Simulations of population dynamics of hemlock woolly adelgid and potential impact of biological control agents

    Treesearch

    Joseph S. Elkinton; Robert T. Trotter; Ann F. Paradis

    2011-01-01

    The hemlock woolly adelgid (Adelges tsugae) is a small invasive Hemipteran herbivore that threatens the continued presence and abundance of hemlock in eastern North America. Efforts to control the adelgid have focused on the introduction of classical biological control agents. These biological controls include six different species of predatory...

  18. Understanding Federal regulations as guidelines for classical biological control programs

    Treesearch

    Michael E. Montgomery

    2011-01-01

    This chapter reviews the legislation and rules that provide the foundation for federal regulation of the introduction of natural enemies of insects as biological control agents. It also outlines the steps for complying with regulatory requirements, using biological control of Adelges tsugae Annand, the hemlock woolly adelgid (HWA), as an example. The...

  19. Biodiversity, ecosystem functioning, and classical biological control.

    PubMed

    Evans, Edward W

    Increasing concern over worldwide loss of biodiversity has led ecologists to focus intently on how ecosystem functioning may depend on diversity. In applied entomology, there is longstanding interest in the issue, especially as regards the importance of natural enemy diversity for pest control. Here I review parallels in interest, conceptual framework, and conclusions concerning biodiversity as it affects ecosystem functioning in general and classical biological control in particular. Whereas the former focuses on implications of loss of diversity, the latter focuses on implications of increase in diversity as additional species of natural enemies are introduced to novel communities in new geographic regions for insect pest and weed control. Many field studies now demonstrate that ecosystem functioning, e.g., as reflected in primary productivity, is enhanced and stabilized over time by high diversity as the community increases in its efficiency in exploiting available resources. Similarly, there is growing field support for the generalization that increasing species and functional diversity of natural enemies leads to increasing pest suppression. Nonetheless a central concern of classical biological control in particular, as it seeks to minimize non-target effects, remains as to whether one or a few species of natural enemies can provide sufficient pest control.

  20. Mutual benefits through formalized international collaboration on biological control of weeds with plant pathogens

    USDA-ARS?s Scientific Manuscript database

    In the U.S., introduced invasive weeds have catastrophic effects on agricultural, aquatic, rangeland, riparian, and natural ecosystems. Often the only economically feasible means for controlling these weeds is classical biological control through the introduction of natural enemies, including plant ...

  1. Biology, host specificity tests, and risk assessment of the sawfly Heteroperreyia hubrichi, a potential biological control agent of Schinus terebinthifolius in Hawaii

    USDA-ARS?s Scientific Manuscript database

    Abstract. Heteroperreyia hubrichi Malaise (Hymenoptera: Pergidae), a foliage feeding sawfly of Schinus terebinthifolius Raddi (Sapindales: Anacardiaceae), was studied to assess its suitability as a classical biological control agent of this invasive weed in Hawaii. Nochoice host-specificity tests we...

  2. Host Specificity of Argopistes tsekooni (Coleoptera: Chrysomelidae), a Potential Biological Control Agent of Chinese Privet

    Treesearch

    Yan Zhuo Zhang; James Hanula; Jiang Hua Sun

    2008-01-01

    Chinese privet, Ligustrum sinense Lour., is a perennial semi-evergreen shrub that is aserious invasive weed in the United States. Classical biological control offers the best hope forcontrolling it in an economic, effective, and persistent way. Host...

  3. Hybridization between a native and introduced predator of Adelgidae: An unintended result of classical biological control

    Treesearch

    N.P. Havill; Gina Davis; David Mausel; Joanne Klein; Richard McDonald; Cera Jones; Melissa Fischer; Scott Salom; Adelgisa Caccone

    2012-01-01

    Hybridization between introduced biological control agents and native species has the potential to impact native biodiversity and pest control efforts. This study reports progress towards predicting the outcome of hybridization between two beetle species, the introduced Laricobius nigrinus Fender and the native L. rubidus LeConte...

  4. Status of biological control projects on terrestrial invasive alien weeds in California

    USDA-ARS?s Scientific Manuscript database

    In cooperation with foreign scientists, we are currently developing new classical biological control agents for five species of invasive alien terrestrial weeds. Cape-Ivy. A gall-forming fly, Parafreutreta regalis, and a stem-boring moth, Digitivalva delaireae, have been favorably reviewed by TAG...

  5. Biology and host range of Tecmessa elegans (Lepidoptera:Notodontidae) a leaf-feeding moth evaluated as a potential biological control agent for Schinus terebinthifolius (Sapindales: Anacardiaceae) in the USA

    USDA-ARS?s Scientific Manuscript database

    During surveys for natural enemies that could potentially be used as classical biological control agents of Schinus terebinthifolius Raddi (Brazilian pepper) which is invasive in the USA, the caterpillar, Tecmessa elegans Schaus (Lepidoptera: Notodontidae), was recorded feeding on the leaves of the ...

  6. Improvement of mass-rearing procedures for an olive fruit fly parasitoid – duration of exposure to hosts affects production of Psyttalia lounsburyi

    USDA-ARS?s Scientific Manuscript database

    The olive fruit fly, Bactrocera oleae (Diptera: Tephritidae), causes severe economic damage in California. Control of this fly is currently limited to pesticides. The USDA-ARS European Biological Control Laboratory in Montpellier, France established a classical biological control program nearly 15 y...

  7. Finalizing host range determination of a weed biological control pathogen with BLUPs and damage assessment

    USDA-ARS?s Scientific Manuscript database

    Colletotrichum gloeosporioides f. sp. salsolae (Penz.) Penz. & Sacc. in Penz. (CGS) is a facultative parasitic fungus being evaluated as a classical biological control agent of Russian thistle or tumbleweed (Salsola tragus L.). In initial host range determination tests, Henderson’s mixed model equat...

  8. Status of biological control projects on yellow starthistle, Russian thistle, Scotch thistle, Cape-ivy and French broom

    USDA-ARS?s Scientific Manuscript database

    The USDA-ARS quarantine laboratory in Albany, CA, in cooperation with foreign scientists, is currently developing classical biological control agents for five species of invasive alien terrestrial weeds. Host specificity testing of the yellow starthistle rosette weevil, Ceratapion basicorne, indica...

  9. Host plant oviposition preference of Ceratapion basicorne (Coleoptera:Apionidae), a potential biological control agent of yellow starthistle

    USDA-ARS?s Scientific Manuscript database

    Ceratapion basicorne (Coleoptera: Apionidae) is a weevil native to Europe and western Asia that is being evaluated as a prospective classical biological control agent of Centaurea solstitialis (yellow starthistle) in the United States. Choice oviposition experiments were conducted under laboratory ...

  10. Diapause in Abrostola asclepiadis (Lepidoptera: Noctuidae) may make for an ineffective weed biological control agent

    USDA-ARS?s Scientific Manuscript database

    Pale and black swallow-wort (Vincetoxicum rossicum and V. nigrum; Apocynaceae, subfamily Asclepiadoideae) are perennial vines from Europe that are invasive in various terrestrial habitats in the northeastern USA and southeastern Canada. A classical weed biological control program has been in develop...

  11. Recent progress in a classical biological control program for olive fruit fly in California

    USDA-ARS?s Scientific Manuscript database

    The olive fruit fly, Bactrocera oleae (Diptera: Tephritidae), causes severe damage to olive production worldwide. Control of olive fruit fly typically relies on pesticides, and under such conditions the impact of natural enemies is relatively low. About 15 years ago, the USDA-ARS European Biologic...

  12. Russian olive - a suitable target for classical biological control in North America? In: Wu, Yun; Johnson, Tracy; Sing, Sharlene; Raghu, S.; Wheeler, Greg; Pratt, Paul; Warner, Keith; Center, Ted; Goolsby, John; Reardon, Richard, eds

    Treesearch

    K. Delaney; E. Espeland; A. Norton; S. Sing; K. Keever; J. L. Baker; M. Cristofaro; R. Jashenko; J. Gaskin; U. Schaffner

    2013-01-01

    Projects to develop biological control solutions against invasive plants are midto long-term endeavors that require considerable financial support over several years. Discussions of concerns and potential conflicts of interests often occur when biological control agents are first being proposed for release into the environment. Such late discussion, which in some cases...

  13. Egg Parasitoids from Pakistan as possible classical biological control agents of the invasive pest, Bagrada hilaris (Heteroptera: Pentatomidae)

    USDA-ARS?s Scientific Manuscript database

    The newly invasive pest stink bug, Bagrada hilaris, threatens the cole crop industry and certain ornamentals in the U.S. Without its co-evolved natural enemies, it is likely to spread from the Southwest U.S. to the east coast, requiring millions more dollars to control it. If key biological control ...

  14. Monitoring the establishment and abundance of introduced parasitoids of emerald ash borer larvae in Maryland, U.S.A

    USDA-ARS?s Scientific Manuscript database

    Classical biological control can be an important tool for managing invasive species such as emerald ash borer, Agrilus planipennis Fairmaire. Emerald ash borer is now widespread throughout the United States, and was first detected in Maryland in 2003. The biological control program to manage emera...

  15. Potential classical biological control of invasive Himalayan yellow raspberry, Rubus ellipticus

    USDA-ARS?s Scientific Manuscript database

    Rubus ellipticus is one of the world's worst invasive alien species. It is a serious problem in Hawaii and Queensland and has naturalized in many other countries. Biological control is being considered as a means to suppress it by introducing natural enemies from Asia, its native region. In this pap...

  16. Using a Classic Paper by I. E. Lawton and N. B. Schwartz to Consider the Array of Factors that Control Luteinizing Hormone Production

    ERIC Educational Resources Information Center

    Bauer-Dantoin, Angela C.; Hanke, Craig J.

    2007-01-01

    Two significant benefits derived from reading and discussing classic scientific papers in undergraduate biology courses are 1) providing students with the realistic perspective that science is an ongoing process (rather than a set of inarguable facts) and 2) deepening the students' understanding of physiological processes. A classic paper that is…

  17. Economic value of biological control in integrated pest management of managed plant systems.

    PubMed

    Naranjo, Steven E; Ellsworth, Peter C; Frisvold, George B

    2015-01-07

    Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.

  18. Field Monitoring of Drosophila suzukii and Associated Communities in South Eastern France as a Pre-Requisite for Classical Biological Control

    PubMed Central

    Kremmer, Laurent; Thaon, Marcel; Borowiec, Nicolas; David, Jean; Poirié, Marylène; Ris, Nicolas

    2017-01-01

    The spotted wing Drosophila, Drosophila suzukii (Ds), became a major economic pest for fruit production since its establishment in Europe and America. Among potential control methods, only classical biological control appears to be a mean of sustainably regulating Ds in both cultivated and natural habitats. In the frame of risk assessment, pre-release surveys were carried out in a restricted but highly heterogeneous area in the south-east of France using traps and deliberate field exposures of Ds and D. melanogaster larvae/pupae. Although Ds abundance varied according to sampling methods, it was found to be pervasive and to produce offspring and adults in most conditions (spatial and seasonal). Its main limits are some specific abiotic conditions (i.e., desiccation) as well as interspecific competition. Indeed, Ds mostly co-occurred with D. busckii and D. hydei, probably due to common phenology and/or ecological requirements. These two species thus deserve more attention for risk assessment. The main indigenous parasitoids collected belonged to two pupal species, Trichopria cf drosophilae and Pachycrepoideus vindemmiae, but their presence was observed late in the autumn and mainly in cultivated areas. Results are discussed in a comparison of the methodological approaches for monitoring Drosophilids and the benefits-risks assessment of classical biological control. PMID:29144440

  19. Effect of exposure time on mass-rearing production of the olive fruit fly parasitoid, Psyttalia lounsburyi (Hymenoptera: Braconidae)

    USDA-ARS?s Scientific Manuscript database

    Classical biological control programs rely on mass-production of high quality beneficial insects for subsequent releases into the field. Psyttalia lounsburyi (Silvestri) (Hymenoptera: Braconidae) is a koinobiont larval-pupal endoparasitoid of tephritid flies that is being reared to support a classic...

  20. Laboratory and field experimental evaluation of host plant specificity of Aceria solstitialis, a prospective biological control agent of yellow starthistle

    USDA-ARS?s Scientific Manuscript database

    Yellow starthistle (Centaurea solstitialis) is an invasive annual weed in the western USA that is native to the Mediterranean Region and is a target for classical biological control. Aceria solstitialis is an eriophyid mite that has been found exclusively in association with yellow starthistle in I...

  1. Genetic and morphological studies of Trichosirocalus species introduced to North America, Australia and New Zealand for the biological control of thistles

    USDA-ARS?s Scientific Manuscript database

    Trichosirocalus horridus sensu lato has been used as a classical biological control agent of several invasive alien thistles (Carduus spp., Cirsium spp. and Onopordum spp.) since 1974. Trichosirocalus horridus was recognized as a single species until 2002, when it was split into three species based ...

  2. Progress and challenges of protecting North American ash trees from the emerald ash borer using biological control

    Treesearch

    Jian Duan; Leah Bauer; Roy van Driesche; Juli Gould

    2018-01-01

    After emerald ash borer (EAB), Agrilus planipennis Fairmaire, was discovered in the United States, a classical biological control program was initiated against this destructive pest of ash trees (Fraxinus spp.). This biocontrol program began in 2007 after federal regulatory agencies and the state of Michigan approved release of...

  3. Lack of native vegetation recovery following biological control of leafy spurge

    Treesearch

    Jack L. Butler; Stefanie D. Wacker

    2010-01-01

    Leafy spurge (Euphorbia esula L.) is an aggressive exotic species that has been successfully suppressed in a variety of situations using classical biological control (flea beetles; Aphthona spp.). This 9-yr study investigated patterns of vegetation responses following significant reductions in leafy spurge cover and density by flea beetles in southeastern Montana. We...

  4. Cold tolerance of Trissolcus japonicus and T. cultratus, potential biological control agents of Halyomorpha halys, the brown marmorated stink bug

    Treesearch

    Erica Nystrom Santacruz; Robert C. Venette; Christine Dieckhoff; Kim Hoelmer; Robert L. Koch

    2017-01-01

    Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) is native to Asia and has become a severe agricultural and nuisance pest in the U.S. Therefore, foreign exploration was conducted in Asia to identify potential classical biological control agents. Several Trissolcus spp. (Hymenoptera: Scelionidae) parasitize H. halys...

  5. Current knowledge and attitudes: Russian olive biology, ecology and management

    Treesearch

    Sharlene E. Sing; Kevin J. Delaney

    2016-01-01

    The primary goals of a two-day Russian olive symposium held in February 2014 were to disseminate current knowledge and identify data gaps regarding Russian olive biology and ecology, distributions, integrated management, and to ascertain the feasibility and acceptance of a proposed program for classical biological control of Russian olive. The symposium was...

  6. Design and control strategies for CELSS - Integrating mechanistic paradigms and biological complexities

    NASA Technical Reports Server (NTRS)

    Moore, B., III; Kaufmann, R.; Reinhold, C.

    1981-01-01

    Systems analysis and control theory consideration are given to simulations of both individual components and total systems, in order to develop a reliable control strategy for a Controlled Ecological Life Support System (CELSS) which includes complex biological components. Because of the numerous nonlinearities and tight coupling within the biological component, classical control theory may be inadequate and the statistical analysis of factorial experiments more useful. The range in control characteristics of particular species may simplify the overall task by providing an appropriate balance of stability and controllability to match species function in the overall design. The ultimate goal of this research is the coordination of biological and mechanical subsystems in order to achieve a self-supporting environment.

  7. F1 Sterile insect technique: a novel approach for risk assessment of Episimus unguiculus (Lepidoptera: Tortricidae), a candidate biological control agent of Schinus terebinthifolus in the Continental USA

    USDA-ARS?s Scientific Manuscript database

    Federal regulations mandate that researchers in the field of classical weed biological control follow the precautionary principle when proposing the release of an organism that can affect our environment. However, the host range observed in traditional laboratory cage experiments typically is broad...

  8. External rostral characters for differentiation of sexes in the biological control agent Mecinus janthinus (Coleoptera: Curculionidae)

    Treesearch

    Marjolein Schat; Sharlene E. Sing; Robert K. D. Peterson

    2007-01-01

    The stem-boring weevil, Mecinus janthinus (Germar), is a promising, well established classical biological control agent for the exotic invasive weed Dalmatian toadflax (Linaria dalmatica (L.) Mill.) (Scrophulariaceae). In this paper we present readily apparent rostral characters that can be used for sex differentiation of live stem-boring weevils at low magnification....

  9. Releases of natural enemies in Hawaii since 1980 for classical biological control of weeds

    Treesearch

    P. Conant; J. N. Garcia; M. T. Johnson; W. T. Nagamine; C. K. Hirayama; G. P. Markin; R. L. Hill

    2013-01-01

    A comprehensive review of biological control of weeds in Hawaii was last published in 1992, covering 74 natural enemy species released from 1902 through 1980. The present review summarizes releases of 21 natural enemies targeting seven invasive weeds from 1981 to 2010. These projects were carried out by Hawaii Department of Agriculture (HDOA), USDA Forest Service (USFS...

  10. Effect of Fopius arisanus Sonan oviposition experience on parasitization of Bactrocera dorsalis Hendel

    USDA-ARS?s Scientific Manuscript database

    Fopius arisanus (Sonan) (Hymenoptera: Braconidae) is an important fruit fly parasitoid, successfully introduced in programs of classical biological control around the world. One aspect of its reproductive biology that has received increasing attention is the role of learning on parasitization by ind...

  11. Effect of mechanical damage on emission of volatile organic compounds from plant leaves and implications for evaluation of host plant specificity of prospective biological control agents of weeds

    USDA-ARS?s Scientific Manuscript database

    Assessment of host plant specificity is a critical step in the evaluation of classical biological control agents of weeds, which is necessary for avoiding possible damage to nontarget plants. Volatile organic compounds (VOC) emitted by plants likely play an important role in determining which plant...

  12. Yellow starthistle rust: summary of release, establishment and biology in California

    USDA-ARS?s Scientific Manuscript database

    The rust pathogen, Puccinia jaceae var. solstitialis, was collected in Turkey for use as a classical biological control of yellow starthistle, which is an invasive alien weed. During pre-release evaluation of risk to 65 nontarget plant species, the rust infected only the target weed and bachelor's b...

  13. Biology and host preferences of Cryptorhynchus melastomae (Coleoptera: Curculionidae), a possible biocontrol agent for Miconia calvescens (Melastomataceae) in Hawaii

    Treesearch

    E. Reichert; M.T. Johnson; E. Chacon; R.S. Anderson; T.A. Wheeler

    2010-01-01

    The introduced plant Miconia calvescens (Melastomataceae) poses a grave threat to Hawaii's native ecosystems and biodiversity. One potential candidate for classical biological control is Cryptorhynchus melastomae (Coleoptera: Curculionidae: Cryptorhynchinae), a stem-boring weevil from Central and South America. This weevil...

  14. Establishment and abundance of Tetrastichus planipennisi (Hymenoptera: Eulophidae) in Michigan: potential for success in classical biocontrol of the invasive emerald ash borer (Coleoptera: Buprestidae)

    Treesearch

    Jian J. Duan; Leah S. Bauer; Kristopher J. Abell; Jonathan P. Lelito; Roy. Van Driesche

    2013-01-01

    Tetrastichus planipennisi Yang is a gregarious larval endoparasitoid native to China and has been introduced to the United States since 2007 for classical biological control of the invasive emerald ash borer, Agrilus planipennis Fairmaire, an exotic beetle responsible for widespread ash mortality. Between 2007-2010, T....

  15. Factors affecting the flight capacity of Tetrastichus planipennisi (Hymenoptera: Eulophidae), a classical biological control agent of Agrilus planipennis (Coleoptera: Buprestidae).

    PubMed

    Fahrner, Samuel J; Lelito, Jonathan P; Blaedow, Karen; Heimpel, George E; Aukema, Brian H

    2014-12-01

    The dispersal characteristics of a biological control agent can have direct implications on the ability of that agent to control populations of a target host. Tetrastichus planipennisi Yang (Hymenoptera: Eulophidae) is a parasitic wasp native to eastern Asia that has been introduced into the United States as part of a classical biological control program against the emerald ash borer Agrilus planipennis Fairmaire (Coleoptera: Buprestidae). We used computer-monitored flight mills to investigate the role of age, feeding status, mating status, and size on the flight capacity of female T. planipennisi over a 24-h period. We also compared flight capacity between sexes. Flight distance of female T. planipennisi representative of populations released in the biological control program averaged 1.26 km in 24 h with a maximum flight of just over 7 km. Median flight distance, however, was 422 m. The flight capacity of females fed a honey-water solution was 41× that of females provided only water, who flew very little. Larger females were capable of flying farther distances, but age did not affect the flight capacity of females up to 70 d posteclosion. Females dispersed 6× farther than did their smaller, male counterparts. The implications of our findings to host-parasitoid interactions and release protocols for distributing T. planipennisi are discussed.

  16. Biomedical implications of information processing in chemical systems: non-classical approach to photochemistry of coordination compounds.

    PubMed

    Szaciłowski, Konrad

    2007-01-01

    Analogies between photoactive nitric oxide generators and various electronic devices: logic gates and operational amplifiers are presented. These analogies have important biological consequences: application of control parameters allows for better targeting and control of nitric oxide drugs. The same methodology may be applied in the future for other therapeutic strategies and at the same time helps to understand natural regulatory and signaling processes in biological systems.

  17. Erythrocyte shape abnormalities, membrane oxidative damage, and β-actin alterations: an unrecognized triad in classical autism.

    PubMed

    Ciccoli, Lucia; De Felice, Claudio; Paccagnini, Eugenio; Leoncini, Silvia; Pecorelli, Alessandra; Signorini, Cinzia; Belmonte, Giuseppe; Guerranti, Roberto; Cortelazzo, Alessio; Gentile, Mariangela; Zollo, Gloria; Durand, Thierry; Valacchi, Giuseppe; Rossi, Marcello; Hayek, Joussef

    2013-01-01

    Autism spectrum disorders (ASDs) are a complex group of neurodevelopment disorders steadily rising in frequency and treatment refractory, where the search for biological markers is of paramount importance. Although red blood cells (RBCs) membrane lipidomics and rheological variables have been reported to be altered, with some suggestions indicating an increased lipid peroxidation in the erythrocyte membrane, to date no information exists on how the oxidative membrane damage may affect cytoskeletal membrane proteins and, ultimately, RBCs shape in autism. Here, we investigated RBC morphology by scanning electron microscopy in patients with classical autism, that is, the predominant ASDs phenotype (age range: 6-26 years), nonautistic neurodevelopmental disorders (i.e., "positive controls"), and healthy controls (i.e., "negative controls"). A high percentage of altered RBCs shapes, predominantly elliptocytes, was observed in autistic patients, but not in both control groups. The RBCs altered morphology in autistic subjects was related to increased erythrocyte membrane F2-isoprostanes and 4-hydroxynonenal protein adducts. In addition, an oxidative damage of the erythrocyte membrane β-actin protein was evidenced. Therefore, the combination of erythrocyte shape abnormalities, erythrocyte membrane oxidative damage, and β-actin alterations constitutes a previously unrecognized triad in classical autism and provides new biological markers in the diagnostic workup of ASDs.

  18. Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

    PubMed

    Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

    2018-04-01

    Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Guiding Classical Biological Control of an Invasive Mealybug Using Integrative Taxonomy

    PubMed Central

    Beltrà, Aleixandre; Addison, Pia; Ávalos, Juan Antonio; Crochard, Didier; Garcia-Marí, Ferran; Guerrieri, Emilio; Giliomee, Jan H.; Malausa, Thibaut; Navarro-Campos, Cristina; Palero, Ferran; Soto, Antonia

    2015-01-01

    Delottococcus aberiae De Lotto (Hemiptera: Pseudococcidae) is a mealybug of Southern African origin that has recently been introduced into Eastern Spain. It causes severe distortions on young citrus fruits and represents a growing threat to Mediterranean citrus production. So far, biological control has proven unsatisfactory due to the absence of efficient natural enemies in Spain. Hence, the management of this pest currently relies only on chemical control. The introduction of natural enemies of D. aberiae from the native area of the pest represents a sustainable and economically viable alternative to reduce the risks linked to pesticide applications. Since biological control of mealybugs has been traditionally challenged by taxonomic misidentification, an intensive survey of Delottococcus spp. and their associated parasitoids in South Africa was required as a first step towards a classical biological control programme. Combining morphological and molecular characterization (integrative taxonomy) a total of nine mealybug species were identified in this study, including three species of Delottococcus. Different populations of D. aberiae were found on wild olive trees, in citrus orchards and on plants of Chrysanthemoides monilifera, showing intra-specific divergences according to their host plants. Interestingly, the invasive mealybug populations from Spanish orchards clustered together with the population on citrus from Limpopo Province (South Africa), sharing COI haplotypes. This result pointed to an optimum location to collect natural enemies against the invasive mealybug. A total of 14 parasitoid species were recovered from Delottococcus spp. and identified to genus and species level, by integrating morphological and molecular data. A parasitoid belonging to the genus Anagyrus, collected from D. aberiae in citrus orchards in Limpopo, is proposed here as a good biological control agent to be introduced into Spain. PMID:26047349

  20. Effect of individualized goal-setting on college biology students' locus of control

    NASA Astrophysics Data System (ADS)

    Schafer, John E.

    This study investigated the effect of Individualized Goal-Setting A-T, relative to Classic A-T, on a student's locus of control (generalized and academic). This study also examined the effect of pretesting, relative to no pretesting, on a student's locus of control. Sixty students in an introductory, Audio-Tutorial, college zoology course were randomly assigned to treatment and control groups. Control groups (Classic A-T) completed the course in the usual manner. Treatment groups (IGS A-T) completed the course in the usual manner with one exception. That is, they used a different format for Optional Minicourse mastery. This new format released greater control to students over means as well as ends of minicourse mastery. Data were collected through use of the Solomon Four-Group design, with two levels of treatment (Classic A-T, IGS A-T) and two levels of pretesting (pretest, no pretest). Instruments included the Rotter I-E and Schafer Academic I-E Locus of Control Scales. Posttest scores were analyzed by a 2 × 2 multivariate analysis of variance (MANOVA).The following conclusions were made (p < 0.10).1IGS A-T, relative to Classic A-T, has no significant effect on a student's locus of control.2Pretesting, relative to no pretesting, has no significant effect on posttest locus of control.

  1. Classical biological control of invasive species: fighting fire with fire

    USDA-ARS?s Scientific Manuscript database

    Invasive species cost the US over $130 billion in losses and control costs every year. Exotic insects, weeds and pathogens are the primary invaders that frequently move across continents, exploding in numbers in areas where they have been newly introduced. There are many reasons that these pests r...

  2. Fine control of nuclear confinement identifies a threshold deformation leading to lamina rupture and induction of specific genes.

    PubMed

    Le Berre, Maël; Aubertin, Johannes; Piel, Matthieu

    2012-11-01

    The quest to understand how the mechanical and geometrical environment of cells impacts their behavior and fate has been a major force driving the recent development of new technologies in cell biology research. Despite rapid advances in this field, many challenges remain in order to bridge the gap between the classical and simple cell culture plate and the biological reality of actual tissue. In tissues, cells have their physical space constrained by neighboring cells and the extracellular matrix. Here, we propose a simple and versatile device to precisely and dynamically control this confinement parameter in cultured cells. We show that there is a precise threshold deformation above which the nuclear lamina breaks and reconstructs, whereas nuclear volume changes. We also show that different nuclear deformations correlate with the expression of specific sets of genes, including nuclear factors and classical mechanotransduction pathways. This versatile device thus enables the precise control of cell and nuclear deformation by confinement and the correlative study of the associated molecular events.

  3. The impacts of a stem boring weevil, Mecinus janthinus, on dalmatian toadflax, Linaria dalmatica

    Treesearch

    Marjolein Schat

    2008-01-01

    Classical biological control of weeds is generally considered an effective, safe, and cost effective tool for controlling widespread weeds in natural areas. However, only 60% of releases have become established and, of those, only 50% have led to control. Therefore, understanding the impacts of agents on target weeds across spatial scales, at different insect densities...

  4. Establishment, dispersal, and competitive impacts of a third fire ant decapitating fly (Pseudacteon obtusus) in North Central Florida

    USDA-ARS?s Scientific Manuscript database

    Self-sustaining classical biological control agents offer a hope for permanent wide-area control of imported Solenopsis fire ants in the United States because escape from abundant natural enemies left behind in Argentina is a likely reason for unusually high fire ant densities in the United States. ...

  5. Augmentative Biological Control Using Parasitoids for Fruit Fly Management in Brazil

    PubMed Central

    Garcia, Flávio R. M.; Ricalde, Marcelo P.

    2012-01-01

    The history of classical biological control of fruit flies in Brazil includes two reported attempts in the past 70 years. The first occurred in 1937 when an African species of parasitoid larvae (Tetrastichus giffardianus) was introduced to control the Mediterranean fruit fly, Ceratitis capitata and other tephritids. The second occurred in September 1994 when the exotic parasitoid Diachasmimorpha longicaudata, originally from Gainesville, Florida, was introduced by a Brazilian agricultural corporation (EMBRAPA) to evaluate the parasitoid’s potential for the biological control of Anastrepha spp. and Ceratitis capitata. Although there are numerous native Brazilian fruit fly parasitoids, mass rearing of these native species is difficult. Thus, D. longicaudata was chosen due to its specificity for the family Tephritidae and its ease of laboratory rearing. In this paper we review the literature on Brazilian fruit fly biological control and suggest that those tactics can be used on a large scale, together creating a biological barrier to the introduction of new fruit fly populations, reducing the source of outbreaks and the risk of species spread, while decreasing the use of insecticides on fruit destined for domestic and foreign markets. PMID:26466795

  6. Impact of introduction of Bactrocera dorsalis (Diptera: Tephritidae) and classical biological control releases of Fopius arisanus (Hymenoptera: Braconidae) on economically important fruit flies in French Polynesia.

    PubMed

    Vargas, Roger I; Leblanc, Luc; Putoa, Rudolph; Eitam, Avi

    2007-06-01

    Oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), was discovered on Tahiti Island in July 1996. Eradication programs were conducted from 1997 to 2001, but failed. From 1998 to 2006, B. dorsalis was recovered from 29 different host fruit from the five Society Islands: Tahiti, Moorea, Raiatea, Tahaa, and Huahine. Analysis of coinfestation patterns by B. dorsalis, Bactrocera tryoni (Froggatt), and Bactrocera kirki (Froggatt) suggested B. dorsalis had displaced these two species and become the most abundant fruit fly in coastal areas. To suppress B. dorsalis populations, a classical biological control program was initiated to introduce the natural enemy Fopius arisanus (Sonan) (Hymenoptera: Braconidae) into French Polynesia from Hawaii. Wasps were released and established on Tahiti, Moorea, Raiatea, Tahaa, and Huahine Islands. In guava, Psidium guajava L., collections for Tahiti, F. arisanus parasitism of fruit flies was 2.1, 31.8, 37.5, and 51.9% for fruit collected for 2003, 2004, 2005 and 2006, respectively. Based on guava collections in 2002 (before releases) and 2006 (after releases), there was a subsequent decrease in numbers of B. dorsalis, B. tryoni, and B. kirki fruit flies emerging (per kilogram of fruit) by 75.6, 79.3, and 97.9%, respectively. These increases in F. arisanus parasitism and decreases in infestation were similar for other host fruit. Establishment of F. arisanus is the most successful example of classical biological control of fruit flies in the Pacific area outside of Hawaii and serves as a model for introduction into South America, Africa, and China where species of the B. dorsalis complex are established.

  7. Synthetic Biology: Life, Jim, but Not As We Know It

    NASA Astrophysics Data System (ADS)

    Hallinan, Jennifer

    Frankenstein, Mary Shelley's classic tale of horror, warns of the perils of hubris: of the terrible fate that awaits when Man plays God and attempts to create life. Molecular biologists are clearly not listening. Not content with merely inserting the occasional gene into the genome of an existing organism. they are developing a whole new field, Synthetic Biology, which aims to engineer from first principles organisms with desirable, controllable qualities.

  8. Key to Nearctic Trissolcus Ashmead

    USDA-ARS?s Scientific Manuscript database

    Trissolcus japonicus (Ashmead) and T. cultratus (Mayr) comb. rev. are under study as classical biological agents to control the brown marmorated stink bug Halyomorpha halys (Stål) in North America. Here we present diagnoses for all Nearctic species of Trissolcus, including T. japonicus and T. cultra...

  9. Biology and host range of Tecmessa elegans (Lepidoptera: Notodontidae), a leaf-feeding moth evaluated as a potential biological control agent for Schinus terebinthifolius (Sapindales: Anacardiaceae) in the United States.

    PubMed

    Oleiro, Marina; Mc Kay, Fernando; Wheeler, Gregory S

    2011-06-01

    During surveys for natural enemies that could be used as classical biological control agents of Schinus terebinthifolius Raddi (Brazilian pepper), the caterpillar, Tecmessa elegans Schaus (Lepidoptera: Notodontidae), was recorded feeding on the leaves of the shrub in South America. The biology and larval and adult host range of this species were examined to determine the insect's suitability for biological control of this invasive weed in North America and Hawaii. Biological observations indicate that the larvae have five instars. When disturbed, the late instar larvae emit formic acid from a prothoracic gland that may protect larvae from generalist predators. Larval host range tests conducted both in South and North America indicated that this species feeds and completes development primarily on members of the Anacardiaceae within the tribe Rhoeae. Oviposition tests indicated that when given a choice in large cages the adults will select the target weed over Pistacia spp. However, considering the many valued plant species in its host range, especially several North American natives, this species will not be considered further for biological control of S. terebinthifolius in North America.

  10. Erythrocyte Shape Abnormalities, Membrane Oxidative Damage, and β-Actin Alterations: An Unrecognized Triad in Classical Autism

    PubMed Central

    Ciccoli, Lucia; De Felice, Claudio; Pecorelli, Alessandra; Belmonte, Giuseppe; Guerranti, Roberto; Cortelazzo, Alessio; Durand, Thierry; Valacchi, Giuseppe; Rossi, Marcello; Hayek, Joussef

    2013-01-01

    Autism spectrum disorders (ASDs) are a complex group of neurodevelopment disorders steadily rising in frequency and treatment refractory, where the search for biological markers is of paramount importance. Although red blood cells (RBCs) membrane lipidomics and rheological variables have been reported to be altered, with some suggestions indicating an increased lipid peroxidation in the erythrocyte membrane, to date no information exists on how the oxidative membrane damage may affect cytoskeletal membrane proteins and, ultimately, RBCs shape in autism. Here, we investigated RBC morphology by scanning electron microscopy in patients with classical autism, that is, the predominant ASDs phenotype (age range: 6–26 years), nonautistic neurodevelopmental disorders (i.e., “positive controls”), and healthy controls (i.e., “negative controls”). A high percentage of altered RBCs shapes, predominantly elliptocytes, was observed in autistic patients, but not in both control groups. The RBCs altered morphology in autistic subjects was related to increased erythrocyte membrane F2-isoprostanes and 4-hydroxynonenal protein adducts. In addition, an oxidative damage of the erythrocyte membrane β-actin protein was evidenced. Therefore, the combination of erythrocyte shape abnormalities, erythrocyte membrane oxidative damage, and β-actin alterations constitutes a previously unrecognized triad in classical autism and provides new biological markers in the diagnostic workup of ASDs. PMID:24453417

  11. What magnitude are observed non-target impacts from weed biocontrol?

    PubMed

    Suckling, David Maxwell; Sforza, René François Henri

    2014-01-01

    A systematic review focused by plant on non-target impacts from agents deliberately introduced for the biological control of weeds found significant non-target impacts to be rare. The magnitude of direct impact of 43 biocontrol agents on 140 non-target plants was retrospectively categorized using a risk management framework for ecological impacts of invasive species (minimal, minor, moderate, major, massive). The vast majority of agents introduced for classical biological control of weeds (>99% of 512 agents released) have had no known significant adverse effects on non-target plants thus far; major effects suppressing non-target plant populations could be expected to be detectable. Most direct non-target impacts on plants (91.6%) were categorized as minimal or minor in magnitude with no known adverse long-term impact on non-target plant populations, but a few cacti and thistles are affected at moderate (n = 3), major (n = 7) to massive (n = 1) scale. The largest direct impacts are from two agents (Cactoblastis cactorum on native cacti and Rhinocyllus conicus on native thistles), but these introductions would not be permitted today as more balanced attitudes exist to plant biodiversity, driven by both society and the scientific community. Our analysis shows (as far as is known), weed biological control agents have a biosafety track record of >99% of cases avoiding significant non-target impacts on plant populations. Some impacts could have been overlooked, but this seems unlikely to change the basic distribution of very limited adverse effects. Fewer non-target impacts can be expected in future because of improved science and incorporation of wider values. Failure to use biological control represents a significant opportunity cost from the certainty of ongoing adverse impacts from invasive weeds. It is recommended that a simple five-step scale be used to better communicate the risk of consequences from both action (classical biological control) and no action (ongoing impacts from invasive weeds).

  12. Habitat affinity of resident natural enemies of the invasive Aphis glycines (Hemiptera: Aphididae), on soybean, with comments on biological control.

    PubMed

    Brewer, Michael J; Noma, Takuji

    2010-06-01

    We integrated a natural enemy survey of the broader landscape into a more traditional survey for Aphis glycines Matsumura (Hemiptera: Aphididae), parasitoids and predatory flies on soybean using A. glycines-infested soybean, Glycine max (L.) Merr., placed in cropped and noncropped plant systems to complement visual field observations. Across three sites and 5 yr, 18 parasitoids and predatory flies in total (Hymenoptera: Aphelinidae [two species] and Bracondae [seven species], Diptera: Cecidomyiidae [one species], Syrphidae [seven species], Chamaemyiidae [one species]) were detected, with significant variability in recoveries detected across plant system treatments and strong contrasts in habitat affinity detected among species. Lysiphlebus testaceipes Cresson was the most frequently detected parasitoid, and no differences in abundance were detected in cropped (soybean, wheat [Triticum aestivum L.], corn [Zea mays L.], and alfalfa [Medicago sativa L.]) and noncropped (poplar [Populus euramericana (Dode) Guinier] and early successional vegetation) areas. In contrast, Binodoxys kelloggensis Pike, Starý & Brewer had strong habitat affinity for poplar and early successional vegetation. The low recoveries seasonally and across habitats of Aphelinus asychis Walker, Aphelinus sp., and Aphidius colemoni Viereck make their suitability to A. glycines on soybean highly suspect. The widespread occurrence of many of the flies reflects their broad habitat affinity and host aphid ranges. The consistent low field observations of parasitism and predation suggest that resident parasitoids and predatory flies are unlikely to contribute substantially to A. glycines suppression, at least during the conventional time period early in the pest invasion when classical biological control activities are considered. For selected species that were relatively well represented across plant systems (i.e., L. testaceipes and Aphidoletes aphidimyza Rondani), conservation biological control efforts may be fruitful. The additional information gained from expanding the natural enemy survey into the broader landscape was essential in making these distinctions relevant to conservation biological control, while adding agroecosystem-specific information valuable to classical biological control.

  13. What Magnitude Are Observed Non-Target Impacts from Weed Biocontrol?

    PubMed Central

    Suckling, David Maxwell; Sforza, René François Henri

    2014-01-01

    A systematic review focused by plant on non-target impacts from agents deliberately introduced for the biological control of weeds found significant non-target impacts to be rare. The magnitude of direct impact of 43 biocontrol agents on 140 non-target plants was retrospectively categorized using a risk management framework for ecological impacts of invasive species (minimal, minor, moderate, major, massive). The vast majority of agents introduced for classical biological control of weeds (>99% of 512 agents released) have had no known significant adverse effects on non-target plants thus far; major effects suppressing non-target plant populations could be expected to be detectable. Most direct non-target impacts on plants (91.6%) were categorized as minimal or minor in magnitude with no known adverse long-term impact on non-target plant populations, but a few cacti and thistles are affected at moderate (n = 3), major (n = 7) to massive (n = 1) scale. The largest direct impacts are from two agents (Cactoblastis cactorum on native cacti and Rhinocyllus conicus on native thistles), but these introductions would not be permitted today as more balanced attitudes exist to plant biodiversity, driven by both society and the scientific community. Our analysis shows (as far as is known), weed biological control agents have a biosafety track record of >99% of cases avoiding significant non-target impacts on plant populations. Some impacts could have been overlooked, but this seems unlikely to change the basic distribution of very limited adverse effects. Fewer non-target impacts can be expected in future because of improved science and incorporation of wider values. Failure to use biological control represents a significant opportunity cost from the certainty of ongoing adverse impacts from invasive weeds. It is recommended that a simple five-step scale be used to better communicate the risk of consequences from both action (classical biological control) and no action (ongoing impacts from invasive weeds). PMID:24454755

  14. Classical biological control for the protection of native ecosystems

    USDA-ARS?s Scientific Manuscript database

    Native ecosystems and their component species are undergoing catastrophic and irreparable change globally as habitat is destroyed for human use and invaded by species from other biogeographical areas (Simberloff et al., 1997; Cox, 1999; Lockwood et al., 2006). Political solutions may be devised to s...

  15. Duration of emission of volatile organic compounds from mechanically damaged plant leaves

    USDA-ARS?s Scientific Manuscript database

    Classical biological control of invasive alien weeds depends on the use of arthropod herbivores that are sufficiently host specific to avoid risk of injuring nontarget plants. Host plant specificity is usually evaluated by using a combination of behavioral and developmental experiments under choice...

  16. Impact of Abrostola asclepiadis and plant competition on invasive swallow-worts (Vincetoxicum spp.)

    USDA-ARS?s Scientific Manuscript database

    Pale and black swallow-wort (Vincetoxicum rossicum and V. nigrum; Apocynaceae, subfamily Asclepiadoideae) are perennial vines from Europe that have become invasive in various terrestrial habitats in the northeastern USA and southeastern Canada. A classical weed biological control program has been in...

  17. Release and establishment of Megamelus scutellaris (Hemiptera: Delphacidae) in Florida

    USDA-ARS?s Scientific Manuscript database

    Megamelus scutellaris (Berg) (Hemiptera: Delphacidae) was recently developed as a classical biological control agent for waterhyacinth, Eichhornia crassipes Mart. Solms, and released in Florida. Releases were conducted at 10 sites around the state every 4-6 weeks until late fall then halted until t...

  18. Discovery and molecular characterization of an ambisense densovirus from South American populations of Solenopsis invicta

    USDA-ARS?s Scientific Manuscript database

    In an effort to expand and utilize viruses as classical biological control agents, a metatranscriptomic/pyrosequencing approach was used to examine Solenopsis invicta populations collected exclusively in Argentina. A new virus with characteristics consistent with the family Parvoviridae, subfamily D...

  19. Seasonal parasitism and host specificity of Trissolcus japonicus in northern China

    USDA-ARS?s Scientific Manuscript database

    The Asian egg parasitoid Trissolcus japonicus is considered the most promising species for classical biological control of Halyomorpha halys. We investigated the fundamental and ecological host range of T. japonicus in northern China to define its host specificity, and we determined that T. japonicu...

  20. On quantum effects in a theory of biological evolution.

    PubMed

    Martin-Delgado, M A

    2012-01-01

    We construct a descriptive toy model that considers quantum effects on biological evolution starting from Chaitin's classical framework. There are smart evolution scenarios in which a quantum world is as favorable as classical worlds for evolution to take place. However, in more natural scenarios, the rate of evolution depends on the degree of entanglement present in quantum organisms with respect to classical organisms. If the entanglement is maximal, classical evolution turns out to be more favorable.

  1. On Quantum Effects in a Theory of Biological Evolution

    PubMed Central

    Martin-Delgado, M. A.

    2012-01-01

    We construct a descriptive toy model that considers quantum effects on biological evolution starting from Chaitin's classical framework. There are smart evolution scenarios in which a quantum world is as favorable as classical worlds for evolution to take place. However, in more natural scenarios, the rate of evolution depends on the degree of entanglement present in quantum organisms with respect to classical organisms. If the entanglement is maximal, classical evolution turns out to be more favorable. PMID:22413059

  2. Establishing Research and Management Priorities for Monoecious Hydrilla

    DTIC Science & Technology

    2014-01-01

    strategies. While use of high stocking rates of non-selective sterile grass carp (Ctenopharyngodon idella) has successfully controlled hydrilla in many...discussions of classical biological control agents (e.g. insects that feed specifically on hydrilla) did not yield any promising near-term candidates...possible. Diver- assisted dredging techniques and hand removal techniques were explored on the infestation in the Lake Cayuga inlet; initial results were

  3. Retrospective analysis of the successful establishment of a biocontrol agent based upon microsatellite data

    USDA-ARS?s Scientific Manuscript database

    The tarnished plant bug Lygus lineolaris is an important pest of cotton and many other crops in North America. Since the 1970s prevalence of insecticide resistant populations coupled with environmental concerns have raised interest in classical biological control of this pest. Peristenus digoneutis,...

  4. Origins and diversity of rush Skeletonweed (Chondrilla juncea) from three continents

    Treesearch

    J. Gaskin; C. L. Kinter; M. Schwarzlander; G. P. Markin; S. Novak; J. F. Smith

    2013-01-01

    Rush skeletonweed (Chondrilla juncea L.) is an invasive apomictic perennial plant in Australia, South- and North America, accidentally introduced from Eurasia, which shows differential resistance/tolerance to some herbicides and classical biological control agents. Rush skeletonweed biotypes have been locally described using morphology, phenology, isozyme patterns, and...

  5. Prospects for Classical Biological Control of Saharan Mustard (Brassica tournefortii)

    USDA-ARS?s Scientific Manuscript database

    Saharan mustard (Brassica tournefortii) is a winter annual plant that is native to the Mediterranean Basin and is becoming highly invasive in the Sonoran and Mojave Deserts and adjacent areas and has spread great distances along highways from its original infestation. It is becoming a serious probl...

  6. Trissolcus japonicus (Ashmead) emerges in North America

    USDA-ARS?s Scientific Manuscript database

    Trissolcus japonicus (Ashmead) is an Asian egg parasitoid of the brown marmorated stink bug, Halyomorpha halys (Stål). It has been under study in U.S. quarantine facilities since 2007 to evaluate its efficacy as a candidate classical biological control agent and its host specificity with regard to t...

  7. Progress in the classical biological control of Agrilus planipennis Fairmaire (Coleoptera: Buprestidae) in North America

    USDA-ARS?s Scientific Manuscript database

    Discovered in North America in 2002, Agrilus planipennis Fairmaire (Coleoptera: Buprestidae) is a phloem-feeding beetle from Asia that attacks and kills ash trees (Fraxinus spp.). Emerald Ash Borer (EAB) populations surveyed for natural enemies in North America reveal low prevalence of native larva...

  8. Virulence of selected entomopathogenic fungi against the olive fruit fly and their potential for biocontrol

    USDA-ARS?s Scientific Manuscript database

    The olive fruit fly, Bactrocera oleae (Diptera: Tephritidae), is the most serious pest of cultivated olives worldwide. Its recent invasion into North America, specifically California, has initiated renewed interest in management strategies for this pest. Research into classical biological control ha...

  9. Enhancing the effectiveness of biological control programs of invasive species through a more comprehensive pest management approach.

    PubMed

    DiTomaso, Joseph M; Van Steenwyk, Robert A; Nowierski, Robert M; Vollmer, Jennifer L; Lane, Eric; Chilton, Earl; Burch, Patrick L; Cowan, Phil E; Zimmerman, Kenneth; Dionigi, Christopher P

    2017-01-01

    Invasive species are one of the greatest economic and ecological threats to agriculture and natural areas in the US and the world. Among the available management tools, biological control provides one of the most economical and long-term effective strategies for managing widespread and damaging invasive species populations of nearly all taxa. However, integrating biological control programs in a more complete integrated pest management approach that utilizes increased information and communication, post-release monitoring, adaptive management practices, long-term stewardship strategies, and new and innovative ecological and genetic technologies can greatly improve the effectiveness of biological control. In addition, expanding partnerships among relevant national, regional, and local agencies, as well as academic scientists and land managers, offers far greater opportunities for long-term success in the suppression of established invasive species. In this paper we direct our recommendations to federal agencies that oversee, fund, conduct research, and develop classical biological control programs for invasive species. By incorporating these recommendations into adaptive management strategies, private and public land managers will have far greater opportunities for long-term success in suppression of established invasive species. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  10. Hybridization of an invasive shrub affects tolerance and resistance to defoliation by a biological control agent

    USGS Publications Warehouse

    Williams, Wyatt I.; Friedman, Jonathan M.; Gaskin, John F.; Norton, Andrew P.

    2014-01-01

    Evolution has contributed to the successful invasion of exotic plant species in their introduced ranges, but how evolution affects particular control strategies is still under evaluation. For instance, classical biological control, a common strategy involving the utilization of highly specific natural enemies to control exotic pests, may be negatively affected by host hybridization because of shifts in plant traits, such as root allocation or chemical constituents. We investigated introgression between two parent species of the invasive shrub tamarisk (Tamarix spp.) in the western United States, and how differences in plant traits affect interactions with a biological control agent. Introgression varied strongly with latitude of origin and was highly correlated with plant performance. Increased levels of T. ramosissima introgression resulted in both higher investment in roots and tolerance to defoliation and less resistance to insect attack. Because tamarisk hybridization occurs predictably on the western U.S. landscape, managers may be able to exploit this information to maximize control efforts. Genetic differentiation in plant traits in this system underpins the importance of plant hybridization and may explain why some biological control releases are more successful than others.

  11. Biological control of weeds: research by the United States Department of Agriculture-Agricultural Research Service: selected case studies.

    PubMed

    Quimby, Paul C; DeLoach, C Jack; Wineriter, Susan A; Goolsby, John A; Sobhian, Rouhollah; Boyette, C Douglas; Abbas, Hamed K

    2003-01-01

    Research by the USDA-Agricultural Research Service (ARS) on biological control of weeds has been practiced for many years because of its inherent ecological and economic advantages. Today, it is further driven by ARS adherence to Presidential Executive Order 13112 (3 February 1999) on invasive species and to USDA-ARS policy toward developing technology in support of sustainable agriculture with reduced dependence on non-renewable petrochemical resources. This paper reports examples or case studies selected to demonstrate the traditional or classical approach for biological control programs using Old World arthropods against Tamarix spp, Melaleuca quinquenervia (Cav) ST Blake and Galium spurium L/G aparine L, and the augmentative approach with a native plant pathogen against Pueraria lobata Ohwi = P montana. The examples illustrated various conflicts of interest with endangered species and ecological complexities of arthropods with associated microbes such as nematodes.

  12. Variable Demographic Rates in an Invasive Plant Species: Differences Among Populations and Management Implications

    USDA-ARS?s Scientific Manuscript database

    Population managers are frequently faced with the challenge of selecting the most effective management strategy from a set of available strategies. In the case of classical weed biological control, this requires predicting a priori which of a group of candidate biocontrol agent species has the great...

  13. Progress in the classical biological control of Agrilus planipennis Fairmaire (Coleoptera: Buprestidae) in North America

    Treesearch

    Leah S. Bauer; Jian J. Duan; Juli R. Gould; Roy. Van Driesche

    2015-01-01

    First detected in North America in 2002, the emerald ash borer (EAB) (Agrilus planipennis Fairmaire; Coleoptera: Buprestidae), an invasive phloem-feeding beetle from Asia, has killed tens of millions of ash (Fraxinus Linnaeus; Oleaceae) trees. Although few parasitoids attack EAB in North America, three parasitoid species were found...

  14. Classical biological control of cassava pests in Latin America and Africa

    USDA-ARS?s Scientific Manuscript database

    Anthony (Tony) Bellotti’s career took him to El Salvador with the Peace Corps in 1962, New Mexico State for a Masters, Paraguay (again with the Peace Corps), Cornell University for a Ph.D., and Colombia where he worked for the Centro Internacional de Agricultura Tropical (CIAT) from 1974 until his p...

  15. Release and monitoring of Laricobius nigrinus (Coleoptera: Derodontidae) for classical biological control of the hemlock woolly adelgid in the Eastern U.S.

    Treesearch

    David L. Mausel; Scott M. Salom; Loke T. Kok

    2007-01-01

    Studies are being conducted to determine optimal release procedures for establishment and sampling methodology of Laricobius nigrinus Fender (Coleoptera: Derodontidae), a predator of the hemlock woolly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae) on eastern hemlock, Tsuga canadensis (L.) Carriere, trees...

  16. Laboratory and field-based temperature-dependent development of a monophagous weevil: implications for integrated weed management

    USDA-ARS?s Scientific Manuscript database

    The stem-boring weevil, Rhinoncomimus latipes Korotyaev (Coleoptera: Curculionidae) was imported from Asia to North America and approved for release as a classical biological control agent for the invasive annual vine Persicaria perfoliata (L.) H. Gross (Polygonaceae) in 2004. Its impact on the weed...

  17. Development of immature tiger-fly Coenosia attenuata (Stein) reared on larvae of the fungus gnat Bradysia impatiens (Johannsen) in coir substrate

    USDA-ARS?s Scientific Manuscript database

    The ability to rear a beneficial predatory insect is often required for its use in inoculative releases for classical biological control applications. However, affordable mass production is required before a beneficial predatory insect will be commercialized for large scale repetitive releases. The...

  18. Semiochemicals to enhance herbivory by Diorhabda carinulata aggregations in saltcedar (Tamarix spp.) infestations

    Treesearch

    Alexander M. Gaffke; Sharlene E. Sing; Tom L. Dudley; Daniel W. Bean; Justin A. Russak; Agenor Mafra-Neto; Paul A. Grieco; Robert K. D. Peterson; David K. Weaver

    2018-01-01

    BACKGROUND: Semiochemicals formonitoring, attracting or repelling pest and beneficial organisms are increasingly deployed in agricultural and forest systems for pest management. However, the use of aggregation pheromones and host-plant attractants for the express purpose of increasing the efficacy of classical biological control agents of weeds has not been widely...

  19. Enhanced energy transport in genetically engineered excitonic networks.

    PubMed

    Park, Heechul; Heldman, Nimrod; Rebentrost, Patrick; Abbondanza, Luigi; Iagatti, Alessandro; Alessi, Andrea; Patrizi, Barbara; Salvalaggio, Mario; Bussotti, Laura; Mohseni, Masoud; Caruso, Filippo; Johnsen, Hannah C; Fusco, Roberto; Foggi, Paolo; Scudo, Petra F; Lloyd, Seth; Belcher, Angela M

    2016-02-01

    One of the challenges for achieving efficient exciton transport in solar energy conversion systems is precise structural control of the light-harvesting building blocks. Here, we create a tunable material consisting of a connected chromophore network on an ordered biological virus template. Using genetic engineering, we establish a link between the inter-chromophoric distances and emerging transport properties. The combination of spectroscopy measurements and dynamic modelling enables us to elucidate quantum coherent and classical incoherent energy transport at room temperature. Through genetic modifications, we obtain a significant enhancement of exciton diffusion length of about 68% in an intermediate quantum-classical regime.

  20. Plasticity of gene-regulatory networks controlling sex determination: of masters, slaves, usual suspects, newcomers, and usurpators.

    PubMed

    Herpin, Amaury; Schartl, Manfred

    2015-10-01

    Sexual dimorphism is one of the most pervasive and diverse features of animal morphology, physiology, and behavior. Despite the generality of the phenomenon itself, the mechanisms controlling how sex is determined differ considerably among various organismic groups, have evolved repeatedly and independently, and the underlying molecular pathways can change quickly during evolution. Even within closely related groups of organisms for which the development of gonads on the morphological, histological, and cell biological level is undistinguishable, the molecular control and the regulation of the factors involved in sex determination and gonad differentiation can be substantially different. The biological meaning of the high molecular plasticity of an otherwise common developmental program is unknown. While comparative studies suggest that the downstream effectors of sex-determining pathways tend to be more stable than the triggering mechanisms at the top, it is still unclear how conserved the downstream networks are and how all components work together. After many years of stasis, when the molecular basis of sex determination was amenable only in the few classical model organisms (fly, worm, mouse), recently, sex-determining genes from several animal species have been identified and new studies have elucidated some novel regulatory interactions and biological functions of the downstream network, particularly in vertebrates. These data have considerably changed our classical perception of a simple linear developmental cascade that makes the decision for the embryo to develop as male or female, and how it evolves. © 2015 The Authors.

  1. From noise to synthetic nucleoli: can synthetic biology achieve new insights?

    PubMed

    Ciechonska, Marta; Grob, Alice; Isalan, Mark

    2016-04-18

    Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."

  2. Some perspectives on the risks and benefits of biological control of invasive alien plants in the management of natural ecosystems.

    PubMed

    van Wilgen, B W; Moran, V C; Hoffmann, J H

    2013-09-01

    Globally, invasions by alien plants are rapidly increasing in extent and severity, leading to large-scale ecosystem degradation. Weed biological control offers opportunities to arrest or even reverse these trends and, although it is not always effective or appropriate as a management strategy, this practice has an excellent record of safety and many notable successes over two centuries. In recent years, growing concerns about the potential for unintended, non-target damage by biological control agents, and fears about other unpredictable effects on ecosystems, have created an increasingly demanding risk-averse regulatory environment. This development may be counter-productive because it tends to overemphasize potential problems and ignores or underestimates the benefits of weed biological control; it offers no viable alternatives; and it overlooks the inherent risks of a decision not to use biological control. The restoration of badly degraded ecosystems to a former pristine condition is not a realistic objective, but the protection of un-invaded or partial restoration of invaded ecosystems can be achieved safely, at low cost and sustainably through the informed and responsible application of biological control. This practice should therefore be given due consideration when management of invasive alien plants is being planned. This discussion paper provides a perspective on the risks and benefits of classical weed biological control, and it is aimed at assisting environmental managers in their deliberations on whether or not to use this strategy in preference, or as a supplement to other alien invasive plant control practices.

  3. Some Perspectives on the Risks and Benefits of Biological Control of Invasive Alien Plants in the Management of Natural Ecosystems

    NASA Astrophysics Data System (ADS)

    van Wilgen, B. W.; Moran, V. C.; Hoffmann, J. H.

    2013-09-01

    Globally, invasions by alien plants are rapidly increasing in extent and severity, leading to large-scale ecosystem degradation. Weed biological control offers opportunities to arrest or even reverse these trends and, although it is not always effective or appropriate as a management strategy, this practice has an excellent record of safety and many notable successes over two centuries. In recent years, growing concerns about the potential for unintended, non-target damage by biological control agents, and fears about other unpredictable effects on ecosystems, have created an increasingly demanding risk-averse regulatory environment. This development may be counter-productive because it tends to overemphasize potential problems and ignores or underestimates the benefits of weed biological control; it offers no viable alternatives; and it overlooks the inherent risks of a decision not to use biological control. The restoration of badly degraded ecosystems to a former pristine condition is not a realistic objective, but the protection of un-invaded or partial restoration of invaded ecosystems can be achieved safely, at low cost and sustainably through the informed and responsible application of biological control. This practice should therefore be given due consideration when management of invasive alien plants is being planned. This discussion paper provides a perspective on the risks and benefits of classical weed biological control, and it is aimed at assisting environmental managers in their deliberations on whether or not to use this strategy in preference, or as a supplement to other alien invasive plant control practices.

  4. Biological forcing controls the chemistry of reef-building coral skeleton

    NASA Astrophysics Data System (ADS)

    Meibom, Anders; Mostefaoui, Smail; Cuif, Jean-Pierre; Dauphin, Yannicke; Houlbreque, Fanny; Dunbar, Robert; Constantz, Brent

    2007-01-01

    We present analyses of major elements C and Ca and trace elements N, S, Mg and Sr in a Porites sp. exoskeleton with a spatial resolution better than ˜150 nm. Trace element variations are evaluated directly against the ultra-structure of the skeleton and are ascribed to dynamic biological forcing. Individual growth layers in the bulk fibrous aragonite skeleton form on sub-daily timescales. Magnesium concentration variations are dramatically correlated with the growth layers, but are uncorrelated with Sr concentration variations. Observed (sub)seasonal relationships between water temperature and skeletal trace-element chemistry are secondary, mediated by sensitive biological processes to which classical thermodynamic formalism does not apply.

  5. Releasing biocontrol agents: Risk assessment and overdue reform

    Treesearch

    Bob Peterson; Sharlene Sing

    2007-01-01

    Although the need for universally instituting formal risk assessment (RA) in the screening and approval process for non-native biological control (BC) agent releases has been widely acknowledged for the past several years, little seems to have been accomplished in terms of codifying this practice within a regulatory framework. Given the low success rate of classical BC...

  6. Developing a classical biological control program for Agrilus planipennis (Coleoptera: Buprestidae), an invasive ash pest in North America

    Treesearch

    Leah S. Bauer; Houping Liu; Deborah Miller; Juli Gould

    2008-01-01

    The emerald ash borer (EAB), Agrilus planipennis, a buprestid beetle native to northeast Asia, was determined as the cause of ash tree (Fraxinus spp.) mortality in areas of southern Michigan and Ontario in 2002. Infestations have since been found in Ohio, Indiana, Illinois, Maryland, Virginia, Pennsylvania, West Virginia,...

  7. Classical biological control of invasive teasels (Dipsacus spp.) and other weeds in areas of limited or restricted weed management

    USDA-ARS?s Scientific Manuscript database

    Invasive teasels (Dipsacus spp.) are considered noxious in five states and listed as invasive in more than a dozen others, despite having little effect on agriculture. They are problematic in areas of limited weed management such as along highways and railroads and in ditches, wetlands and parks. A ...

  8. Evaluation of the host specificity of Spathius galinae (Hymenoptera: Braconidae), a larval parasitoid of the emerald ash borer (Coleoptera: Buprestidae) in Northeast Asia

    USDA-ARS?s Scientific Manuscript database

    Host-specificity determination prior to the introduction of non-native natural enemies (predators and parasitoids) is a critical component of the risk assessment for modern classical biological control programs. In the present study, we assessed the host specificity of a newly described parasitoid,...

  9. Classical biological control of the olive fruit fly, Bactrocera olea (Diptera: Tephritidae), using the exotic parasitoie, Psyttalia lounsburyi (Hymenoptera: Braconidae) in France.

    USDA-ARS?s Scientific Manuscript database

    The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae) is an important pest of olives which is worldwide distributed and responsible for economic losses of approximately US$800 million per year. Since the 2000s both economical and environmental concerns have raised interested in clas...

  10. Developing rearing methods for Tetrastichus planipennisi (Hymenoptera: Eulophidae), a larval endoparasitoid of the emerald ash borer (Coleoptera: Buprestidae)

    Treesearch

    Philip Taylor; Jian J. Duan; Roger Fuester

    2011-01-01

    Classical biological control efforts against emerald ash borer (EAB) (Agrilus planipennis Fairmaire) in North America primarily have focused on introduction and releases of exotic parasitoid species collected from northern parts of China. Recently, field surveys in Michigan, Pennsylvania, Ohio, and Ontario also indicate that some existing parasitoids...

  11. Benefits of pre-release population genetics: a case study using Psyttalia lounsburyi, a biocontrol agent of the olive fruit fly in California

    USDA-ARS?s Scientific Manuscript database

    From a pest management perspective, limited knowledge on the genetics of released biocontrol agents has been repeatedly considered as one possible cause of failures in classical biological control. Introduced biocontrol agents are expected to experience a loss in genetic diversity as the result of s...

  12. Huntington II Simulation Program - MALAR. Student Workbook, Teacher's Guide, and Resource Handbook.

    ERIC Educational Resources Information Center

    Friedland, James; Frishman, Austin

    Described is the computer model "MALAR" which deals with malaria and its eradication. A computer program allows the tenth- to twelfth-grade student to attempt to control a malaria epidemic. This simulation provides a context within which to study the biological, economic, social, political, and ecological aspects of a classic world health problem.…

  13. Entomopathogenic fungi and their potential for the management of Aedes aegypti (Diptera: Culicidae) in the Americas

    PubMed Central

    Evans, Harry C; Elliot, Simon L; Barreto, Robert W

    2018-01-01

    Classical biological control has been used extensively for the management of exotic weeds and agricultural pests, but never for alien insect vectors of medical importance. This simple but elegant control strategy involves the introduction of coevolved natural enemies from the centre of origin of the target alien species. Aedes aegypti - the primary vector of the dengue, yellow fever and Zika flaviviruses - is just such an invasive alien in the Americas where it arrived accidentally from its West African home during the slave trade. Here, we introduce the concept of exploiting entomopathogenic fungi from Africa for the classical biological control of Ae. aegypti in the Americas. Fungal pathogens attacking arthropods are ubiquitous in tropical forests and are important components in the natural balance of arthropod populations. They can produce a range of specialised spore forms, as well as inducing a variety of bizarre behaviours in their hosts, in order to maximise infection. The fungal groups recorded as specialised pathogens of mosquito hosts worldwide are described and discussed. We opine that similar fungal pathogens will be found attacking and manipulating Ae. aegypti in African forests and that these could be employed for an economic, environmentally-safe and long-term solution to the flavivirus pandemics in the Americas. PMID:29412361

  14. Entomopathogenic fungi and their potential for the management of Aedes aegypti (Diptera: Culicidae) in the Americas.

    PubMed

    Evans, Harry C; Elliot, Simon L; Barreto, Robert W

    2018-03-01

    Classical biological control has been used extensively for the management of exotic weeds and agricultural pests, but never for alien insect vectors of medical importance. This simple but elegant control strategy involves the introduction of coevolved natural enemies from the centre of origin of the target alien species. Aedes aegypti - the primary vector of the dengue, yellow fever and Zika flaviviruses - is just such an invasive alien in the Americas where it arrived accidentally from its West African home during the slave trade. Here, we introduce the concept of exploiting entomopathogenic fungi from Africa for the classical biological control of Ae. aegypti in the Americas. Fungal pathogens attacking arthropods are ubiquitous in tropical forests and are important components in the natural balance of arthropod populations. They can produce a range of specialised spore forms, as well as inducing a variety of bizarre behaviours in their hosts, in order to maximise infection. The fungal groups recorded as specialised pathogens of mosquito hosts worldwide are described and discussed. We opine that similar fungal pathogens will be found attacking and manipulating Ae. aegypti in African forests and that these could be employed for an economic, environmentally-safe and long-term solution to the flavivirus pandemics in the Americas.

  15. Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions.

    PubMed

    Foo, Mathias; Sawlekar, Rucha; Kulkarni, Vishwesh V; Bates, Declan G

    2016-08-01

    The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators. Here, we propose an alternative design approach that utilises the abstract chemical reactions involved in cellular signalling cycles to implement a biomolecular controller - termed a signalling-cycle (SC) controller. We compare the performance of the PI and SC controllers in closed-loop with a nonlinear second-order chemical process. Our results show that the SC controller outperforms the PI controller in terms of both performance and robustness, and also requires fewer abstract chemical reactions to implement, highlighting its potential usefulness in the construction of biomolecular control circuits.

  16. Classic hallucinogens in the treatment of addictions.

    PubMed

    Bogenschutz, Michael P; Johnson, Matthew W

    2016-01-04

    Addictive disorders are very common and have devastating individual and social consequences. Currently available treatment is moderately effective at best. After many years of neglect, there is renewed interest in potential clinical uses for classic hallucinogens in the treatment of addictions and other behavioral health conditions. In this paper we provide a comprehensive review of both historical and recent clinical research on the use of classic hallucinogens in the treatment of addiction, selectively review other relevant research concerning hallucinogens, and suggest directions for future research. Clinical trial data are very limited except for the use of LSD in the treatment of alcoholism, where a meta-analysis of controlled trials has demonstrated a consistent and clinically significant beneficial effect of high-dose LSD. Recent pilot studies of psilocybin-assisted treatment of nicotine and alcohol dependence had strikingly positive outcomes, but controlled trials will be necessary to evaluate the efficacy of these treatments. Although plausible biological mechanisms have been proposed, currently the strongest evidence is for the role of mystical or other meaningful experiences as mediators of therapeutic effects. Classic hallucinogens have an excellent record of safety in the context of clinical research. Given our limited understanding of the clinically relevant effects of classic hallucinogens, there is a wealth of opportunities for research that could contribute important new knowledge and potentially lead to valuable new treatments for addiction. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Species Diversity in the Parasitoid Genus Asobara (Hymenoptera: Braconidae) from the Native Area of the Fruit Fly Pest Drosophila suzukii (Diptera: Drosophilidae).

    PubMed

    Guerrieri, Emilio; Giorgini, Massimo; Cascone, Pasquale; Carpenito, Simona; van Achterberg, Cees

    2016-01-01

    Drosophila suzukii (Matsumura), commonly known as Spotted Wing Drosophila (SWD), is a worldwide serious economic threat to the production of berries and stone fruits. The chemical control widely used against this pest is often not able to preventing yield losses because wild flora offers an abundance of fruits to D. suzukii where the pest is able to reproduce and from where it recolonizes neighbouring cultivated fields. Alternatively, within Integrated Pest Management protocols for D. suzukii, biological control could play a key role by reducing its populations particularly in non-cultivated habitats, thus increasing the effectiveness and reducing the side negative effects of other management strategies. Because of the scarcity and of the low efficiency of autochthonous parasitoids in the new invaded territories, in the last few years, a number of surveys started in the native area of D. suzukii to find parasitoid species to be evaluated in quarantine structures and eventually released in the field, following a classical biological control approach. This paper reports the results of these surveys carried out in South Korea and for the first time in China. Among the parasitoids collected, those belonging to the genus Asobara Foerster resulted dominant both by number and species diversity. By combining morphological characters and the mitochondrial COI gene as a molecular marker, we identified seven species of Asobara, of which two associated with D. suzukii, namely A. japonica and A leveri, and five new to science, namely Asobara brevicauda, A. elongata, A mesocauda, A unicolorata, A. triangulata. Our findings offer new opportunity to find effective parasitoids to be introduced in classical biological control programmes in the territories recently invaded by D. suzukii.

  18. Two new species of Oobius Trjapitzin (Hymenoptera, Encyrtidae) egg parasitoids of Agrilus spp. (Coleoptera, Buprestidae) from the USA, including a key and taxonomic notes on other congeneric Nearctic taxa

    Treesearch

    Serguei V. Triapitsyn; Toby R. Petrice; Michael W. Gates; Leah S. Bauer

    2015-01-01

    Oobius Trjapitzin (Hymenoptera, Encyrtidae) species are egg parasitoids that are important for the biological control of some Buprestidae and Cerambycidae (Coleoptera). Two species, O. agrili Zhang & Huang and O. longoi (Siscaro), were introduced into North America for classical biocontrol and have...

  19. Biological control of emerald ash borer in North America: current progress and potential for success

    Treesearch

    Jian J. Duan; Leah S. Bauer; Juli R. Gould; Jonathan P. Lelito

    2012-01-01

    The emerald ash borer (EAB) (Agrilus planipennis), a buprestid native to north-east Asia, was first discovered in North America near Detroit in 2002. EAB has since spread to at least 15 U.S. States and two Canadian provinces, threatening the existence of native ash trees (Fraxinus spp.). A classical biocontrol program was initiated...

  20. A new species of Aculops (Acari: Prostigmata: Eriophyidae) from Serbia on Dipsacus laciniatus L. (Dipsacaceae), a weed target of classical biological control in the United States of America

    USDA-ARS?s Scientific Manuscript database

    The new eriophyid mite species Aculops dipsaci n. sp. (Acari: Prostigmata: Eriophyidae) collected from Dipsacus laciniatus L. (Dipsacaceae) in northern Serbia is described and illustrated. Differential diagnosis is provided in comparison with Aculops salixis Xue, Song and Hong. This is the first e...

  1. The Scotch Broom gall mite: Accidental introduction to classical biological control agent?

    Treesearch

    J. Andreas; T. Wax; E. Coombs; J. Gaskin; G. Markin; S. Sing

    2013-01-01

    The gall mite, Aceria genistae (Nal.) Castagnoli s.l., an accidentally introduced natural enemy of Scotch broom (Cytisus scoparius (L.) Link), was first discovered in the Portland OR and Tacoma WA region in 2005. It has since been reported from southern British Columbia to southern Oregon. Observationally, the mite appears to reduce Scotch broom seed production and at...

  2. Two new species of Oobius Trjapitzin (Hymenoptera: Encyrtidae) egg parasitoids of Agrilus spp. (Coleoptera: Buprestidae) from the USA, including a key and taxonomic notes on other congeneric Nearctic taxa

    USDA-ARS?s Scientific Manuscript database

    Oobius Trjapitzin (Hymenoptera, Encyrtidae) species are egg parasitoids that are important for the biological control of some Buprestidae and Cerambycidae (Coleoptera); two species were introduced into North America for classical biocontrol and have successfully established. Two new native North Ame...

  3. A Model of Controlled Growth

    NASA Astrophysics Data System (ADS)

    Bressan, Alberto; Lewicka, Marta

    2018-03-01

    We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric shape of the growing tissue is determined by the instantaneous minimization of an elastic deformation energy, subject to a constraint on the volumetric growth. For an initial domain with C}^{2,α boundary, our main result establishes the local existence and uniqueness of a classical solution, up to a rigid motion.

  4. Metals and lipid oxidation. Contemporary issues.

    PubMed

    Schaich, K M

    1992-03-01

    Lipid oxidation is now recognized to be a critically important reaction in physiological and toxicological processes as well as in food products. This provides compelling reasons to understand what causes lipid oxidation in order to be able to prevent or control the reactions. Redox-active metals are major factors catalyzing lipid oxidation in biological systems. Classical mechanisms of direct electron transfer to double bonds by higher valence metals and of reduction of hydroperoxides by lower valence metals do not always account for patterns of metal catalysis of lipid oxidation in multiphasic or compartmentalized biological systems. To explain why oxidation kinetics, mechanisms, and products in molecular environments which are both chemically and physically complex often do not follow classical patterns predicted by model system studies, increased consideration must be given to five contemporary issues regarding metal catalysis of lipid oxidation: hypervalent non-heme iron or iron-oxygen complexes, heme catalysis mechanism(s), compartmentalization of reactions and lipid phase reactions of metals, effects of metals on product mixes, and factors affecting the mode of metal catalytic action.

  5. Extinction Phenomena: A Biologic Perspective on How and Why Psychoanalysis Works

    PubMed Central

    Brakel, Linda A. W.

    2011-01-01

    This article presents the view that much of the success of classical psychoanalysis is centrally predicated on its biological potency; focusing not on neuropsychology, but on the biology of conditioning. The argument suggests that features of classic psychoanalytic technique – the couch, meetings several times per week with both parties present, and free association – uniquely facilitate intense transferences of various sorts, and that these in turn constitute the multiple and diverse extinction trials necessary to best approximate extinction. PMID:21927610

  6. Generation of a tunable environment for electrical oscillator systems.

    PubMed

    León-Montiel, R de J; Svozilík, J; Torres, Juan P

    2014-07-01

    Many physical, chemical, and biological systems can be modeled by means of random-frequency harmonic oscillator systems. Even though the noise-free evolution of harmonic oscillator systems can be easily implemented, the way to experimentally introduce, and control, noise effects due to a surrounding environment remains a subject of lively interest. Here, we experimentally demonstrate a setup that provides a unique tool to generate a fully tunable environment for classical electrical oscillator systems. We illustrate the operation of the setup by implementing the case of a damped random-frequency harmonic oscillator. The high degree of tunability and control of our scheme is demonstrated by gradually modifying the statistics of the oscillator's frequency fluctuations. This tunable system can readily be used to experimentally study interesting noise effects, such as noise-induced transitions in systems driven by multiplicative noise, and noise-induced transport, a phenomenon that takes place in quantum and classical coupled oscillator networks.

  7. Dynamics of a Subterranean Trophic Cascade in Space and Time

    PubMed Central

    Ram, Karthik; Gruner, Daniel S.; McLaughlin, John P.; Preisser, Evan L.; Strong, Donald R.

    2008-01-01

    Trophic cascades, whereby predators indirectly benefit plant biomass by reducing herbivore pressure, form the mechanistic basis for classical biological control of pest insects. Entomopathogenic nematodes (EPN) are lethal to a variety of insect hosts with soil-dwelling stages, making them promising biocontrol agents. EPN biological control programs, however, typically fail because nematodes do not establish, persist and/or recycle over multiple host generations in the field. A variety of factors such as local abiotic conditions, host quantity and quality, and rates of movement affect the probability of persistence. Here, we review results from 13 years of study on the biology and ecology of an endemic population of Heterorhabditis marelatus (Rhabditida: Heterorhabditidae) in a California coastal prairie. In a highly seasonal abiotic environment with intrinsic variation in soils, vegetation structure, and host availability, natural populations of H. marelatus persisted at high incidence at some but not all sites within our study area. Through a set of field and lab experiments, we describe mechanisms and hypotheses to understand the persistence of H. marelatus. We suggest that further ecological study of naturally occurring EPN populations can yield significant insight to improve the practice and management of biological control of soil-dwelling insect pests. PMID:19259524

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

    Cuda, J.P.; Dunford, J.C.; Leavengood, J.M. Jr.

    Torpedograss, Panicum repens L., is an adventive, rhizomatous grass species that has become an invasive weed of terrestrial, wetland, and aquatic environments in tropical and subtropical regions worldwide. Until recently, strategies for controlling torpedograss in the USA have focused almost exclusively on mechanical and chemical methods, either alone or in combination, with varied results. A survey of the arthropods and nematodes currently associated with the plant in Lake Okeechobee, Florida, was conducted as part of a feasibility study to determine whether torpedograss is an appropriate target for a classical biological control program. Overall, approximately 4,000 arthropods and 400 nematode specimensmore » were collected. Sweep, clipped vegetation, and soil core samples were dominated by representatives of the arthropod orders Hemiptera, Hymenoptera, Diptera, and Acari. Lesion nematodes of the genus Pratylenchus were commonly associated with the roots of torpedograss. None of the organisms collected were torpedograss specialists. Although classical biological control of torpedograss is feasible based on the extent of the infestation, economic losses, resistance to conventional controls, and the report of a potentially host specific natural enemy in India, the botanical position of this grass weed will require a formal risk assessment before proceeding with a classical biological control program. (author) [Spanish] La conota, Panicum repens L., es una especie foranea de pasto que produce rizomas que ha convertido en ser una maleza invasora de ambientes terrestres, pantanosos y acuaticos en regiones tropicales y subtropicales en todo el mundo. Hasta hace un tiempo reciente, las estrategias para controlar conota en los EEUU eran enfocadas casi exclusivamente en los metodos mecanicos y quimicos, solos o en combinacion, con resultados variables. Un muestreo de los artropodos y nematodos asociados corrientemente con esta planta en el Lago de Okeechobee, Florida, fue realizado como parte de un estudio de factibilidad para determinar si conota es una candidata apropiada para un programa de control biologico clasico. En general, especimenes de aproximadamente unos 4,000 artropodos y unos 400 nematodos fueron recolectados. Muestras recolectadas pasando una red sobre vegetacion mezclada, cortando la vegetacion y tomando centros del suelo fueron dominados por representantes de artropodos de los ordenes de Hemiptera, Hymenoptera, Diptera, y Acari. Nematodos en el genero Pratylenchus, que causan lesiones sobre tejido, fueron asociados regularmente con las raices de conota. Ninguno de los organismos recolectados eran especialistas sobre conota. Aunque el control biologico clasico de la conota es factible basado sobre la magnitud de la infestacion, las perdidas economicas, la resistencia hacia los metodos de control convencionales y el informe en la India de un posible enemigo natural especifico a esta planta, la posicion botanica de este pasto maleza requiere una evaluacion de riesgo economico formal antes de continuar con un programa de control biologico clasico. (author)« less

  9. Steps towards the synthetic biology of polyketide biosynthesis.

    PubMed

    Cummings, Matthew; Breitling, Rainer; Takano, Eriko

    2014-02-01

    Nature is providing a bountiful pool of valuable secondary metabolites, many of which possess therapeutic properties. However, the discovery of new bioactive secondary metabolites is slowing down, at a time when the rise of multidrug-resistant pathogens and the realization of acute and long-term side effects of widely used drugs lead to an urgent need for new therapeutic agents. Approaches such as synthetic biology are promising to deliver a much-needed boost to secondary metabolite drug development through plug-and-play optimized hosts and refactoring novel or cryptic bacterial gene clusters. Here, we discuss this prospect focusing on one comprehensively studied class of clinically relevant bioactive molecules, the polyketides. Extensive efforts towards optimization and derivatization of compounds via combinatorial biosynthesis and classical engineering have elucidated the modularity, flexibility and promiscuity of polyketide biosynthetic enzymes. Hence, a synthetic biology approach can build upon a solid basis of guidelines and principles, while providing a new perspective towards the discovery and generation of novel and new-to-nature compounds. We discuss the lessons learned from the classical engineering of polyketide synthases and indicate their importance when attempting to engineer biosynthetic pathways using synthetic biology approaches for the introduction of novelty and overexpression of products in a controllable manner. © 2013 The Authors FEMS Microbiology Letters published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.

  10. Evolving Concepts and Translational Relevance of Enteroendocrine Cell Biology.

    PubMed

    Drucker, Daniel J

    2016-03-01

    Classical enteroenteroendocrine cell (EEC) biology evolved historically from identification of scattered hormone-producing endocrine cells within the epithelial mucosa of the stomach, small and large intestine. Purification of functional EEC hormones from intestinal extracts, coupled with molecular cloning of cDNAs and genes expressed within EECs has greatly expanded the complexity of EEC endocrinology, with implications for understanding the contribution of EECs to disease pathophysiology. Pubmed searches identified manuscripts highlighting new concepts illuminating the molecular biology, classification and functional role(s) of EECs and their hormonal products. Molecular interrogation of EECs has been transformed over the past decade, raising multiple new questions that challenge historical concepts of EEC biology. Evidence for evolution of the EEC from a unihormonal cell type with classical endocrine actions, to a complex plurihormonal dynamic cell with pleiotropic interactive functional networks within the gastrointestinal mucosa is critically assessed. We discuss gaps in understanding how EECs sense and respond to nutrients, cytokines, toxins, pathogens, the microbiota, and the microbial metabolome, and highlight the expanding translational relevance of EECs in the pathophysiology and therapy of metabolic and inflammatory disorders. The EEC system represents the largest specialized endocrine network in human physiology, integrating environmental and nutrient cues, enabling neural and hormonal control of metabolic homeostasis. Updating EEC classification systems will enable more accurate comparative analyses of EEC subpopulations and endocrine networks in multiple regions of the gastrointestinal tract.

  11. Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature

    PubMed Central

    O’Reilly, Edward J.; Olaya-Castro, Alexandra

    2014-01-01

    Advancing the debate on quantum effects in light-initiated reactions in biology requires clear identification of non-classical features that these processes can exhibit and utilize. Here we show that in prototype dimers present in a variety of photosynthetic antennae, efficient vibration-assisted energy transfer in the sub-picosecond timescale and at room temperature can manifest and benefit from non-classical fluctuations of collective pigment motions. Non-classicality of initially thermalized vibrations is induced via coherent exciton–vibration interactions and is unambiguously indicated by negativities in the phase–space quasi-probability distribution of the effective collective mode coupled to the electronic dynamics. These quantum effects can be prompted upon incoherent input of excitation. Our results therefore suggest that investigation of the non-classical properties of vibrational motions assisting excitation and charge transport, photoreception and chemical sensing processes could be a touchstone for revealing a role for non-trivial quantum phenomena in biology. PMID:24402469

  12. New and old roles of the peripheral and brain renin-angiotensin-aldosterone system (RAAS): Focus on cardiovascular and neurological diseases.

    PubMed

    Mascolo, A; Sessa, M; Scavone, C; De Angelis, A; Vitale, C; Berrino, L; Rossi, F; Rosano, G; Capuano, A

    2017-01-15

    It is commonly accepted that the renin-angiotensin-aldosterone system (RAAS) is a cardiovascular circulating hormonal system that plays also an important role in the modulation of several patterns in the brain. The pathway of the RAAS can be divided into two classes: the traditional pathway of RAAS, also named classic RAAS, and the non-classic RAAS. Both pathways play a role in both cardiovascular and neurological diseases through a peripheral or central control. In this regard, renewed interest is growing in the last years for the consideration that the brain RAAS could represent a new important therapeutic target to regulate not only the blood pressure via central nervous control, but also neurological diseases. However, the development of compounds able to cross the blood-brain barrier and to act on the brain RAAS is challenging, especially if the metabolic stability and the half-life are taken into consideration. To date, two drug classes (aminopeptidase type A inhibitors and angiotensin IV analogues) acting on the brain RAAS are in development in pre-clinical or clinical stages. In this article, we will present an overview of the biological functions played by peripheral and brain classic and non-classic pathways of the RAAS in several clinical conditions, focusing on the brain RAAS and on the new pharmacological targets of the RAAS. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  13. Add Control: plant virtualization for control solutions in WWTP.

    PubMed

    Maiza, M; Bengoechea, A; Grau, P; De Keyser, W; Nopens, I; Brockmann, D; Steyer, J P; Claeys, F; Urchegui, G; Fernández, O; Ayesa, E

    2013-01-01

    This paper summarizes part of the research work carried out in the Add Control project, which proposes an extension of the wastewater treatment plant (WWTP) models and modelling architectures used in traditional WWTP simulation tools, addressing, in addition to the classical mass transformations (transport, physico-chemical phenomena, biological reactions), all the instrumentation, actuation and automation & control components (sensors, actuators, controllers), considering their real behaviour (signal delays, noise, failures and power consumption of actuators). Its ultimate objective is to allow a rapid transition from the simulation of the control strategy to its implementation at full-scale plants. Thus, this paper presents the application of the Add Control simulation platform for the design and implementation of new control strategies at the WWTP of Mekolalde.

  14. Phenotypic and genotypic characterization of phenanthrene-degrading fluorescent Pseudomonas biovars.

    PubMed Central

    Johnsen, K; Andersen, S; Jacobsen, C S

    1996-01-01

    A total of 41 phenanthrene degraders were isolated from a former coal gasification site by using Pseudomonas-selective Gould's S1 medium. All isolates were found to belong to the fluorescent Pseudomonas group and were subjected to characterization by phenotypic methods, including classical taxonomic tests, API 20NE, and Biolog GN, and the strains were further characterized by the genotypic method repetitive extragenic palindromic PCR (REP-PCR). By using classical tests, the population was found to consist of 38 strains belonging to P. fluorescens, 2 P. putida strains, and 1 Pseudomonas sp. Bacteria in phenograms from Biolog GN and REP-PCR data were divided into groups, which were in good agreement with classical test and API 20NE results. We found a nonfluorescent group of 22 bacteria inconsistent with any Pseudomonas sp. in Bergey's Manual of Systematic Bacteriology. The group showed small differences in the genotypic test, indicating that all 22 isolates were not recent clones of the same isolate. Analyses of the nonfluorescent group indicated that it belonged to Pseudomonas, but the group could not be affiliated with P. fluorescens because of differences in DNA-DNA hybridization. Identifications using classical tests and API 20NE were found to correlate, but Biolog GN identifications after 24-h incubation resulted very often in the distantly related P. corrugata. The reproducibilities of individual tests of each phenotypic method were assessed, and low reproducibilities were mainly found to be associated with specific Biolog GN test wells. Classical tests and API 20NE proved to be the best for identification of isolates, whereas Biolog GN and REP-PCR were found to be the best tests for high resolution among these closely related isolates. PMID:8837438

  15. Apparent synergy among defense mechanisms in subterranean termites (Rhinotermitidae) against epizootic events: limits and potential for biological control.

    PubMed

    Chouvenc, Thomas; Su, Nan-Yao

    2010-08-01

    The use of entomopathogens for biological control of subterranean termites (Rhinotermitidae) has attracted attention in the past four decades, and several laboratory studies have shown promising results with fungal agents. This approach was based on the concept of classical biological control with the use of a virulent agent that can self-replicate in a termite nest and be transmitted among individuals, resulting in an epizootic to kill the entire colony. However, the absence of positive results in field studies challenged the potential of fungal pathogens as a realistic approach for subterranean termite control, and the relationship between fungi and subterranean termites remains poorly understood. A multimodal approach of the currently identified defense mechanisms allowed us to show that subterranean termites have the ability to prevent an epizootic from occurring. The defense mechanisms involved in such resistance are reviewed and documented. Finally, the interactions among three major defense mechanisms (grooming, cellular encapsulation, and gut antifungal activity) were analyzed, and it is suggested that these mechanisms act synergistically to produce an efficient defense against the infection of the fungus at the individual and group level so as to protect the colony from epizootics.

  16. An embodied biologically constrained model of foraging: from classical and operant conditioning to adaptive real-world behavior in DAC-X.

    PubMed

    Maffei, Giovanni; Santos-Pata, Diogo; Marcos, Encarni; Sánchez-Fibla, Marti; Verschure, Paul F M J

    2015-12-01

    Animals successfully forage within new environments by learning, simulating and adapting to their surroundings. The functions behind such goal-oriented behavior can be decomposed into 5 top-level objectives: 'how', 'why', 'what', 'where', 'when' (H4W). The paradigms of classical and operant conditioning describe some of the behavioral aspects found in foraging. However, it remains unclear how the organization of their underlying neural principles account for these complex behaviors. We address this problem from the perspective of the Distributed Adaptive Control theory of mind and brain (DAC) that interprets these two paradigms as expressing properties of core functional subsystems of a layered architecture. In particular, we propose DAC-X, a novel cognitive architecture that unifies the theoretical principles of DAC with biologically constrained computational models of several areas of the mammalian brain. DAC-X supports complex foraging strategies through the progressive acquisition, retention and expression of task-dependent information and associated shaping of action, from exploration to goal-oriented deliberation. We benchmark DAC-X using a robot-based hoarding task including the main perceptual and cognitive aspects of animal foraging. We show that efficient goal-oriented behavior results from the interaction of parallel learning mechanisms accounting for motor adaptation, spatial encoding and decision-making. Together, our results suggest that the H4W problem can be solved by DAC-X building on the insights from the study of classical and operant conditioning. Finally, we discuss the advantages and limitations of the proposed biologically constrained and embodied approach towards the study of cognition and the relation of DAC-X to other cognitive architectures. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Risk assessment, eradication, and biological control: global efforts to limit Australian acacia invasions

    USGS Publications Warehouse

    Wilson, John R.U.; Gairifo, Carla; Gibson, Michelle R.; Arianoutsou, Margarita; Bakar, Baki B.; Baret, Stephane; Celesti-Grapow, Laura; DiTomaso, Joseph M.; Dufour-Dror, Jean-Marc; Kueffer, Christoph; Kull, Christian A.; Hoffman, John H.; Impson, Fiona A.C.; Loope, Lloyd L.; Marchante, Elizabete; Harchante, Helia; Moore, Joslin L.; Murphy, Daniel J.; Tassin, Jacques; Witt, Arne; Zenni, Rafael D.; Richardson, David M.

    2011-01-01

    Aim Many Australian Acacia species have been planted around the world, some are highly valued, some are invasive, and some are both highly valued and invasive. We review global efforts to minimize the risk and limit the impact of invasions in this widely used plant group. Location Global. Methods Using information from literature sources, knowledge and experience of the authors, and the responses from a questionnaire sent to experts around the world, we reviewed: (1) a generalized life cycle of Australian acacias and how to control each life stage, (2) different management approaches and (3) what is required to help limit or prevent invasions. Results Relatively few Australian acacias have been introduced in large numbers, but all species with a long and extensive history of planting have become invasive somewhere. Australian acacias, as a group, have a high risk of becoming invasive and causing significant impacts as determined by existing assessment schemes. Moreover, in most situations, long-lived seed banks mean it is very difficult to control established infestations. Control has focused almost exclusively on widespread invaders, and eradication has rarely been attempted. Classical biological control is being used in South Africa with increasing success. Main conclusions A greater emphasis on pro-active rather than reactive management is required given the difficulties managing established invasions of Australian acacias. Adverse effects of proposed new introductions can be minimized by conducting detailed risk assessments in advance, planning for on-going monitoring and management, and ensuring resources are in place for long-term mitigation. Benign alternatives (e.g. sterile hybrids) could be developed to replace existing utilized taxa. Eradication should be set as a management goal more often to reduce the invasion debt. Introducing classical biological control agents that have a successful track-record in South Africa to other regions and identifying new agents (notably vegetative feeders) can help mitigate existing widespread invasions. Trans-boundary sharing of information will assist efforts to limit future invasions, in particular, management strategies need to be better evaluated, monitored, published and publicised so that global best-practice procedures can be developed.

  18. Boolean Networks in Inference and Dynamic Modeling of Biological Systems at the Molecular and Physiological Level

    NASA Astrophysics Data System (ADS)

    Thakar, Juilee; Albert, Réka

    The following sections are included: * Introduction * Boolean Network Concepts and History * Extensions of the Classical Boolean Framework * Boolean Inference Methods and Examples in Biology * Dynamic Boolean Models: Examples in Plant Biology, Developmental Biology and Immunology * Conclusions * References

  19. Single-molecule imaging in live bacteria cells.

    PubMed

    Ritchie, Ken; Lill, Yoriko; Sood, Chetan; Lee, Hochan; Zhang, Shunyuan

    2013-02-05

    Bacteria, such as Escherichia coli and Caulobacter crescentus, are the most studied and perhaps best-understood organisms in biology. The advances in understanding of living systems gained from these organisms are immense. Application of single-molecule techniques in bacteria have presented unique difficulties owing to their small size and highly curved form. The aim of this review is to show advances made in single-molecule imaging in bacteria over the past 10 years, and to look to the future where the combination of implementing such high-precision techniques in well-characterized and controllable model systems such as E. coli could lead to a greater understanding of fundamental biological questions inaccessible through classic ensemble methods.

  20. Biological control via "ecological" damping: An approach that attenuates non-target effects.

    PubMed

    Parshad, Rana D; Quansah, Emmanuel; Black, Kelly; Beauregard, Matthew

    2016-03-01

    In this work we develop and analyze a mathematical model of biological control to prevent or attenuate the explosive increase of an invasive species population, that functions as a top predator, in a three-species food chain. We allow for finite time blow-up in the model as a mathematical construct to mimic the explosive increase in population, enabling the species to reach "disastrous", and uncontrollable population levels, in a finite time. We next improve the mathematical model and incorporate controls that are shown to drive down the invasive population growth and, in certain cases, eliminate blow-up. Hence, the population does not reach an uncontrollable level. The controls avoid chemical treatments and/or natural enemy introduction, thus eliminating various non-target effects associated with such classical methods. We refer to these new controls as "ecological damping", as their inclusion dampens the invasive species population growth. Further, we improve prior results on the regularity and Turing instability of the three-species model that were derived in Parshad et al. (2014). Lastly, we confirm the existence of spatiotemporal chaos. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. The perils of the imperfect expectation of the perfect baby.

    PubMed

    Chervenak, Frank A; McCullough, Laurence B; Brent, Robert L

    2010-08-01

    Advances in modern medicine invite the assumption that medicine can control human biology. There is a perilous logic that leads from expectations of medicine's control over reproductive biology to the expectation of having a perfect baby. This article proposes that obstetricians should take a preventive ethics approach to the care of pregnant women with expectations for a perfect baby. We use Nathaniel Hawthorne's classic short story, "The Birthmark," to illustrate the perils of the logic of control and perfection through science and then identify possible contemporary sources of the expectation of the perfect baby. We propose that the informed consent process should be used as a preventive ethics tool throughout the course of pregnancy to educate pregnant women about the inherent errors of human reproduction, the highly variable clinical outcomes of these errors, the limited capacity of medicine to detect these errors, and the even more limited capacity to correct them. Copyright (c) 2010 Mosby, Inc. All rights reserved.

  2. Inverse biomimetics: how robots can help to verify concepts concerning sensorimotor control of human arm and leg movements.

    PubMed

    Kalveram, Karl Theodor; Seyfarth, André

    2009-01-01

    Simulation test, hardware test and behavioral comparison test are proposed to experimentally verify whether a technical control concept for limb movements is logically precise, physically sound, and biologically relevant. Thereby, robot test-beds may play an integral part by mimicking functional limb movements. The procedure is exemplarily demonstrated for human aiming movements with the forearm: when comparing competitive control concepts, these movements are described best by a spring-like operating muscular-skeletal device which is assisted by feedforward control through an inverse internal model of the limb--without regress to a forward model of the limb. In a perspective on hopping, the concept of exploitive control is addressed, and its comparison to concepts derived from classical control theory advised.

  3. Inference of developmental gene regulatory networks beyond classical model systems: new approaches in the post-genomic era.

    PubMed

    Fernandez-Valverde, Selene L; Aguilera, Felipe; Ramos-Díaz, René Alexander

    2018-06-18

    The advent of high-throughput sequencing technologies has revolutionized the way we understand the transformation of genetic information into morphological traits. Elucidating the network of interactions between genes that govern cell differentiation through development is one of the core challenges in genome research. These networks are known as developmental gene regulatory networks (dGRNs) and consist largely of the functional linkage between developmental control genes, cis-regulatory modules and differentiation genes, which generate spatially and temporally refined patterns of gene expression. Over the last 20 years, great advances have been made in determining these gene interactions mainly in classical model systems, including human, mouse, sea urchin, fruit fly, and worm. This has brought about a radical transformation in the fields of developmental biology and evolutionary biology, allowing the generation of high-resolution gene regulatory maps to analyse cell differentiation during animal development. Such maps have enabled the identification of gene regulatory circuits and have led to the development of network inference methods that can recapitulate the differentiation of specific cell-types or developmental stages. In contrast, dGRN research in non-classical model systems has been limited to the identification of developmental control genes via the candidate gene approach and the characterization of their spatiotemporal expression patterns, as well as to the discovery of cis-regulatory modules via patterns of sequence conservation and/or predicted transcription-factor binding sites. However, thanks to the continuous advances in high-throughput sequencing technologies, this scenario is rapidly changing. Here, we give a historical overview on the architecture and elucidation of the dGRNs. Subsequently, we summarize the approaches available to unravel these regulatory networks, highlighting the vast range of possibilities of integrating multiple technical advances and theoretical approaches to expand our understanding on the global of gene regulation during animal development in non-classical model systems. Such new knowledge will not only lead to greater insights into the evolution of molecular mechanisms underlying cell identity and animal body plans, but also into the evolution of morphological key innovations in animals.

  4. Bayesian Statistics for Biological Data: Pedigree Analysis

    ERIC Educational Resources Information Center

    Stanfield, William D.; Carlton, Matthew A.

    2004-01-01

    The use of Bayes' formula is applied to the biological problem of pedigree analysis to show that the Bayes' formula and non-Bayesian or "classical" methods of probability calculation give different answers. First year college students of biology can be introduced to the Bayesian statistics.

  5. Citation classics in periodontology: a controlled study.

    PubMed

    Nieri, Michele; Saletta, Daniele; Guidi, Luisa; Buti, Jacopo; Franceschi, Debora; Mauro, Saverio; Pini-Prato, Giovanpaolo

    2007-04-01

    The aims of this study were to identify the most cited articles in Periodontology published from January 1990 to March 2005; and to analyse the differences between citation Classics and less cited articles. The search was carried out in four international periodontal journals: Journal of Periodontology, Journal of Clinical Periodontology, International Journal of Periodontics and Restorative Dentistry and Journal of Periodontal Research. The Classics, that are articles cited at least 100 times, were identified using the Science Citation Index database. From every issue of the journals that contained a Classic, another article was randomly selected and used as a Control. Fifty-five Classics and 55 Controls were identified. Classic articles were longer, used more images, had more authors, and contained more self-references than Controls. Moreover Classics had on the average a bigger sample size, often dealt with etiopathogenesis and prognosis, but were rarely controlled or randomized studies. Classic articles play an instructive role, but are often non-Controlled studies.

  6. Studies on the Biology of Hypogeococcus pungens (sensu stricto) (Hemiptera: Pseudococcidae) in Argentina to Aid the Identification of the Mealybug Pest of Cactaceae in Puerto Rico

    PubMed Central

    Aguirre, M. B.; Diaz-Soltero, H.; Claps, L. E.; Saracho Bottero, A.; Triapitsyn, S.; Hasson, E.; Logarzo, G. A.

    2016-01-01

    Hypogeococcus pungens Granara de Willink, sensu stricto, is a serious pest of cacti in Puerto Rico threating many Caribbean islands. A classical biological control program for H. pungens was initiated for Puerto Rico in 2010 with a survey for natural enemies of H. pungens in its native range of Argentina. Biological differences were observed between populations of H. pungens sampled on Amaranthaceae and Cactaceae. Molecular studies suggested that H. pungens populations from different host plant families are likely a complex of species. Our objective was to study the biology of H. pungens sensu stricto on specimens collected in the same locality and host plant as the holotype [Tucumán Province, Argentina; Alternanthera pungens Kunth (Amaranthaceae)]. We were interested in the reproductive biology of females, longevity and survival of adults, the effect of temperature on the development, and nymph performance (survival and development) on five Cactaceae species. We found that H. pungens s.s. showed marked biological differences from the populations collected on Cactaceae and exported to Australia for the biological control of the cactus Harrisia spp. The main differences were the presence of deuterotoky parthenogenesis and the fact that H. pungens did not attack Cactaceae in the laboratory. Our results provide biological evidence that H. pungens is a species complex. We propose that the population introduced to Australia is neither Hypogeococcus festerianus Lizer y Trelles nor H. pungens, but an undescribed species with three circuli, and that the Hypogeococcus pest of cacti in Puerto Rico is not H. pungens. PMID:27324585

  7. Population Biology of Schistosoma Mating, Aggregation, and Transmission Breakpoints: More Reliable Model Analysis for the End-Game in Communities at Risk

    PubMed Central

    Gurarie, David; King, Charles H.

    2014-01-01

    Mathematical modeling is widely used for predictive analysis of control options for infectious agents. Challenging problems arise for modeling host-parasite systems having complex life-cycles and transmission environments. Macroparasites, like Schistosoma, inhabit highly fragmented habitats that shape their reproductive success and distribution. Overdispersion and mating success are important factors to consider in modeling control options for such systems. Simpler models based on mean worm burden (MWB) formulations do not take these into account and overestimate transmission. Proposed MWB revisions have employed prescribed distributions and mating factor corrections to derive modified MWB models that have qualitatively different equilibria, including ‘breakpoints’ below which the parasite goes to extinction, suggesting the possibility of elimination via long-term mass-treatment control. Despite common use, no one has attempted to validate the scope and hypotheses underlying such MWB approaches. We conducted a systematic analysis of both the classical MWB and more recent “stratified worm burden” (SWB) modeling that accounts for mating and reproductive hurdles (Allee effect). Our analysis reveals some similarities, including breakpoints, between MWB and SWB, but also significant differences between the two types of model. We show the classic MWB has inherent inconsistencies, and propose SWB as a reliable alternative for projection of long-term control outcomes. PMID:25549362

  8. Parallel firing strategy on Petri nets: A review

    NASA Astrophysics Data System (ADS)

    Mavlankulov, Gairatzhan; Turaev, Sherzod; Zhumabaeva, Laula; Zhukabayeva, Tamara

    2015-05-01

    In this paper we review the recent results related on Petri net controlled grammars and the close related topics. Though the theme of regulated grammars is one of the classic topics in formal language theory, a Petri net controlled grammar is still interesting subject for the investigation for many reasons. This type of grammars can successfully be used in modeling new problems emerging in manufacturing systems, systems biology and other areas. Moreover, the graphically illustrability, the ability to represent both a grammar and its control in one structure, and the possibility to unify different regulated rewritings make this formalization attractive for the study. We also summarize the obtained results and propose a new conception such as parallel firing strategy on Petri Nets.

  9. Integrating Genetic and Functional Genomic Data to Elucidate Common Disease Tra

    NASA Astrophysics Data System (ADS)

    Schadt, Eric

    2005-03-01

    The reconstruction of genetic networks in mammalian systems is one of the primary goals in biological research, especially as such reconstructions relate to elucidating not only common, polygenic human diseases, but living systems more generally. Here I present a statistical procedure for inferring causal relationships between gene expression traits and more classic clinical traits, including complex disease traits. This procedure has been generalized to the gene network reconstruction problem, where naturally occurring genetic variations in segregating mouse populations are used as a source of perturbations to elucidate tissue-specific gene networks. Differences in the extent of genetic control between genders and among four different tissues are highlighted. I also demonstrate that the networks derived from expression data in segregating mouse populations using the novel network reconstruction algorithm are able to capture causal associations between genes that result in increased predictive power, compared to more classically reconstructed networks derived from the same data. This approach to causal inference in large segregating mouse populations over multiple tissues not only elucidates fundamental aspects of transcriptional control, it also allows for the objective identification of key drivers of common human diseases.

  10. Genetic tool development and systemic regulation in biosynthetic technology.

    PubMed

    Dai, Zhongxue; Zhang, Shangjie; Yang, Qiao; Zhang, Wenming; Qian, Xiujuan; Dong, Weiliang; Jiang, Min; Xin, Fengxue

    2018-01-01

    With the increased development in research, innovation, and policy interest in recent years, biosynthetic technology has developed rapidly, which combines engineering, electronics, computer science, mathematics, and other disciplines based on classical genetic engineering and metabolic engineering. It gives a wider perspective and a deeper level to perceive the nature of life via cell mechanism, regulatory networks, or biological evolution. Currently, synthetic biology has made great breakthrough in energy, chemical industry, and medicine industries, particularly in the programmable genetic control at multiple levels of regulation to perform designed goals. In this review, the most advanced and comprehensive developments achieved in biosynthetic technology were represented, including genetic engineering as well as synthetic genomics. In addition, the superiority together with the limitations of the current genome-editing tools were summarized.

  11. Molecular biology of bladder cancer.

    PubMed

    Martin-Doyle, William; Kwiatkowski, David J

    2015-04-01

    Classic as well as more recent large-scale genomic analyses have uncovered multiple genes and pathways important for bladder cancer development. Genes involved in cell-cycle control, chromatin regulation, and receptor tyrosine and PI3 kinase-mammalian target of rapamycin signaling pathways are commonly mutated in muscle-invasive bladder cancer. Expression-based analyses have identified distinct types of bladder cancer that are similar to subsets of breast cancer, and have prognostic and therapeutic significance. These observations are leading to novel therapeutic approaches in bladder cancer, providing optimism for therapeutic progress. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Bacterial RNA Biology on a Genome Scale.

    PubMed

    Hör, Jens; Gorski, Stanislaw A; Vogel, Jörg

    2018-06-07

    Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms. Collectively, this creates a need for global RNA biology approaches that can rapidly and comprehensively analyze the RNA composition of a bacterium of interest. We review such approaches with a focus on RNA-seq as a versatile tool to investigate the different layers of gene expression in which RNA is made, processed, regulated, modified, translated, and turned over. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Regional Suppression of Bactrocera Fruit Flies (Diptera: Tephritidae) in the Pacific through Biological Control and Prospects for Future Introductions into Other Areas of the World

    PubMed Central

    Vargas, Roger I.; Leblanc, Luc; Harris, Ernest J.; Manoukis, Nicholas C.

    2012-01-01

    Bactrocera fruit fly species are economically important throughout the Pacific. The USDA, ARS U.S. Pacific Basin Agricultural Research Center has been a world leader in promoting biological control of Bactrocera spp. that includes classical, augmentative, conservation and IPM approaches. In Hawaii, establishment of Bactrocera cucurbitae (Coquillett) in 1895 resulted in the introduction of the most successful parasitoid, Psyttalia fletcheri (Silvestri); similarly, establishment of Bactrocera dorsalis (Hendel) in 1945 resulted in the introduction of 32 natural enemies of which Fopius arisanus (Sonan), Diachasmimorpha longicaudata (Ashmead) and Fopius vandenboschi (Fullaway) were most successful. Hawaii has also been a source of parasitoids for fruit fly control throughout the Pacific region including Australia, Pacific Island Nations, Central and South America, not only for Bactrocera spp. but also for Ceratitis and Anastrepha spp. Most recently, in 2002, F. arisanus was introduced into French Polynesia where B. dorsalis had invaded in 1996. Establishment of D. longicaudata into the new world has been important to augmentative biological control releases against Anastrepha spp. With the rapid expansion of airline travel and global trade there has been an alarming spread of Bactrocera spp. into new areas of the world (i.e., South America and Africa). Results of studies in Hawaii and French Polynesia, support parasitoid introductions into South America and Africa, where B. carambolae and B. invadens, respectively, have become established. In addition, P. fletcheri is a candidate for biological control of B. cucurbitae in Africa. We review past and more recent successes against Bactrocera spp. and related tephritids, and outline simple rearing and release methods to facilitate this goal. PMID:26466626

  14. Analysis of a predator-prey model with Holling II functional response concerning impulsive control strategy

    NASA Astrophysics Data System (ADS)

    Liu, Bing; Teng, Zhidong; Chen, Lansun

    2006-08-01

    According to biological and chemical control strategy for pest control, we investigate the dynamic behavior of a Holling II functional response predator-prey system concerning impulsive control strategy-periodic releasing natural enemies and spraying pesticide at different fixed times. By using Floquet theorem and small amplitude perturbation method, we prove that there exists a stable pest-eradication periodic solution when the impulsive period is less than some critical value. Further, the condition for the permanence of the system is also given. Numerical results show that the system we consider can take on various kinds of periodic fluctuations and several types of attractor coexistence and is dominated by periodic, quasiperiodic and chaotic solutions, which implies that the presence of pulses makes the dynamic behavior more complex. Finally, we conclude that our impulsive control strategy is more effective than the classical one if we take chemical control efficiently.

  15. A 2cM genome-wide scan of European Holstein cattle affected by classical BSE

    PubMed Central

    2010-01-01

    Background Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease that is invariably fatal in cattle and has been implicated as a significant human health risk. Polymorphisms that alter the prion protein of sheep or humans have been associated with variations in transmissible spongiform encephalopathy susceptibility or resistance. In contrast, there is no strong evidence that non-synonymous mutations in the bovine prion gene (PRNP) are associated with classical BSE disease susceptibility. However, two bovine PRNP insertion/deletion polymorphisms, one within the promoter region and the other in intron 1, have been associated with susceptibility to classical BSE. These associations do not explain the full extent of BSE susceptibility, and loci outside of PRNP appear to be associated with disease incidence in some cattle populations. To test for associations with BSE susceptibility, we conducted a genome wide scan using a panel of 3,072 single nucleotide polymorphism (SNP) markers on 814 animals representing cases and control Holstein cattle from the United Kingdom BSE epidemic. Results Two sets of BSE affected Holstein cattle were analyzed in this study, one set with known family relationships and the second set of paired cases with controls. The family set comprises half-sibling progeny from six sires. The progeny from four of these sires had previously been scanned with microsatellite markers. The results obtained from the current analysis of the family set yielded both some supporting and new results compared with those obtained in the earlier study. The results revealed 27 SNPs representing 18 chromosomes associated with incidence of BSE disease. These results confirm a region previously reported on chromosome 20, and identify additional regions on chromosomes 2, 14, 16, 21 and 28. This study did not identify a significant association near the PRNP in the family sample set. The only association found in the PRNP region was in the case-control sample set and this was not significant after multiple test correction. The genome scan of the case-control animals did not identify any associations that passed a stringent genome-wide significance threshold. Conclusions Several regions of the genome are statistically associated with the incidence of classical BSE in European Holstein cattle. Further investigation of loci on chromosomes 2, 14, 16, 20, 21 and 28 will be required to uncover any biological significance underlying these marker associations. PMID:20350325

  16. Studies on the Biology of Hypogeococcus pungens (sensu stricto) (Hemiptera: Pseudococcidae) in Argentina to Aid the Identification of the Mealybug Pest of Cactaceae in Puerto Rico.

    PubMed

    Aguirre, M B; Diaz-Soltero, H; Claps, L E; Saracho Bottero, A; Triapitsyn, S; Hasson, E; Logarzo, G A

    2016-01-01

    Hypogeococcus pungens Granara de Willink, sensu stricto, is a serious pest of cacti in Puerto Rico threating many Caribbean islands. A classical biological control program for H. pungens was initiated for Puerto Rico in 2010 with a survey for natural enemies of H. pungens in its native range of Argentina. Biological differences were observed between populations of H. pungens sampled on Amaranthaceae and Cactaceae. Molecular studies suggested that H. pungens populations from different host plant families are likely a complex of species. Our objective was to study the biology of H. pungens sensu stricto on specimens collected in the same locality and host plant as the holotype [Tucumán Province, Argentina; Alternanthera pungens Kunth (Amaranthaceae)]. We were interested in the reproductive biology of females, longevity and survival of adults, the effect of temperature on the development, and nymph performance (survival and development) on five Cactaceae species. We found that H. pungens s.s showed marked biological differences from the populations collected on Cactaceae and exported to Australia for the biological control of the cactus Harrisia spp. The main differences were the presence of deuterotoky parthenogenesis and the fact that H. pungens did not attack Cactaceae in the laboratory. Our results provide biological evidence that H. pungens is a species complex. We propose that the population introduced to Australia is neither Hypogeococcus festerianus Lizer y Trelles nor H. pungens, but an undescribed species with three circuli, and that the Hypogeococcus pest of cacti in Puerto Rico is not H. pungens. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America.

  17. Evolution of critical day length for diapause induction enables range expansion of Diorhabda carinulata, a biological control agent against tamarisk (Tamarix spp.)

    PubMed Central

    Bean, Dan W; Dalin, Peter; Dudley, Tom L

    2012-01-01

    In classical weed biological control, small collections of arthropods are made from one or a few sites in the native range of the target plant and are introduced to suppress the plant where it has become invasive, often across a wide geographic range. Ecological mismatches in the new range are likely, and success using the biocontrol agent may depend on postrelease evolution of beneficial life history traits. In this study, we measure the evolution of critical day length for diapause induction (day length at which 50% of the population enters dormancy), in a beetle (Diorhabda carinulata) introduced into North America from China to control an exotic shrub, Tamarix spp. Beetle populations were sampled from four sites in North America 7 years after introduction, and critical day length was shown to have declined, forming a cline over a latitudinal gradient At one field site, decreased critical day length was correlated with 16 additional days of reproductive activity, resulting in a closer match between beetle life history and the phenology of Tamarix. These findings indicate an enhanced efficacy and an increasingly wider range for D. carinulata in Tamarix control. PMID:22949926

  18. Mistaken gender identity in non-classical congenital adrenal hyperplasia.

    PubMed

    Kukreti, Prerna; Kandpal, Manish; Jiloha, R C

    2014-04-01

    Gender identity is the sense of belonging that one feels for a particular sex psychologically and socially, independent of one's biological sex. There is much less systematic data on gender identity in females with congenital adrenal hyperplasia (CAH). We report a case of non-classical CAH presenting as a case of gender identity disorder.

  19. A Model Plant for a Biology Curriculum: Spider Flower ("Cleome Hasslerana L.")

    ERIC Educational Resources Information Center

    Marquard, Robert D.; Steinback, Rebecca

    2009-01-01

    Major advances in fundamental science are developed using model systems. Classic examples of model systems include Mendel's work with the common garden pea ("Pisium sativa"), classic inheritance work by Morgan with the fruit fly ("Drosophila"), developmental studies with the nematode ("C. elegans"), and transposable elements in maize ("Zea…

  20. Unexpected Levels of Biological Activity during the Polar Night Offer New Perspectives on a Warming Arctic.

    PubMed

    Berge, Jørgen; Daase, Malin; Renaud, Paul E; Ambrose, William G; Darnis, Gerald; Last, Kim S; Leu, Eva; Cohen, Jonathan H; Johnsen, Geir; Moline, Mark A; Cottier, Finlo; Varpe, Øystein; Shunatova, Natalia; Bałazy, Piotr; Morata, Nathalie; Massabuau, Jean-Charles; Falk-Petersen, Stig; Kosobokova, Ksenia; Hoppe, Clara J M; Węsławski, Jan Marcin; Kukliński, Piotr; Legeżyńska, Joanna; Nikishina, Daria; Cusa, Marine; Kędra, Monika; Włodarska-Kowalczuk, Maria; Vogedes, Daniel; Camus, Lionel; Tran, Damien; Michaud, Emma; Gabrielsen, Tove M; Granovitch, Andrei; Gonchar, Anya; Krapp, Rupert; Callesen, Trine A

    2015-10-05

    The current understanding of Arctic ecosystems is deeply rooted in the classical view of a bottom-up controlled system with strong physical forcing and seasonality in primary-production regimes. Consequently, the Arctic polar night is commonly disregarded as a time of year when biological activities are reduced to a minimum due to a reduced food supply. Here, based upon a multidisciplinary ecosystem-scale study from the polar night at 79°N, we present an entirely different view. Instead of an ecosystem that has entered a resting state, we document a system with high activity levels and biological interactions across most trophic levels. In some habitats, biological diversity and presence of juvenile stages were elevated in winter months compared to the more productive and sunlit periods. Ultimately, our results suggest a different perspective regarding ecosystem function that will be of importance for future environmental management and decision making, especially at a time when Arctic regions are experiencing accelerated environmental change [1]. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Polymer-mediated growth of crystals and mesocrystals.

    PubMed

    Cölfen, Helmut

    2013-01-01

    Polymers are important additives for the control of mineralization reactions in both biological and bioinspired mineralization. The reason is that they allow for a number of interactions with the growing crystals and even amorphous minerals. These can substantially influence the way the mineral grows on several levels. Already in the prenucleation phase, polymers can control the formation of prenucleation clusters and subsequently the nucleation event. Also, polymers can control whether the further crystallization follows a classical or nonclassical particle-mediated growth path. In this chapter, the main ways in which polymers can be used to control a crystallization reaction will be highlighted. In addition, polymers that are useful for this purpose and the experimental conditions suitable for directing a crystallization reaction into the desired direction through the use of polymers will be described. © 2013 Elsevier Inc. All rights reserved.

  2. Dynamic sensitivity analysis of biological systems

    PubMed Central

    Wu, Wu Hsiung; Wang, Feng Sheng; Chang, Maw Shang

    2008-01-01

    Background A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differential equation (ODE) system. How to simulate the dynamic behavior and dynamic parameter sensitivities of systems described by ODEs efficiently and accurately is a critical job. In many practical applications, e.g., the fed-batch fermentation systems, the system admissible input (corresponding to independent variables of the system) can be time-dependent. The main difficulty for investigating the dynamic log gains of these systems is the infinite dimension due to the time-dependent input. The classical dynamic sensitivity analysis does not take into account this case for the dynamic log gains. Results We present an algorithm with an adaptive step size control that can be used for computing the solution and dynamic sensitivities of an autonomous ODE system simultaneously. Although our algorithm is one of the decouple direct methods in computing dynamic sensitivities of an ODE system, the step size determined by model equations can be used on the computations of the time profile and dynamic sensitivities with moderate accuracy even when sensitivity equations are more stiff than model equations. To show this algorithm can perform the dynamic sensitivity analysis on very stiff ODE systems with moderate accuracy, it is implemented and applied to two sets of chemical reactions: pyrolysis of ethane and oxidation of formaldehyde. The accuracy of this algorithm is demonstrated by comparing the dynamic parameter sensitivities obtained from this new algorithm and from the direct method with Rosenbrock stiff integrator based on the indirect method. The same dynamic sensitivity analysis was performed on an ethanol fed-batch fermentation system with a time-varying feed rate to evaluate the applicability of the algorithm to realistic models with time-dependent admissible input. Conclusion By combining the accuracy we show with the efficiency of being a decouple direct method, our algorithm is an excellent method for computing dynamic parameter sensitivities in stiff problems. We extend the scope of classical dynamic sensitivity analysis to the investigation of dynamic log gains of models with time-dependent admissible input. PMID:19091016

  3. The sociobiology of genes: the gene's eye view as a unifying behavioural-ecological framework for biological evolution.

    PubMed

    De Tiège, Alexis; Van de Peer, Yves; Braeckman, Johan; Tanghe, Koen B

    2017-11-22

    Although classical evolutionary theory, i.e., population genetics and the Modern Synthesis, was already implicitly 'gene-centred', the organism was, in practice, still generally regarded as the individual unit of which a population is composed. The gene-centred approach to evolution only reached a logical conclusion with the advent of the gene-selectionist or gene's eye view in the 1960s and 1970s. Whereas classical evolutionary theory can only work with (genotypically represented) fitness differences between individual organisms, gene-selectionism is capable of working with fitness differences among genes within the same organism and genome. Here, we explore the explanatory potential of 'intra-organismic' and 'intra-genomic' gene-selectionism, i.e., of a behavioural-ecological 'gene's eye view' on genetic, genomic and organismal evolution. First, we give a general outline of the framework and how it complements the-to some extent-still 'organism-centred' approach of classical evolutionary theory. Secondly, we give a more in-depth assessment of its explanatory potential for biological evolution, i.e., for Darwin's 'common descent with modification' or, more specifically, for 'historical continuity or homology with modular evolutionary change' as it has been studied by evolutionary developmental biology (evo-devo) during the last few decades. In contrast with classical evolutionary theory, evo-devo focuses on 'within-organism' developmental processes. Given the capacity of gene-selectionism to adopt an intra-organismal gene's eye view, we outline the relevance of the latter model for evo-devo. Overall, we aim for the conceptual integration between the gene's eye view on the one hand, and more organism-centred evolutionary models (both classical evolutionary theory and evo-devo) on the other.

  4. EMBAYMENT CHARACTERISTIC TIME AND BIOLOGY VIA TIDAL PRISM MODEL

    EPA Science Inventory

    Transport time scales in water bodies are classically based on their physical and chemical aspects rather than on their ecological and biological character. The direct connection between a physical time scale and ecological effects has to be investigated in order to quantitativel...

  5. Host range testing of Tamarixia radiata (Hymenoptera: Eulophidae) sourced from the Punjab of Pakistan for classical biological control of Diaphorina citri (Hemiptera: Liviidae: Euphyllurinae: Diaphorinini) in California.

    PubMed

    Hoddle, Mark S; Pandey, Raju

    2014-02-01

    ABSTRACT Tests evaluating the host range of Tamarixia radiata (Waterson) (Hymenoptera: Eulophidae), a parasitoid of the pestiferous Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), sourced from the Punjab of Pakistan, were conducted in quarantine at the University of California, Riverside, CA. Seven nontarget psyllid species (five native and two self-introduced species) representing five families were exposed to T radiata under the following three different exposure scenarios: 1) sequential no-choice tests, 2) static no-choice tests, and 3) choice tests. Nontarget species were selected for testing based on the following criteria: 1) taxonomic relatedness to the target, D. citri; 2) native psyllids inhabiting native host plants related to citrus that could release volatiles attractive to T. radiata; 3) native psyllids with a high probability of occurrence in native vegetation surrounding commercial citrus groves that could be encountered by T. radiata emigrating from D. citri-infested citrus orchards; 4) a common native pest psyllid species; and 5) a beneficial psyllid attacking a noxious weed. The results of host range testing were unambiguous; T radiata exhibited a narrow host range and high host specificity, with just one species of nontarget psyllid, the abundant native pest Bactericera cockerelli Sulc, being parasitized at low levels (< 5%). These results suggest that the likelihood of significant nontarget impacts is low, and the establishment of T. radiata in southern California for the classical biological control of D. citri poses negligible environmental risk.

  6. Masters change, slaves remain.

    PubMed

    Graham, Patricia; Penn, Jill K M; Schedl, Paul

    2003-01-01

    Sex determination offers an opportunity to address many classic questions of developmental biology. In addition, because sex determination evolves rapidly, it offers an opportunity to investigate the evolution of genetic hierarchies. Sex determination in Drosophila melanogaster is controlled by the master regulatory gene, Sex lethal (Sxl). DmSxl controls the alternative splicing of a downstream gene, transformer (tra), which acts with tra2 to control alternative splicing of doublesex (dsx). DmSxl also controls its own splicing, creating an autoregulatory feedback loop that ensures expression of Sxl in females, but not males. A recent paper has shown that in the dipteran Ceratitis capitata later (downstream) steps in the regulatory hierarchy are conserved, while earlier (upstream) steps are not. Cctra is regulated by alternative splicing and apparently controls the alternative splicing of Ccdsx. However, Cctra is not regulated by CcSxl. Instead it appears to autoregulate in a manner similar to the autoregulation seen with DmSxl. Copyright 2002 Wiley Periodicals, Inc.

  7. Detecting Rhythms in Time Series with RAIN

    PubMed Central

    Thaben, Paul F.; Westermark, Pål O.

    2014-01-01

    A fundamental problem in research on biological rhythms is that of detecting and assessing the significance of rhythms in large sets of data. Classic methods based on Fourier theory are often hampered by the complex and unpredictable characteristics of experimental and biological noise. Robust nonparametric methods are available but are limited to specific wave forms. We present RAIN, a robust nonparametric method for the detection of rhythms of prespecified periods in biological data that can detect arbitrary wave forms. When applied to measurements of the circadian transcriptome and proteome of mouse liver, the sets of transcripts and proteins with rhythmic abundances were significantly expanded due to the increased detection power, when we controlled for false discovery. Validation against independent data confirmed the quality of these results. The large expansion of the circadian mouse liver transcriptomes and proteomes reflected the prevalence of nonsymmetric wave forms and led to new conclusions about function. RAIN was implemented as a freely available software package for R/Bioconductor and is presently also available as a web interface. PMID:25326247

  8. Mistaken gender identity in non-classical congenital adrenal hyperplasia

    PubMed Central

    Kukreti, Prerna; Kandpal, Manish; Jiloha, R. C.

    2014-01-01

    Gender identity is the sense of belonging that one feels for a particular sex psychologically and socially, independent of one's biological sex. There is much less systematic data on gender identity in females with congenital adrenal hyperplasia (CAH). We report a case of non-classical CAH presenting as a case of gender identity disorder. PMID:24891708

  9. Models for integrated pest control and their biological implications.

    PubMed

    Tang, Sanyi; Cheke, Robert A

    2008-09-01

    Successful integrated pest management (IPM) control programmes depend on many factors which include host-parasitoid ratios, starting densities, timings of parasitoid releases, dosages and timings of insecticide applications and levels of host-feeding and parasitism. Mathematical models can help us to clarify and predict the effects of such factors on the stability of host-parasitoid systems, which we illustrate here by extending the classical continuous and discrete host-parasitoid models to include an IPM control programme. The results indicate that one of three control methods can maintain the host level below the economic threshold (ET) in relation to different ET levels, initial densities of host and parasitoid populations and host-parasitoid ratios. The effects of host intrinsic growth rate and parasitoid searching efficiency on host mean outbreak period can be calculated numerically from the models presented. The instantaneous pest killing rate of an insecticide application is also estimated from the models. The results imply that the modelling methods described can help in the design of appropriate control strategies and assist management decision-making. The results also indicate that a high initial density of parasitoids (such as in inundative releases) and high parasitoid inter-generational survival rates will lead to more frequent host outbreaks and, therefore, greater economic damage. The biological implications of this counter intuitive result are discussed.

  10. (Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis.

    PubMed

    He, Fei; Fromion, Vincent; Westerhoff, Hans V

    2013-11-21

    Metabolic control analysis (MCA) and supply-demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic regulation. Supply-demand theory has not yet considered gene-expression regulation explicitly whilst a variant of MCA, i.e. Hierarchical Control Analysis (HCA), has done so. Existing analyses based on control engineering approaches have not been very explicit about whether metabolic or gene-expression regulation would be involved, but designed different ways in which regulation could be organized, with the potential of causing adaptation to be perfect. This study integrates control engineering and classical MCA augmented with supply-demand theory and HCA. Because gene-expression regulation involves time integration, it is identified as a natural instantiation of the 'integral control' (or near integral control) known in control engineering. This study then focuses on robustness against and adaptation to perturbations of process activities in the network, which could result from environmental perturbations, mutations or slow noise. It is shown however that this type of 'integral control' should rarely be expected to lead to the 'perfect adaptation': although the gene-expression regulation increases the robustness of important metabolite concentrations, it rarely makes them infinitely robust. For perfect adaptation to occur, the protein degradation reactions should be zero order in the concentration of the protein, which may be rare biologically for cells growing steadily. A proposed new framework integrating the methodologies of control engineering and metabolic and hierarchical control analysis, improves the understanding of biological systems that are regulated both metabolically and by gene expression. In particular, the new approach enables one to address the issue whether the intracellular biochemical networks that have been and are being identified by genomics and systems biology, correspond to the 'perfect' regulatory structures designed by control engineering vis-à-vis optimal functions such as robustness. To the extent that they are not, the analyses suggest how they may become so and this in turn should facilitate synthetic biology and metabolic engineering.

  11. "Fathers" and "sons" of theories in cell physiology: the membrane theory.

    PubMed

    Matveev, V V; Wheatley, D N

    2005-12-16

    The last 50 years in the history of life sciences are remarkable for a new important feature that looks as a great threat for their future. A profound specialization dominating in quickly developing fields of science causes a crisis of the scientific method. The essence of the method is a unity of two elements, the experimental data and the theory that explains them. To us, "fathers" of science, classically, were the creators of new ideas and theories. They were the true experts of their own theories. It is only they who have the right to say: "I am the theory". In other words, they were carriers of theories, of the theoretical knowledge. The fathers provided the necessary logical integrity to their theories, since theories in biology have still to be based on strict mathematical proofs. It is not true for sons. As a result of massive specialization, modern experts operate in very confined close spaces. They formulate particular rules far from the level of theory. The main theories of science are known to them only at the textbook level. Nowadays, nobody can say: "I am the theory". With whom, then is it possible to discuss today on a broader theoretical level? How can a classical theory--for example, the membrane one--be changed or even disproved under these conditions? How can the "sons" with their narrow education catch sight of membrane theory defects? As a result, "global" theories have few critics and control. Due to specialization, we have lost the ability to work at the experimental level of biology within the correct or appropriate theoretical context. The scientific method in its classic form is now being rapidly eroded. A good case can be made for "Membrane Theory", to which we will largely refer throughout this article.

  12. Along the Central Dogma-Controlling Gene Expression with Small Molecules.

    PubMed

    Schneider-Poetsch, Tilman; Yoshida, Minoru

    2018-05-04

    The central dogma of molecular biology, that DNA is transcribed into RNA and RNA translated into protein, was coined in the early days of modern biology. Back in the 1950s and 1960s, bacterial genetics first opened the way toward understanding life as the genetically encoded interaction of macromolecules. As molecular biology progressed and our knowledge of gene control deepened, it became increasingly clear that expression relied on many more levels of regulation. In the process of dissecting mechanisms of gene expression, specific small-molecule inhibitors played an important role and became valuable tools of investigation. Small molecules offer significant advantages over genetic tools, as they allow inhibiting a process at any desired time point, whereas mutating or altering the gene of an important regulator would likely result in a dead organism. With the advent of modern sequencing technology, it has become possible to monitor global cellular effects of small-molecule treatment and thereby overcome the limitations of classical biochemistry, which usually looks at a biological system in isolation. This review focuses on several molecules, especially natural products, that have played an important role in dissecting gene expression and have opened up new fields of investigation as well as clinical venues for disease treatment. Expected final online publication date for the Annual Review of Biochemistry Volume 87 is June 20, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  13. Impaired associative learning in schizophrenia: behavioral and computational studies

    PubMed Central

    Diwadkar, Vaibhav A.; Flaugher, Brad; Jones, Trevor; Zalányi, László; Ujfalussy, Balázs; Keshavan, Matcheri S.

    2008-01-01

    Associative learning is a central building block of human cognition and in large part depends on mechanisms of synaptic plasticity, memory capacity and fronto–hippocampal interactions. A disorder like schizophrenia is thought to be characterized by altered plasticity, and impaired frontal and hippocampal function. Understanding the expression of this dysfunction through appropriate experimental studies, and understanding the processes that may give rise to impaired behavior through biologically plausible computational models will help clarify the nature of these deficits. We present a preliminary computational model designed to capture learning dynamics in healthy control and schizophrenia subjects. Experimental data was collected on a spatial-object paired-associate learning task. The task evinces classic patterns of negatively accelerated learning in both healthy control subjects and patients, with patients demonstrating lower rates of learning than controls. Our rudimentary computational model of the task was based on biologically plausible assumptions, including the separation of dorsal/spatial and ventral/object visual streams, implementation of rules of learning, the explicit parameterization of learning rates (a plausible surrogate for synaptic plasticity), and learning capacity (a plausible surrogate for memory capacity). Reductions in learning dynamics in schizophrenia were well-modeled by reductions in learning rate and learning capacity. The synergy between experimental research and a detailed computational model of performance provides a framework within which to infer plausible biological bases of impaired learning dynamics in schizophrenia. PMID:19003486

  14. (Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis

    PubMed Central

    2013-01-01

    Background Metabolic control analysis (MCA) and supply–demand theory have led to appreciable understanding of the systems properties of metabolic networks that are subject exclusively to metabolic regulation. Supply–demand theory has not yet considered gene-expression regulation explicitly whilst a variant of MCA, i.e. Hierarchical Control Analysis (HCA), has done so. Existing analyses based on control engineering approaches have not been very explicit about whether metabolic or gene-expression regulation would be involved, but designed different ways in which regulation could be organized, with the potential of causing adaptation to be perfect. Results This study integrates control engineering and classical MCA augmented with supply–demand theory and HCA. Because gene-expression regulation involves time integration, it is identified as a natural instantiation of the ‘integral control’ (or near integral control) known in control engineering. This study then focuses on robustness against and adaptation to perturbations of process activities in the network, which could result from environmental perturbations, mutations or slow noise. It is shown however that this type of ‘integral control’ should rarely be expected to lead to the ‘perfect adaptation’: although the gene-expression regulation increases the robustness of important metabolite concentrations, it rarely makes them infinitely robust. For perfect adaptation to occur, the protein degradation reactions should be zero order in the concentration of the protein, which may be rare biologically for cells growing steadily. Conclusions A proposed new framework integrating the methodologies of control engineering and metabolic and hierarchical control analysis, improves the understanding of biological systems that are regulated both metabolically and by gene expression. In particular, the new approach enables one to address the issue whether the intracellular biochemical networks that have been and are being identified by genomics and systems biology, correspond to the ‘perfect’ regulatory structures designed by control engineering vis-à-vis optimal functions such as robustness. To the extent that they are not, the analyses suggest how they may become so and this in turn should facilitate synthetic biology and metabolic engineering. PMID:24261908

  15. Evidence of non-classical (squeezed) light in biological systems

    NASA Astrophysics Data System (ADS)

    Popp, F. A.; Chang, J. J.; Herzog, A.; Yan, Z.; Yan, Y.

    2002-01-01

    By use of coincidence measurements on “ultraweak” photon emission, the photocount statistics (PCS) of artificial visible light turns out to follow-as expected-super-Poissonian PCS. Biophotons, originating from spontaneous or light-induced living systems, display super-Poissonian, Poissonian and even sub-Poissonian PCS. This result shows the first time evidence of non-classical (squeezed) light in living tissues.

  16. The biology of gall-inducing arthropods.

    Treesearch

    Gyuri Csoka; William J. Mattson; Graham N. Stone; Peter W. Price

    1998-01-01

    This proceedings explores many facets of the ever intriguing and enigmatic relationships between plants and their gall-forming herbivores. The research reported herein ranges from studies on classical biology and systematics of galling to molecular phylogeny, population genetics, and ecological and evolutionary theory. Human kind has much to learn and gain from...

  17. Intramembrane proteolysis: theme and variations.

    PubMed

    Wolfe, Michael S; Kopan, Raphael

    2004-08-20

    Proteases that reside in cellular membranes apparently wield water to hydrolyze the peptide bonds of substrates despite their water-excluding environment. Although these intramembrane proteases bear little or no sequence resemblance to classical water-soluble proteases, they have ostensibly converged on similar hydrolytic mechanisms. Identification of essential amino acid residues of these proteases suggests that they use residue combinations for catalysis in the same way as their soluble cousins. In contrast to classical proteases, however, the catalytic residues of intramembrane proteases lie within predicted hydrophobic transmembrane domains. Elucidating the biological functions of intramembrane proteases, identifying their substrates, and understanding how they hydrolyze peptide bonds within membranes will shed light on the ways these proteases regulate crucial biological processes and contribute to disease.

  18. Human pluripotent stem cells: an emerging model in developmental biology.

    PubMed

    Zhu, Zengrong; Huangfu, Danwei

    2013-02-01

    Developmental biology has long benefited from studies of classic model organisms. Recently, human pluripotent stem cells (hPSCs), including human embryonic stem cells and human induced pluripotent stem cells, have emerged as a new model system that offers unique advantages for developmental studies. Here, we discuss how studies of hPSCs can complement classic approaches using model organisms, and how hPSCs can be used to recapitulate aspects of human embryonic development 'in a dish'. We also summarize some of the recently developed genetic tools that greatly facilitate the interrogation of gene function during hPSC differentiation. With the development of high-throughput screening technologies, hPSCs have the potential to revolutionize gene discovery in mammalian development.

  19. Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities

    PubMed Central

    2011-01-01

    Background Gene regulatory networks play essential roles in living organisms to control growth, keep internal metabolism running and respond to external environmental changes. Understanding the connections and the activity levels of regulators is important for the research of gene regulatory networks. While relevance score based algorithms that reconstruct gene regulatory networks from transcriptome data can infer genome-wide gene regulatory networks, they are unfortunately prone to false positive results. Transcription factor activities (TFAs) quantitatively reflect the ability of the transcription factor to regulate target genes. However, classic relevance score based gene regulatory network reconstruction algorithms use models do not include the TFA layer, thus missing a key regulatory element. Results This work integrates TFA prediction algorithms with relevance score based network reconstruction algorithms to reconstruct gene regulatory networks with improved accuracy over classic relevance score based algorithms. This method is called Gene expression and Transcription factor activity based Relevance Network (GTRNetwork). Different combinations of TFA prediction algorithms and relevance score functions have been applied to find the most efficient combination. When the integrated GTRNetwork method was applied to E. coli data, the reconstructed genome-wide gene regulatory network predicted 381 new regulatory links. This reconstructed gene regulatory network including the predicted new regulatory links show promising biological significances. Many of the new links are verified by known TF binding site information, and many other links can be verified from the literature and databases such as EcoCyc. The reconstructed gene regulatory network is applied to a recent transcriptome analysis of E. coli during isobutanol stress. In addition to the 16 significantly changed TFAs detected in the original paper, another 7 significantly changed TFAs have been detected by using our reconstructed network. Conclusions The GTRNetwork algorithm introduces the hidden layer TFA into classic relevance score-based gene regulatory network reconstruction processes. Integrating the TFA biological information with regulatory network reconstruction algorithms significantly improves both detection of new links and reduces that rate of false positives. The application of GTRNetwork on E. coli gene transcriptome data gives a set of potential regulatory links with promising biological significance for isobutanol stress and other conditions. PMID:21668997

  20. Optics-Integrated Microfluidic Platforms for Biomolecular Analyses

    PubMed Central

    Bates, Kathleen E.; Lu, Hang

    2016-01-01

    Compared with conventional optical methods, optics implemented on microfluidic chips provide small, and often much cheaper ways to interrogate biological systems from the level of single molecules up to small model organisms. The optical probing of single molecules has been used to investigate the mechanical properties of individual biological molecules; however, multiplexing of these measurements through microfluidics and nanofluidics confers many analytical advantages. Optics-integrated microfluidic systems can significantly simplify sample processing and allow a more user-friendly experience; alignments of on-chip optical components are predetermined during fabrication and many purely optical techniques are passively controlled. Furthermore, sample loss from complicated preparation and fluid transfer steps can be virtually eliminated, a particularly important attribute for biological molecules at very low concentrations. Excellent fluid handling and high surface area/volume ratios also contribute to faster detection times for low abundance molecules in small sample volumes. Although integration of optical systems with classical microfluidic analysis techniques has been limited, microfluidics offers a ready platform for interrogation of biophysical properties. By exploiting the ease with which fluids and particles can be precisely and dynamically controlled in microfluidic devices, optical sensors capable of unique imaging modes, single molecule manipulation, and detection of minute changes in concentration of an analyte are possible. PMID:27119629

  1. Crapemyrtle Bark Scale: A New Threat for Crapemyrtles, a Popular Landscape Plant in the U.S.

    PubMed Central

    Wang, Zinan; Chen, Yan; Gu, Mengmeng; Vafaie, Erfan; Merchant, Michael; Diaz, Rodrigo

    2016-01-01

    Crapemyrtle bark scale, Acanthococcus (=Eriococcus) lagerstroemiae (Kuwana) (Hemiptera: Eriococcidae), is a newly introduced insect pest on crapemyrtles, Lagerstroemia spp. (Myrtales: Lythraceae), one of the most popular flowering shrubs in the U.S. Since first detected in Texas in 2004, this pest has spread to twelve states causing losses to stakeholders. To develop a management plan, we reviewed current knowledge about the pest’s biology and ecology, and suggested research approaches including studying its thermal tolerance, host range, plant resistance and biological control. Parasitoids and predators have been reared from A. lagerstroemiae in the U.S. and China. However, new surveys of natural enemies should be conducted in China, and studies on the host range and impacts of natural enemies on A. lagerstroemiae may help determine the potential for classical biological control. The life history, preying efficiency and rearing methods are important for coccinellid predators found in the U.S. including Chilocorus cacti L. and Hyperaspis spp. To enhance natural enemy performance, it is important to evaluate a sustainable insecticide program that considers efficacy, timing, rate and impact on pollinator health. Finally, an integrated management program of A. lagerstroemiae is discussed including planting resistant cultivars, using host specific natural enemies, and prudent use of insecticides. PMID:27999262

  2. The evolution of respect for property.

    PubMed

    Sherratt, T N; Mesterton-Gibbons, M

    2015-06-01

    Although possession is 'nine-tenths of the law', respect for ownership is widespread in the animal kingdom even without third-party enforcement. Thus, the first individuals to find objects are frequently left unchallenged by potential competitors and tend to win contests when disputes arise. Game theory has shown that respect for ownership ('Bourgeois' behaviour) can arise as an arbitrary convention to avoid costly disputes. However, the same theory predicts that a paradoxical respect for lack of ownership ('anti-Bourgeois' behaviour) can evolve under the same conditions and in some cases is the only stable outcome. Despite these predictions, anti-Bourgeois behaviour is rare in nature, whereas respect for ownership is frequently not absolute. Here, we review extensions of the classic models involving repeated interactions, confusion over roles, strategic coordination of behaviour ('secret handshakes'), owner-intruder asymmetries and continuous control of fighting investment. Confusion over roles and owner-intruder asymmetries in fighting ability may explain why respect for ownership is often partial. Moreover, although most model extensions facilitate the evolution of Bourgeois-like behaviour, secret handshakes and continuous control of fighting investment render the alternative anti-Bourgeois convention unstable. We develop these insights to highlight several key areas for future investigation. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

  3. Hybrid Quantum-Classical Approach to Quantum Optimal Control.

    PubMed

    Li, Jun; Yang, Xiaodong; Peng, Xinhua; Sun, Chang-Pu

    2017-04-14

    A central challenge in quantum computing is to identify more computational problems for which utilization of quantum resources can offer significant speedup. Here, we propose a hybrid quantum-classical scheme to tackle the quantum optimal control problem. We show that the most computationally demanding part of gradient-based algorithms, namely, computing the fitness function and its gradient for a control input, can be accomplished by the process of evolution and measurement on a quantum simulator. By posing queries to and receiving answers from the quantum simulator, classical computing devices update the control parameters until an optimal control solution is found. To demonstrate the quantum-classical scheme in experiment, we use a seven-qubit nuclear magnetic resonance system, on which we have succeeded in optimizing state preparation without involving classical computation of the large Hilbert space evolution.

  4. Simulations of molecular self-assembled monolayers on surfaces: packing structures, formation processes and functions tuned by intermolecular and interfacial interactions.

    PubMed

    Wen, Jin; Li, Wei; Chen, Shuang; Ma, Jing

    2016-08-17

    Surfaces modified with a functional molecular monolayer are essential for the fabrication of nano-scale electronics or machines with novel physical, chemical, and/or biological properties. Theoretical simulation based on advanced quantum chemical and classical models is at present a necessary tool in the development, design, and understanding of the interfacial nanostructure. The nanoscale surface morphology, growth processes, and functions are controlled by not only the electronic structures (molecular energy levels, dipole moments, polarizabilities, and optical properties) of building units but also the subtle balance between intermolecular and interfacial interactions. The switchable surfaces are also constructed by introducing stimuli-responsive units like azobenzene derivatives. To bridge the gap between experiments and theoretical models, opportunities and challenges for future development of modelling of ferroelectricity, entropy, and chemical reactions of surface-supported monolayers are also addressed. Theoretical simulations will allow us to obtain important and detailed information about the structure and dynamics of monolayer modified interfaces, which will guide the rational design and optimization of dynamic interfaces to meet challenges of controlling optical, electrical, and biological functions.

  5. Neurobiology of Learning and Memory: Modulation and Mechanisms

    DTIC Science & Technology

    1988-08-01

    Behavioral Biology, 6 (1976) pp. 45-62. Birt, D. and Olds, M., Associative response changes in lateral midbrain tegmentum and medial geniculate during...medial geniculate body of the cat during classical conditioning, Society for Neuroscience Abstracts, 6, (1976), p. 435. Ryugo, D.K. and Weinberger, N.M...Differential plasticity of morphologi- cally distinct neuron populations in the medial geniculate body of the cat during classical conditioning

  6. Ein Klassiker der Padagogik in Evolutionarer Perspektive: Eduard Sprangers "Lebensformen" im Lichte der Modernen Biologie (A Classic of Pedagogics from an Evolutionary Perspective: Edward Spranger's "Forms of Life" in the Light of Modern Biology).

    ERIC Educational Resources Information Center

    Neumann, Dieter

    2002-01-01

    Interprets Edward Spranger's "Forms of Life" against the background of the findings of modern biology. Shows how far Spranger's diagnosis of different human types, which are not affected by external influences on characteristics, conform with research hypotheses of modern biological sciences. (CAJ)

  7. Biology and management of ependymomas

    PubMed Central

    Wu, Jing; Armstrong, Terri S.; Gilbert, Mark R.

    2016-01-01

    Ependymomas are rare primary tumors of the central nervous system in children and adults that comprise histologically similar but genetically distinct subgroups. The tumor biology is typically more associated with the site of origin rather than being age-specific. Genetically distinct subgroups have been identified by genomic studies based on locations in classic grade II and III ependymomas. They are supratentorial ependymomas with C11orf95-RELA fusion or YAP1 fusion, infratentorial ependymomas with or without a hypermethylated phenotype (CIMP), and spinal cord ependymomas. Myxopapillary ependymomas and subependymomas have different biology than ependymomas with typical WHO grade II or III histology. Surgery and radiotherapy are the mainstays of treatment, while the role of chemotherapy has not yet been established. An in-depth understanding of tumor biology, developing reliable animal models that accurately reflect tumor molecule features, and high throughput drug screening are essential for developing new therapies. Collaborative efforts between scientists, physicians, and advocacy groups will enhance the translation of laboratory findings into clinical trials. Improvements in disease control underscore the need to incorporate assessment and management of patients' symptoms to ensure that treatment advances translate into improvement in quality of life. PMID:27022130

  8. Host Specificity of Microsporidia (Protista: Microspora) from European Populations of Lymantria dispar (Lepidoptera: Lymantriidae) to Indigenous North American Lepidoptera

    PubMed

    Solter; Maddox; McManus

    1997-03-01

    Results of traditional laboratory bioassays may not accurately represent ecological (field) host specificity of entomopathogens but, if carefully interpreted, may be used to predict the ecological host specificity of pathogens being considered for release as classical biological control agents. We conducted laboratory studies designed to evaluate the physiological host specificity of microsporidia, which are common protozoan pathogens of insects. In these studies, 49 nontarget lepidopteran species indigenous to North America were fed five biotypes of microsporidia that occur in European populations of Lymantria dispar but are not found in North American populations of L. dispar. These microsporidia, Microsporidium sp. from Portugal, Microsporidium sp. from Romania, Microsporidium sp. from Slovakia, Nosema lymantriae, and Endoreticulatus sp. from Portugal, are candidates for release as classical biological control agents into L. dispar populations in the United States. The microsporidia produced a variety of responses in the nontarget hosts and, based on these responses, the nontarget hosts were placed in the following categories: (1) no infection (refractory), (2) atypical infections, and (3) heavy infections. Endoreticulatus sp. produced patent, host-like infections in nearly two-thirds of the nontarget hosts to which it was fed. Such generalist species should not be recommended for release. Infections comparable to those produced in L. dispar were produced in 2% of the nontarget hosts fed Microsporidium sp. from Portugal, 19% of nontarget hosts fed Microsporidium sp. from Romania, 13% fed spores of Microsporidium sp. from Slovakia, and 11% of nontarget species fed N. lymantriae. The remaining nontarget species developed infections that, despite production of mature spores, were not typical of infection in L. dispar. We believe it is very unlikely that these atypical infections would be horizontally transmitted within nontarget insect populations in the United States.

  9. On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

    PubMed

    Gomez-Ramirez, Jaime; Sanz, Ricardo

    2013-09-01

    One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Protein design in systems metabolic engineering for industrial strain development.

    PubMed

    Chen, Zhen; Zeng, An-Ping

    2013-05-01

    Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Classical investigation of long-range coherence in biological systems

    NASA Astrophysics Data System (ADS)

    Preto, Jordane

    2016-12-01

    Almost five decades ago, H. Fröhlich [H. Fröhlich, "Long-range coherence and energy storage in biological systems," Int. J. Quantum Chem. 2(5), 641-649 (1968)] reported, on a theoretical basis, that the excitation of quantum modes of vibration in contact with a thermal reservoir may lead to steady states, where under high enough rate of energy supply, only specific low-frequency modes of vibration are strongly excited. This nonlinear phenomenon was predicted to occur in biomolecular systems, which are known to exhibit complex vibrational spectral properties, especially in the terahertz frequency domain. However, since the effects of terahertz or lower-frequency modes are mainly classical at physiological temperatures, there are serious doubts that Fröhlich's quantum description can be applied to predict such a coherent behavior in a biological environment, as suggested by the author. In addition, a quantum formalism makes the phenomenon hard to investigate using realistic molecular dynamics simulations (MD) as they are usually based on the classical principles. In the current paper, we provide a general classical Hamiltonian description of a nonlinear open system composed of many degrees of freedom (biomolecular structure) excited by an external energy source. It is shown that a coherent behaviour similar to Fröhlich's effect is to be expected in the classical case for a given range of parameter values. Thus, the supplied energy is not completely thermalized but stored in a highly ordered fashion. The connection between our Hamiltonian description, carried out in the space of normal modes, and a more standard treatment in the physical space is emphasized in order to facilitate the prediction of the effect from MD simulations. It is shown how such a coherent phenomenon may induce long-range resonance effects that could be of critical importance at the biomolecular level. The present work is motivated by recent experimental evidences of long-lived excited low-frequency modes in protein structures, which were reported as a consequence of the Fröhlich's effect.

  12. Experimentally Guided Models Reveal Replication Principles that Shape the Mutation Distribution of RNA Viruses

    DTIC Science & Technology

    2015-01-30

    intracel- lular replication. Two classic replication modes have been described for single-stranded RNA viruses: the ‘stamping machine’ mode ( Stent ...Journal of Theoretical Biology 218:309–321. doi: 10.1006/jtbi.2002.3078. Stent GS. 1963. Molecular Biology of Bacterial Viruses. San Francisco, Calif: W H

  13. Quantum formalism as an optimisation procedure of information flows for physical and biological systems.

    PubMed

    Baladrón, Carlos; Khrennikov, Andrei

    2016-12-01

    The similarities between biological and physical systems as respectively defined in quantum information biology (QIB) and in a Darwinian approach to quantum mechanics (DAQM) have been analysed. In both theories the processing of information is a central feature characterising the systems. The analysis highlights a mutual support on the thesis contended by each theory. On the one hand, DAQM provides a physical basis that might explain the key role played by quantum information at the macroscopic level for bio-systems in QIB. On the other hand, QIB offers the possibility, acting as a macroscopic testing ground, to analyse the emergence of quantumness from classicality in the terms held by DAQM. As an added result of the comparison, a tentative definition of quantum information in terms of classical information flows has been proposed. The quantum formalism would appear from this comparative analysis between QIB and DAQM as an optimal information scheme that would maximise the stability of biological and physical systems at any scale. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. Humoral and cellular immune response in mice induced by the classical swine fever virus E2 protein fused to the porcine CD154 antigen.

    PubMed

    Sordo, Yusmel; Suárez, Marisela; Caraballo, Rosalina; Sardina, Talía; Brown, Emma; Duarte, Carlos; Lugo, Joanna; Gil, Lázaro; Perez, Danny; Oliva, Ayme; Vargas, Milagros; Santana, Elaine; Valdés, Rodolfo; Rodríguez, María Pilar

    2018-03-01

    The development of subunit vaccines against classical swine fever is a desirable goal, because it allows discrimination between vaccinated and infected animals. In this study, humoral and cellular immune response elicited in inbred BALB/c mice by immunization with a recombinant classical swine fever virus (CSFV) E2 protein fused to porcine CD154 antigen (E2CD154) was assessed. This model was used as a predictor of immune response in swine. Mice were immunized with E2CD154 emulsified in Montanide ISA50V2 or dissolved in saline on days 1 and 21. Another group received E2His antigen, without CD154, in the same adjuvant. Montanide ISA50V2 or saline served as negative controls for each experimental group. Animals immunized with 12.5 and 2.5 μg/dose of E2CD154 developed the highest titers (>1:2000) of CSFV neutralizing antibodies. Moreover, CSFV specific splenocyte gamma-interferon production, measured after seven and twenty-eight days of immunization, was significantly higher in mice immunized with 12.5 μg of E2CD154. As a conclusion, E2CD154 emulsified in Montanide ISA50 V2 was able to induce a potent humoral and an early cellular immune response in inbred BALB/c mice. Therefore, this immunogen might be an appropriate candidate to elicit immune response in swine, control CSF disease and to eliminate CSFV in swine. Copyright © 2018 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  15. Developmental biology and tissue engineering.

    PubMed

    Marga, Francoise; Neagu, Adrian; Kosztin, Ioan; Forgacs, Gabor

    2007-12-01

    Morphogenesis implies the controlled spatial organization of cells that gives rise to tissues and organs in early embryonic development. While morphogenesis is under strict genetic control, the formation of specialized biological structures of specific shape hinges on physical processes. Tissue engineering (TE) aims at reproducing morphogenesis in the laboratory, i.e., in vitro, to fabricate replacement organs for regenerative medicine. The classical approach to generate tissues/organs is by seeding and expanding cells in appropriately shaped biocompatible scaffolds, in the hope that the maturation process will result in the desired structure. To accomplish this goal more naturally and efficiently, we set up and implemented a novel TE method that is based on principles of developmental biology and employs bioprinting, the automated delivery of cellular composites into a three-dimensional (3D) biocompatible environment. The novel technology relies on the concept of tissue liquidity according to which multicellular aggregates composed of adhesive and motile cells behave in analogy with liquids: in particular, they fuse. We emphasize the major role played by tissue fusion in the embryo and explain how the parameters (surface tension, viscosity) that govern tissue fusion can be used both experimentally and theoretically to control and simulate the self-assembly of cellular spheroids into 3D living structures. The experimentally observed postprinting shape evolution of tube- and sheet-like constructs is presented. Computer simulations, based on a liquid model, support the idea that tissue liquidity may provide a mechanism for in vitro organ building. Copyright 2008 Wiley-Liss, Inc.

  16. The potential of pathogens as biological control of parthenium weed (Parthenium hysterophorus L.) in Ethiopia.

    PubMed

    Taye, T; Gossmann, M; Einhorn, G; Büttner, C; Metz, R; Abate, D

    2002-01-01

    P. hsyterophorus is an exotic invasive annual weed now causing severe infestation in Ethiopia. Studies on diagnosis, incidence and distribution of pathogens associated with parthenium weed in Ethiopia were carried out from 1998-2002. Several fungal isolates were obtained from seed and other parts of parthenium plants. Among them were putative pathogenic fungal species of the genus Helminthosporium, Phoma, Curvularia, Chaetomium, Alternaria, and Fusarium. However, pathogenecity test of the isolates obtained showed no or non-specific symptoms. It was concluded that these pathogens could be opportunistic with insignificant potential for biological control of parthenium. Two most important diseases associated with parthenium were a rust disease, caused by Puccinia abrupta var. partheniicola, and a phyllody disease, caused by a phytoplasma of fababean phyllody (PBP) phytoplasma group. The rust was commonly found in cool mid altitude (1500-2500 m) areas while phyllody was observed in low to mid altitude regions (900-2500 m) of Ethiopia, with a disease incidence up to 100% and 75%, respectively, in some locations. Study of the individual effects of the rust and phyllody diseases under field conditions showed a reduction on weed morphological parameters (plant height, leaf area, and dry matter yield). Parthenium seed production was reduced by 42% and 85% due to rust and phyllody, respectively. Phyllody and rust diseases of parthenium showed significant potential for classical biological control of parthenium after further confirmation of insect vectors that transmit phyllody and host range of phyllody disease to the related economic plants in Ethiopia.

  17. Statistical methods for biodosimetry in the presence of both Berkson and classical measurement error

    NASA Astrophysics Data System (ADS)

    Miller, Austin

    In radiation epidemiology, the true dose received by those exposed cannot be assessed directly. Physical dosimetry uses a deterministic function of the source term, distance and shielding to estimate dose. For the atomic bomb survivors, the physical dosimetry system is well established. The classical measurement errors plaguing the location and shielding inputs to the physical dosimetry system are well known. Adjusting for the associated biases requires an estimate for the classical measurement error variance, for which no data-driven estimate exists. In this case, an instrumental variable solution is the most viable option to overcome the classical measurement error indeterminacy. Biological indicators of dose may serve as instrumental variables. Specification of the biodosimeter dose-response model requires identification of the radiosensitivity variables, for which we develop statistical definitions and variables. More recently, researchers have recognized Berkson error in the dose estimates, introduced by averaging assumptions for many components in the physical dosimetry system. We show that Berkson error induces a bias in the instrumental variable estimate of the dose-response coefficient, and then address the estimation problem. This model is specified by developing an instrumental variable mixed measurement error likelihood function, which is then maximized using a Monte Carlo EM Algorithm. These methods produce dose estimates that incorporate information from both physical and biological indicators of dose, as well as the first instrumental variable based data-driven estimate for the classical measurement error variance.

  18. A quantum–quantum Metropolis algorithm

    PubMed Central

    Yung, Man-Hong; Aspuru-Guzik, Alán

    2012-01-01

    The classical Metropolis sampling method is a cornerstone of many statistical modeling applications that range from physics, chemistry, and biology to economics. This method is particularly suitable for sampling the thermal distributions of classical systems. The challenge of extending this method to the simulation of arbitrary quantum systems is that, in general, eigenstates of quantum Hamiltonians cannot be obtained efficiently with a classical computer. However, this challenge can be overcome by quantum computers. Here, we present a quantum algorithm which fully generalizes the classical Metropolis algorithm to the quantum domain. The meaning of quantum generalization is twofold: The proposed algorithm is not only applicable to both classical and quantum systems, but also offers a quantum speedup relative to the classical counterpart. Furthermore, unlike the classical method of quantum Monte Carlo, this quantum algorithm does not suffer from the negative-sign problem associated with fermionic systems. Applications of this algorithm include the study of low-temperature properties of quantum systems, such as the Hubbard model, and preparing the thermal states of sizable molecules to simulate, for example, chemical reactions at an arbitrary temperature. PMID:22215584

  19. Evaluation on the Corrosion of the Three Ni-Cr Alloys with Different Composition

    PubMed Central

    Rao, Srinivasa B.; Chowdhary, Ramesh

    2011-01-01

    Dental casting alloys are widely used in contact with oral tissue for many years now. With the development of new dental alloys over the past 15 years, many questions remain unanswered about their biologic safety. Concepts and current issues concerning the response to the biologic effects of dental casting alloys are presented. In this paper, samples of three commercially available nickel-chrome (Ni-cr) casting alloys (Dentaurum, Bego, Sankin) were taken to assess their corrosion behavior, using potentiodynamic polarization method (electrochemical method) with fusayama artificial saliva as an electrolyte medium to check for their biocompatibility. The parameters for corrosion rate and corrosion resistance were obtained from computer-controlled corrosion schematic instrument, namely, potentiostat through corrosion software (power CV). The results obtained were analyzed by classic Tafel analysis. Statistical analysis was done by Student's t-test and ANOVA test. It was concluded that Dentarum and Bego showed satisfactory corrosive behavior, with exception of Sankin which depicted higher corrosion rate and least resistance to corrosion. Thus, the selection of an alloy should be made on the basis of corrosion resistance and biologic data from dental manufactures. PMID:21461232

  20. Density dependence in demography and dispersal generates fluctuating invasion speeds

    PubMed Central

    Li, Bingtuan; Miller, Tom E. X.

    2017-01-01

    Density dependence plays an important role in population regulation and is known to generate temporal fluctuations in population density. However, the ways in which density dependence affects spatial population processes, such as species invasions, are less understood. Although classical ecological theory suggests that invasions should advance at a constant speed, empirical work is illuminating the highly variable nature of biological invasions, which often exhibit nonconstant spreading speeds, even in simple, controlled settings. Here, we explore endogenous density dependence as a mechanism for inducing variability in biological invasions with a set of population models that incorporate density dependence in demographic and dispersal parameters. We show that density dependence in demography at low population densities—i.e., an Allee effect—combined with spatiotemporal variability in population density behind the invasion front can produce fluctuations in spreading speed. The density fluctuations behind the front can arise from either overcompensatory population growth or density-dependent dispersal, both of which are common in nature. Our results show that simple rules can generate complex spread dynamics and highlight a source of variability in biological invasions that may aid in ecological forecasting. PMID:28442569

  1. Human pluripotent stem cells: an emerging model in developmental biology

    PubMed Central

    Zhu, Zengrong; Huangfu, Danwei

    2013-01-01

    Developmental biology has long benefited from studies of classic model organisms. Recently, human pluripotent stem cells (hPSCs), including human embryonic stem cells and human induced pluripotent stem cells, have emerged as a new model system that offers unique advantages for developmental studies. Here, we discuss how studies of hPSCs can complement classic approaches using model organisms, and how hPSCs can be used to recapitulate aspects of human embryonic development ‘in a dish’. We also summarize some of the recently developed genetic tools that greatly facilitate the interrogation of gene function during hPSC differentiation. With the development of high-throughput screening technologies, hPSCs have the potential to revolutionize gene discovery in mammalian development. PMID:23362344

  2. Panaceas, uncertainty, and the robust control framework in sustainability science

    PubMed Central

    Anderies, John M.; Rodriguez, Armando A.; Janssen, Marco A.; Cifdaloz, Oguzhan

    2007-01-01

    A critical challenge faced by sustainability science is to develop strategies to cope with highly uncertain social and ecological dynamics. This article explores the use of the robust control framework toward this end. After briefly outlining the robust control framework, we apply it to the traditional Gordon–Schaefer fishery model to explore fundamental performance–robustness and robustness–vulnerability trade-offs in natural resource management. We find that the classic optimal control policy can be very sensitive to parametric uncertainty. By exploring a large class of alternative strategies, we show that there are no panaceas: even mild robustness properties are difficult to achieve, and increasing robustness to some parameters (e.g., biological parameters) results in decreased robustness with respect to others (e.g., economic parameters). On the basis of this example, we extract some broader themes for better management of resources under uncertainty and for sustainability science in general. Specifically, we focus attention on the importance of a continual learning process and the use of robust control to inform this process. PMID:17881574

  3. Structure-based control of complex networks with nonlinear dynamics

    NASA Astrophysics Data System (ADS)

    Zanudo, Jorge G. T.; Yang, Gang; Albert, Reka

    What can we learn about controlling a system solely from its underlying network structure? Here we use a framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors, regardless of the dynamic details and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of classical structural control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case, but not in specific model instances. This work was supported by NSF Grants PHY 1205840 and IIS 1160995. JGTZ is a recipient of a Stand Up To Cancer - The V Foundation Convergence Scholar Award.

  4. Macroscale delivery systems for molecular and cellular payloads

    NASA Astrophysics Data System (ADS)

    Kearney, Cathal J.; Mooney, David J.

    2013-11-01

    Macroscale drug delivery (MDD) devices are engineered to exert spatiotemporal control over the presentation of a wide range of bioactive agents, including small molecules, proteins and cells. In contrast to systemically delivered drugs, MDD systems act as a depot of drug localized to the treatment site, which can increase drug effectiveness while reducing side effects and confer protection to labile drugs. In this Review, we highlight the key advantages of MDD systems, describe their mechanisms of spatiotemporal control and provide guidelines for the selection of carrier materials. We also discuss the combination of MDD technologies with classic medical devices to create multifunctional MDD devices that improve integration with host tissue, and the use of MDD technology in tissue-engineering strategies to direct cell behaviour. As our ever-expanding knowledge of human biology and disease provides new therapeutic targets that require precise control over their application, the importance of MDD devices in medicine is expected to increase.

  5. Microwave-assisted synthesis of medicinally relevant indoles.

    PubMed

    Patil, S A; Patil, R; Miller, D D

    2011-01-01

    Indoles represent an important structural class in medicinal chemistry with broad spectrum of biological activities. The synthesis of indoles, therefore, has attracted enormous attention from synthetic chemists. Microwave methods for the preparation of indole analogs have been developed to speed up the synthesis, therefore, microwave assisted organic synthesis (MAOS) in controlled conditions is an invaluable technique for medicinal chemistry. In this review, indole forming classical reactions such as Fischer, Madelung, Bischler-Mohlau, Batcho-Leimgruber, Hemetsberger-Knittel, Graebe-Ullmann, Diels-Alder and Wittig type reactions using microwave radiation has been summarized. In addition, metal mediated cyclizations along with solid phase synthesis of indoles have been discussed. © 2011 Bentham Science Publishers Ltd.

  6. Single-crystalline δ-Ni2Si nanowires with excellent physical properties

    PubMed Central

    2013-01-01

    In this article, we report the synthesis of single-crystalline nickel silicide nanowires (NWs) via chemical vapor deposition method using NiCl2·6H2O as a single-source precursor. Various morphologies of δ-Ni2Si NWs were successfully acquired by controlling the growth conditions. The growth mechanism of the δ-Ni2Si NWs was thoroughly discussed and identified with microscopy studies. Field emission measurements show a low turn-on field (4.12 V/μm), and magnetic property measurements show a classic ferromagnetic characteristic, which demonstrates promising potential applications for field emitters, magnetic storage, and biological cell separation. PMID:23782805

  7. Quantum biological channel modeling and capacity calculation.

    PubMed

    Djordjevic, Ivan B

    2012-12-10

    Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general.

  8. Remembering the Forest While Viewing the Trees: Evolutionary Thinking in the Teaching of Molecular Biology

    ERIC Educational Resources Information Center

    Saraswati, Sitaraman; Sitaraman, Ramakrishnan

    2014-01-01

    Given the centrality of evolutionary theory to the study of biology, we present a strategy for reinforcing its importance by appropriately recontextualizing classic and well-known experiments that are not explicitly linked with evolution in conventional texts. This exercise gives students an appreciation of the applicability of the theory of…

  9. Gene Concepts in Higher Education Cell and Molecular Biology Textbooks

    ERIC Educational Resources Information Center

    Albuquerque, Pitombo Maiana; de Almeida, Ana Maria Rocha; El-Hani, Nino Charbel

    2008-01-01

    Despite being a landmark of 20th century biology, the "classical molecular gene concept," according to which a gene is a stretch of DNA encoding a functional product, which may be a single polypeptide or RNA molecule, has been recently challenged by a series of findings (e.g., split genes, alternative splicing, overlapping and nested…

  10. Physical break-down of the classical view on cancer cell invasion and metastasis.

    PubMed

    Mierke, Claudia T

    2013-03-01

    Eight classical hallmarks of cancer have been proposed and are well-defined by using biochemical or molecular genetic methods, but are not yet precisely defined by cellular biophysical processes. To define the malignant transformation of neoplasms and finally reveal the functional pathway, which enables cancer cells to promote cancer progression, these classical hallmarks of cancer require the inclusion of specific biomechanical properties of cancer cells and their microenvironment such as the extracellular matrix and embedded cells such as fibroblasts, macrophages or endothelial cells. Nonetheless a main novel ninth hallmark of cancer is still elusive in classical tumor biological reviews, which is the aspect of physics in cancer disease by the natural selection of an aggressive (highly invasive) subtype of cancer cells. The physical aspects can be analyzed by using state-of-the-art biophysical methods. Thus, this review will present current cancer research in a different light and will focus on novel physical methods to investigate the aggressiveness of cancer cells from a biophysicist's point of view. This may lead to novel insights into cancer disease and will overcome classical views on cancer. In addition, this review will discuss how physics of cancer can help to reveal whether cancer cells will invade connective tissue and metastasize. In particular, this review will point out how physics can improve, break-down or support classical approaches to examine tumor growth even across primary tumor boundaries, the invasion of single or collective cancer cells, transendothelial migration of cancer cells and metastasis in targeted organs. Finally, this review will show how physical measurements can be integrated into classical tumor biological analysis approaches. The insights into physical interactions between cancer cells, the primary tumor and the microenvironment may help to solve some "old" questions in cancer disease progression and may finally lead to novel approaches for development and improvement of cancer diagnostics and therapies. Copyright © 2013 Elsevier GmbH. All rights reserved.

  11. Ferret lung transplant: an orthotopic model of obliterative bronchiolitis.

    PubMed

    Sui, H; Olivier, A K; Klesney-Tait, J A; Brooks, L; Tyler, S R; Sun, X; Skopec, A; Kline, J; Sanchez, P G; Meyerholz, D K; Zavazava, N; Iannettoni, M; Engelhardt, J F; Parekh, K R

    2013-02-01

    Obliterative bronchiolitis (OB) is the primary cause of late morbidity and mortality following lung transplantation. Current animal models do not reliably develop OB pathology. Given the similarities between ferret and human lung biology, we hypothesized an orthotopic ferret lung allograft would develop OB. Orthotopic left lower lobe transplants were successfully performed in 22 outbred domestic ferrets in the absence of immunosuppression (IS; n = 5) and presence of varying IS protocols (n = 17). CT scans were performed to evaluate the allografts. At intervals between 3-6 months the allografts were examined histologically for evidence of acute/chronic rejection. IS protects allografts from acute rejection and early graft loss. Reduction of IS dosage by 50% allowed development of controlled rejection. Allografts developed infiltrates on CT and classic histologic acute rejection and lymphocytic bronchiolitis. Cycling of IS, to induce repeated episodes of controlled rejection, promoted classic histologic hallmarks of OB including fibrosis-associated occlusion of the bronchiolar airways in all allografts of long-term survivors. In conclusion, we have developed an orthotopic lung transplant model in the ferret with documented long-term functional allograft survival. Allografts develop acute rejection and lymphocytic bronchiolitis, similar to humans. Long-term survivors develop histologic changes in the allografts that are hallmarks of OB. © Copyright 2012 The American Society of Transplantation and the American Society of Transplant Surgeons.

  12. Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

    PubMed

    Brohée, Sylvain; Barriot, Roland; Moreau, Yves

    2010-09-01

    In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

  13. A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis

    PubMed Central

    Refahi, Yassin; Brunoud, Géraldine; Farcot, Etienne; Jean-Marie, Alain; Pulkkinen, Minna; Vernoux, Teva; Godin, Christophe

    2016-01-01

    Exploration of developmental mechanisms classically relies on analysis of pattern regularities. Whether disorders induced by biological noise may carry information on building principles of developmental systems is an important debated question. Here, we addressed theoretically this question using phyllotaxis, the geometric arrangement of plant aerial organs, as a model system. Phyllotaxis arises from reiterative organogenesis driven by lateral inhibitions at the shoot apex. Motivated by recurrent observations of disorders in phyllotaxis patterns, we revisited in depth the classical deterministic view of phyllotaxis. We developed a stochastic model of primordia initiation at the shoot apex, integrating locality and stochasticity in the patterning system. This stochastic model recapitulates phyllotactic patterns, both regular and irregular, and makes quantitative predictions on the nature of disorders arising from noise. We further show that disorders in phyllotaxis instruct us on the parameters governing phyllotaxis dynamics, thus that disorders can reveal biological watermarks of developmental systems. DOI: http://dx.doi.org/10.7554/eLife.14093.001 PMID:27380805

  14. Constituent bioconcentration in rainbow trout exposed to a complex chemical mixture

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

    Linder, G.; Bergman, H.L.; Meyer, J.S.

    1984-09-01

    Classically, aquatic contaminant fate models predicting a chemical's bioconcentration factor (BCF) are based upon single-compound derived models, yet such BCF predictions may deviate from observed BCFs when physicochemical interactions or biological responses to complex chemical mixture exposures are not adequately considered in the predictive model. Rainbow trout were exposed to oil-shale retort waters. Such a study was designed to model the potential biological effects precluded by exposure to complex chemical mixtures such as solid waste leachates, agricultural runoff, and industrial process waste waters. Chromatographic analysis of aqueous and nonaqueous liquid-liquid reservoir components yielded differences in mixed extraction solvent HPLC profilesmore » of whole fish exposed for 1 and 3 weeks to the highest dilution of the complex chemical mixture when compared to their corresponding control, yet subsequent whole fish extractions at 6, 9, 12, and 15 weeks into exposure demonstrated no qualitative differences between control and exposed fish. Liver extractions and deproteinized bile samples from exposed fish were qualitatively different than their corresponding controls. These findings support the projected NOEC of 0.0045% dilution, even though the differences in bioconcentration profiles suggest hazard assessment strategies may be useful in evaluating environmental fate processes associated with complex chemical mixtures. 12 references, 4 figures, 2 tables.« less

  15. Comparison of adaptive critic-based and classical wide-area controllers for power systems.

    PubMed

    Ray, Swakshar; Venayagamoorthy, Ganesh Kumar; Chaudhuri, Balarko; Majumder, Rajat

    2008-08-01

    An adaptive critic design (ACD)-based damping controller is developed for a thyristor-controlled series capacitor (TCSC) installed in a power system with multiple poorly damped interarea modes. The performance of this ACD computational intelligence-based method is compared with two classical techniques, which are observer-based state-feedback (SF) control and linear matrix inequality LMI-H(infinity) robust control. Remote measurements are used as feedback signals to the wide-area damping controller for modulating the compensation of the TCSC. The classical methods use a linearized model of the system whereas the ACD method is purely measurement-based, leading to a nonlinear controller with fixed parameters. A comparative analysis of the controllers' performances is carried out under different disturbance scenarios. The ACD-based design has shown promising performance with very little knowledge of the system compared to classical model-based controllers. This paper also discusses the advantages and disadvantages of ACDs, SF, and LMI-H(infinity).

  16. Methods to study maternal regulation of germ cell specification in zebrafish

    PubMed Central

    Kaufman, O.H.; Marlow, F.L.

    2016-01-01

    The process by which the germ line is specified in the zebrafish embryo is under the control of maternal gene products that were produced during oogenesis. Zebrafish are highly amenable to microscopic observation of the processes governing maternal germ cell specification because early embryos are transparent, and the germ line is specified rapidly (within 4–5 h post fertilization). Advantages of zebrafish over other models used to study vertebrate germ cell formation include their genetic tractability, the large numbers of progeny, and the easily manipulable genome, all of which make zebrafish an ideal system for studying the genetic regulators and cellular basis of germ cell formation and maintenance. Classical molecular biology techniques, including expression analysis through in situ hybridization and forward genetic screens, have laid the foundation for our understanding of germ cell development in zebrafish. In this chapter, we discuss some of these classic techniques, as well as recent cutting-edge methodologies that have improved our ability to visualize the process of germ cell specification and differentiation, and the tracking of specific molecules involved in these processes. Additionally, we discuss traditional and novel technologies for manipulating the zebrafish genome to identify new components through loss-of-function studies of putative germ cell regulators. Together with the numerous aforementioned advantages of zebrafish as a genetic model for studying development, we believe these new techniques will continue to advance zebrafish to the forefront for investigation of the molecular regulators of germ cell specification and germ line biology. PMID:27312489

  17. Emerging role of mesenchymal stem cells during tuberculosis: The fifth element in cell mediated immunity.

    PubMed

    Khan, Arshad; Hunter, Robert L; Jagannath, Chinnaswamy

    2016-12-01

    Mesenchymal stem cells (MSCs) are non-hematopoietic cells that occur in almost all human tissues and can be cultured and expanded to large numbers in vitro. They secrete growth factors, cytokines, and chemokines and express Toll-like receptors on their surface, although multiple cell biological mechanisms remain unclear. MSCs are multi-potent and can differentiate into many cell types including adipocytes, neuronal cells and osteoclasts. Despite gaps in cell biology, because of their immunomodulatory and regenerative capacity, several hundred clinical trials have used MSCs for therapy of cancer, autoimmune diseases and control of inflammation during organ transplantation. MSCs secrete immune-modulatory factors and are able to skew T cell responses and shift M1 to M2 differentiation of macrophages. We review the emerging role of MSCs to act as phagocytes for Mycobacterium tuberculosis and its role during the persistence of M. tuberculosis and spread of infection. Paradoxically, MSCs use innate defense mechanisms of autophagy and nitric oxide to inhibit the growth of intracellular M. tuberculosis. In addition, transplantation with autologous MSCs improved the clinical condition of patients with multi-drug resistant tuberculosis. Thus, in addition to the well-known immune defense played by macrophages, DCs, classical T cells and non-classical immune cells, MSCs have emerged as a fifth element capable of regulating immune responses during tuberculosis. We discuss their immunomodulatory properties and innate defense mechanisms in the context of developing immunotherapeutic strategies for tuberculosis. Published by Elsevier Ltd.

  18. Next-Generation Connexin and Pannexin Cell Biology.

    PubMed

    Esseltine, Jessica L; Laird, Dale W

    2016-12-01

    Connexins and pannexins are two families of large-pore channel forming proteins that are capable of passing small signaling molecules. While connexins serve the seminal task of direct gap junctional intercellular communication, pannexins are far less understood but function primarily as single membrane channels in autocrine and paracrine signaling. Advancements in connexin and pannexin biology in recent years has revealed that in addition to well-described classical functions at the plasma membrane, exciting new evidence suggests that connexins and pannexins participate in alternative pathways involving multiple intracellular compartments. Here we briefly highlight classical functions of connexins and pannexins but focus our attention mostly on the transformative findings that suggest that these channel-forming proteins may serve roles far beyond our current understandings. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Advances in the application of genetic manipulation methods to apicomplexan parasites.

    PubMed

    Suarez, C E; Bishop, R P; Alzan, H F; Poole, W A; Cooke, B M

    2017-10-01

    Apicomplexan parasites such as Babesia, Theileria, Eimeria, Cryptosporidium and Toxoplasma greatly impact animal health globally, and improved, cost-effective measures to control them are urgently required. These parasites have complex multi-stage life cycles including obligate intracellular stages. Major gaps in our understanding of the biology of these relatively poorly characterised parasites and the diseases they cause severely limit options for designing novel control methods. Here we review potentially important shared aspects of the biology of these parasites, such as cell invasion, host cell modification, and asexual and sexual reproduction, and explore the potential of the application of relatively well-established or newly emerging genetic manipulation methods, such as classical transfection or gene editing, respectively, for closing important gaps in our knowledge of the function of specific genes and proteins, and the biology of these parasites. In addition, genetic manipulation methods impact the development of novel methods of control of the diseases caused by these economically important parasites. Transient and stable transfection methods, in conjunction with whole and deep genome sequencing, were initially instrumental in improving our understanding of the molecular biology of apicomplexan parasites and paved the way for the application of the more recently developed gene editing methods. The increasingly efficient and more recently developed gene editing methods, in particular those based on the CRISPR/Cas9 system and previous conceptually similar techniques, are already contributing to additional gene function discovery using reverse genetics and related approaches. However, gene editing methods are only possible due to the increasing availability of in vitro culture, transfection, and genome sequencing and analysis techniques. We envisage that rapid progress in the development of novel gene editing techniques applied to apicomplexan parasites of veterinary interest will ultimately lead to the development of novel and more efficient methods for disease control. Published by Elsevier Ltd.

  20. Zsyntax: a formal language for molecular biology with projected applications in text mining and biological prediction.

    PubMed

    Boniolo, Giovanni; D'Agostino, Marcello; Di Fiore, Pier Paolo

    2010-03-03

    We propose a formal language that allows for transposing biological information precisely and rigorously into machine-readable information. This language, which we call Zsyntax (where Z stands for the Greek word zetaomegaeta, life), is grounded on a particular type of non-classical logic, and it can be used to write algorithms and computer programs. We present it as a first step towards a comprehensive formal language for molecular biology in which any biological process can be written and analyzed as a sort of logical "deduction". Moreover, we illustrate the potential value of this language, both in the field of text mining and in that of biological prediction.

  1. Chemical genomics in plant biology.

    PubMed

    Sadhukhan, Ayan; Sahoo, Lingaraj; Panda, Sanjib Kumar

    2012-06-01

    Chemical genomics is a newly emerged and rapidly progressing field in biology, where small chemical molecules bind specifically and reversibly to protein(s) to modulate their function(s), leading to the delineation and subsequent unravelling of biological processes. This approach overcomes problems like lethality and redundancy of classical genetics. Armed with the powerful techniques of combinatorial synthesis, high-throughput screening and target discovery chemical genomics expands its scope to diverse areas in biology. The well-established genetic system of Arabidopsis model allows chemical genomics to enter into the realm of plant biology exploring signaling pathways of growth regulators, endomembrane signaling cascades, plant defense mechanisms and many more events.

  2. Foundations in the Law: Classic Cases in Medical Ethics

    DTIC Science & Technology

    2007-01-01

    Defendant Ms. H, a citizen of the Commonwealth of Virginia, is the biological mother of Baby K, an infant girl born by Caesarean-section at the...defendant Mr. K, a citizen of the Commonwealth of Virginia, to be Baby K’s biological father. 8. Ms. H and Mr. K have never been married. 9. Since Baby K’s...the relative noninvolvement of Baby K’s biological father, the constitutional and common law presumption must be that Ms. H. is the appropriate decision

  3. Socially acquired predator avoidance: is it just classical conditioning?

    PubMed

    Griffin, Andrea S

    2008-06-15

    Associative learning theories presume the existence of a general purpose learning process, the structure of which does not mirror the demands of any particular learning problem. In contrast, learning scientists working within an Evolutionary Biology tradition believe that learning processes have been shaped by ecological demands. One potential means of exploring how ecology may have modified properties of acquisition is to use associative learning theory as a framework within which to analyse a particular learning phenomenon. Recent work has used this approach to examine whether socially transmitted predator avoidance can be conceptualised as a classical conditioning process in which a novel predator stimulus acts as a conditioned stimulus (CS) and acquires control over an avoidance response after it has become associated with alarm signals of social companions, the unconditioned stimulus (US). I review here a series of studies examining the effect of CS/US presentation timing on the likelihood of acquisition. Results suggest that socially acquired predator avoidance may be less sensitive to forward relationships than traditional classical conditioning paradigms. I make the case that socially acquired predator avoidance is an exciting novel one-trial learning paradigm that could be studied along side fear conditioning. Comparisons between social and non-social learning of danger at both the behavioural and neural level may yield a better understanding of how ecology might shape properties and mechanisms of learning.

  4. Impacts of biological control and invasive species on a non-target native Hawaiian insect.

    PubMed

    Johnson, M Tracy; Follett, Peter A; Taylor, Andrew D; Jones, Vincent P

    2005-02-01

    The potential for classical biological control to cause unintended harm to native species was evaluated in the case of the endemic Hawaiian koa bug, Coleotichus blackburniae White (Hemiptera: Scutelleridae), and parasitoids introduced to Hawaii for control of an agricultural pest, the southern green stink bug, Nezara viridula (L.) (Hemiptera: Pentatomidae). Parasitism of C. blackburniae eggs, nymphs and adults by biocontrol agents was quantified across a wide range of habitats and compared to other sources of mortality. Egg mortality due to the biocontrol agent Trissolcus basalis Wollaston (Hymenoptera: Scelionidae) was low (maximum 26%) and confined to elevations below 500 m on a single host plant. Predation, mainly by alien spiders and ants, was the greatest source of egg mortality (maximum 87%). Parasitism of adult C. blackburniae by the biocontrol agent Trichopoda pilipes (F.) (Diptera: Tachinidae) was near zero at 21 of 24 sites surveyed. Three sites with high bug density had higher levels of T. pilipes parasitism, reaching maxima of 70% among adult female bugs, 100% among males and 50% among fifth instars. Male-biased parasitism indicated that T. pilipes is adapted to using male aggregation pheromone for finding C. blackburniae hosts. The relative impacts of biocontrol agents and other sources of mortality were compared using life tables. Invasive species, particularly generalist egg predators, had the greatest impacts on C. blackburniae populations. Effects of intentionally introduced parasitoids were relatively minor, although the tachinid T. pilipes showed potential for large impacts at individual sites. In retrospect, non-target attacks by biological control agents on C. blackburniae were predictable, but the environmental range and magnitude of impacts would have been difficult to foresee.

  5. New Insights to Compare and Choose TKTD Models for Survival Based on an Interlaboratory Study for Lymnaea stagnalis Exposed to Cd.

    PubMed

    Baudrot, Virgile; Preux, Sara; Ducrot, Virginie; Pave, Alain; Charles, Sandrine

    2018-02-06

    Toxicokinetic-toxicodynamic (TKTD) models, as the General Unified Threshold model of Survival (GUTS), provide a consistent process-based framework compared to classical dose-response models to analyze both time and concentration-dependent data sets. However, the extent to which GUTS models (Stochastic Death (SD) and Individual Tolerance (IT)) lead to a better fitting than classical dose-response model at a given target time (TT) has poorly been investigated. Our paper highlights that GUTS estimates are generally more conservative and have a reduced uncertainty through smaller credible intervals for the studied data sets than classical TT approaches. Also, GUTS models enable estimating any x% lethal concentration at any time (LC x,t ), and provide biological information on the internal processes occurring during the experiments. While both GUTS-SD and GUTS-IT models outcompete classical TT approaches, choosing one preferentially to the other is still challenging. Indeed, the estimates of survival rate over time and LC x,t are very close between both models, but our study also points out that the joint posterior distributions of SD model parameters are sometimes bimodal, while two parameters of the IT model seems strongly correlated. Therefore, the selection between these two models has to be supported by the experimental design and the biological objectives, and this paper provides some insights to drive this choice.

  6. Should I fight or should I flight? How studying insect aggression can help integrated pest management.

    PubMed

    Benelli, Giovanni

    2015-07-01

    Aggression plays a key role all across the animal kingdom, as it allows the acquisition and/or defence of limited resources (food, mates and territories) in a huge number of species. A large part of our knowledge on aggressive behaviour has been developed on insects of economic importance. How can this knowledge be exploited to enhance integrated pest management? Here, I highlight how knowledge on intraspecific aggression can help IPM both in terms of insect pests (with a focus on the enhancement of the sterile insect technique) and in terms of biological control agents (with a focus on mass-rearing optimisation). Then, I examine what implications for IPM can be outlined from knowledge about interspecific aggressive behaviour. Besides predator-pest aggressive interactions predicted by classic biological control, I focus on what IPM can learn from (i) interspecific aggression among pest species (with special reference to competitive displacement), (ii) defensive behaviour exhibited by prey against predaceous insects and (iii) conflicts among predaceous arthropods sharing the same trophic niche (with special reference to learning/sensitisation practices and artificial manipulation of chemically mediated interactions). © 2015 Society of Chemical Industry.

  7. Biophysical mechanisms complementing "classical" cell biology.

    PubMed

    Funk, Richard H W

    2018-01-01

    This overview addresses phenomena in cell- and molecular biology which are puzzling by their fast and highly coordinated way of organization. Generally, it appears that informative processes probably involved are more on the biophysical than on the classical biochemical side. The coordination problem is explained within the first part of the review by the topic of endogenous electrical phenomena. These are found e.g. in fast tissue organization and reorganization processes like development, wound healing and regeneration. Here, coupling into classical biochemical signaling and reactions can be shown by modern microscopy, electronics and bioinformatics. Further, one can follow the triggered reactions seamlessly via molecular biology till into genetics. Direct observation of intracellular electric processes is very difficult because of e.g. shielding through the cell membrane and damping by other structures. Therefore, we have to rely on photonic and photon - phonon coupling phenomena like molecular vibrations, which are addressed within the second part. Molecules normally possess different charge moieties and thus small electromagnetic (EMF) patterns arise during molecular vibration. These patterns can now be measured best within the optical part of the spectrum - much less in the lower terahertz till kHz and lower Hz part (third part of this review). Finally, EMFs facilitate quantum informative processes in coherent domains of molecular, charge and electron spin motion. This helps to coordinate such manifold and intertwined processes going on within cells, tissues and organs (part 4). Because the phenomena described in part 3 and 4 of the review still await really hard proofs we need concerted efforts and a combination of biophysics, molecular biology and informatics to unravel the described mysteries in "physics of life".

  8. Local and traditional uses, phytochemistry, and pharmacology of Sophora japonica L.: A review.

    PubMed

    He, Xirui; Bai, Yajun; Zhao, Zefeng; Wang, Xiaoxiao; Fang, Jiacheng; Huang, Linhong; Zeng, Min; Zhang, Qiang; Zhang, Yajun; Zheng, Xiaohui

    2016-07-01

    Sophora japonica (Fabaceae), also known as Huai (Chinese: ), is a medium-sized deciduous tree commonly found in China, Japan, Korea, Vietnam, and other countries. The use of this plant has been recorded in classical medicinal treatises of ancient China, and it is currently recorded in both the Chinese Pharmacopoeia and European Pharmacopoeia. The flower buds and fruits of S. japonica, also known as Flos Sophorae Immaturus and Fructus Sophorae in China, are most commonly used in Asia (especially in China) to treat hemorrhoids, hematochezia, hematuria, hematemesis, hemorrhinia, uterine or intestinal hemorrhage, arteriosclerosis, headache, hypertension, dysentery, dizziness, and pyoderma. To discuss feasible trends for further research on S. japonica, this review highlights the botany, ethnopharmacology, phytochemistry, biological activities, and toxicology of S. japonica based on studies published in the last six decades. Information on the S. japonica was collected from major scientific databases (SciFinder, PubMed, Elsevier, SpringerLink, Web of Science, Google Scholar, Medline Plus, China Knowledge Resource Integrated (CNKI), and "Da Yi Yi Xue Sou Suo (http://www.dayi100.com/login.jsp)" for publications between 1957 and 2015 on S. japonica. Information was also obtained from local classic herbal literature, government reports, conference papers, as well as PhD and MSc dissertations. Approximately 153 chemical compounds, including flavonoids, isoflavonoids, triterpenes, alkaloids, polysaccharides, amino acids, and other compounds, have been isolated from the leaves, branches, flowers, buds, pericarps, and/or fruits of S. japonica. Among these compounds, several flavonoids and isoflavonoids comprise the active constituents of S. japonica, which exhibit a wide range of biological activities in vitro and in vivo such as anti-inflammatory, antibacterial, antiviral, anti-osteoporotic, antioxidant, radical scavenging, antihyperglycemic, antiobesity, antitumor, and hemostatic effects. Furthermore, flavonoids and isoflavonoids can be used as quality control markers for quality identification and evaluation of medicinal materials and their preparations. Information on evaluating the safety of S. japonica is very limited, so further study is required. To enable safer, more effective, and controllable therapeutic preparations, more in-depth information is urgently needed on the quality control, toxicology data, and clinical value of crude extract and active compounds of S. japonica. S. japonica has long been used in traditional Chinese medicine (TCM) due to its wide range of biological activities, and is administered orally. Phytochemical and pharmacological studies of S. japonica have increased in the past few years, and the extract and active components of this plant can be used to develop new drugs based on their traditional application as well as their biological activities. Therefore, this review on the ethnopharmacology, phytochemistry, biological activities, and toxicity of S. japonica offers promising data for further studies as well as the commercial exploitation of this traditional medicine. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  9. Effects of foot massage applied in two different methods on symptom control in colorectal cancer patients: Randomised control trial.

    PubMed

    Uysal, Neşe; Kutlutürkan, Sevinç; Uğur, Işıl

    2017-06-01

    This randomized controlled clinical study aimed to determine the effect of 2 foot massage methods on symptom control in people with colorectal cancer who received chemoradiotherapy. Data were collected between June 16, 2015, and February 10, 2016, in the Department of Radiation Oncology of an oncology training and research hospital. The sample comprised 60 participants. Data were collected using an introductory information form, common terminology criteria for adverse events and European Organization for Research and Treatment of Cancer Quality of Life Questionnaires C30 and CR29. Participants were randomly allocated to 3 groups: classical foot massage, reflexology, and standard care control. The classical massage group received foot massage using classical massage techniques, and the reflexology group received foot reflexology focusing on symptom-oriented reflexes twice a week during a 5-week chemoradiotherapy treatment schedule. The control group received neither classical massage nor reflexology. All patients were provided with the same clinic routine care. The classical massage was effective in reducing pain level and distension incidence while foot reflexology was effective in reducing pain and fatigue level, lowering incidence of distension and urinary frequency and improving life quality. © 2017 John Wiley & Sons Australia, Ltd.

  10. The Operant and the Classical in Conditioned Orientation of Drosophila melanogaster at the Flight Simulator

    PubMed Central

    Brembs, Björn; Heisenberg, Martin

    2000-01-01

    Ever since learning and memory have been studied experimentally, the relationship between operant and classical conditioning has been controversial. Operant conditioning is any form of conditioning that essentially depends on the animal's behavior. It relies on operant behavior. A motor output is called operant if it controls a sensory variable. The Drosophila flight simulator, in which the relevant behavior is a single motor variable (yaw torque), fully separates the operant and classical components of a complex conditioning task. In this paradigm a tethered fly learns, operantly or classically, to prefer and avoid certain flight orientations in relation to the surrounding panorama. Yaw torque is recorded and, in the operant mode, controls the panorama. Using a yoked control, we show that classical pattern learning necessitates more extensive training than operant pattern learning. We compare in detail the microstructure of yaw torque after classical and operant training but find no evidence for acquired behavioral traits after operant conditioning that might explain this difference. We therefore conclude that the operant behavior has a facilitating effect on the classical training. In addition, we show that an operantly learned stimulus is successfully transferred from the behavior of the training to a different behavior. This result unequivocally demonstrates that during operant conditioning classical associations can be formed. PMID:10753977

  11. The operant and the classical in conditioned orientation of Drosophila melanogaster at the flight simulator.

    PubMed

    Brembs, B; Heisenberg, M

    2000-01-01

    Ever since learning and memory have been studied experimentally, the relationship between operant and classical conditioning has been controversial. Operant conditioning is any form of conditioning that essentially depends on the animal's behavior. It relies on operant behavior. A motor output is called operant if it controls a sensory variable. The Drosophila flight simulator, in which the relevant behavior is a single motor variable (yaw torque), fully separates the operant and classical components of a complex conditioning task. In this paradigm a tethered fly learns, operantly or classically, to prefer and avoid certain flight orientations in relation to the surrounding panorama. Yaw torque is recorded and, in the operant mode, controls the panorama. Using a yoked control, we show that classical pattern learning necessitates more extensive training than operant pattern learning. We compare in detail the microstructure of yaw torque after classical and operant training but find no evidence for acquired behavioral traits after operant conditioning that might explain this difference. We therefore conclude that the operant behavior has a facilitating effect on the classical training. In addition, we show that an operantly learned stimulus is successfully transferred from the behavior of the training to a different behavior. This result unequivocally demonstrates that during operant conditioning classical associations can be formed.

  12. Antibacterial Discovery and Development: From Gene to Product and Back

    PubMed Central

    Fedorenko, Victor; Genilloud, Olga; Horbal, Liliya; Marcone, Giorgia Letizia; Marinelli, Flavia; Paitan, Yossi; Ron, Eliora Z.

    2015-01-01

    Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement. PMID:26339625

  13. Toxins as biological weapons for terror-characteristics, challenges and medical countermeasures: a mini-review.

    PubMed

    Berger, Tamar; Eisenkraft, Arik; Bar-Haim, Erez; Kassirer, Michael; Aran, Adi Avniel; Fogel, Itay

    2016-01-01

    Toxins are hazardous biochemical compounds derived from bacteria, fungi, or plants. Some have mechanisms of action and physical properties that make them amenable for use as potential warfare agents. Currently, some toxins are classified as potential biological weapons, although they have several differences from classic living bio-terror pathogens and some similarities to manmade chemical warfare agents. This review focuses on category A and B bio-terror toxins recognized by the Centers for Disease Control and Prevention: Botulinum neurotoxin, staphylococcal enterotoxin B, Clostridium perfringens epsilon toxin, and ricin. Their derivation, pathogenesis, mechanism of action, associated clinical signs and symptoms, diagnosis, and treatment are discussed in detail. Given their expected covert use, the primary diagnostic challenge in toxin exposure is the early detection of morbidity clusters, apart from background morbidity, after a relatively short incubation period. For this reason, it is important that clinicians be familiar with the clinical manifestations of toxins and the appropriate methods of management and countermeasures.

  14. Molecular, biological, and antigenic characterization of a Border disease virus isolated from a pig during classical swine fever surveillance in Japan.

    PubMed

    Nagai, Makoto; Aoki, Hiroshi; Sakoda, Yoshihiro; Kozasa, Takashi; Tominaga-Teshima, Kaho; Mine, Junki; Abe, Yuri; Tamura, Tomokazu; Kobayashi, Tsubasa; Nishine, Kaoru; Tateishi, Kentaro; Suzuki, Yudai; Fukuhara, Mai; Ohmori, Keitaro; Todaka, Reiko; Katayama, Kazuhiko; Mizutani, Tetsuya; Nakamura, Shigeyuki; Kida, Hiroshi; Shirai, Junsuke

    2014-07-01

    In the current study, molecular, biological, and antigenic analyses were performed to characterize Border disease virus (BDV) strain FNK2012-1 isolated from a pig in 2012 in Japan. The complete genome comprises 12,327 nucleotides (nt), including a large open reading frame of 11,685 nt. Phylogenetic analysis revealed that FNK2012-1 was clustered into BDV genotype 1 with ovine strains. FNK2012-1 grew in porcine, bovine, and ovine primary cells and cell lines, but grew better in bovine and ovine cells than in porcine cells. Specific pathogen-free pigs inoculated with FNK2012-1 did not show any clinical signs. Noninoculated contact control pigs also did not show clinical signs and did not seroconvert. The results suggest that FNK2012-1 may be of ruminant origin and is poorly adapted to pigs. Such observations can provide important insights into evidence for infection and transmission of BDV, which may be of ruminant origin, among pigs.

  15. Classical and all-floating FETI methods for the simulation of arterial tissues

    PubMed Central

    Augustin, Christoph M.; Holzapfel, Gerhard A.; Steinbach, Olaf

    2015-01-01

    High-resolution and anatomically realistic computer models of biological soft tissues play a significant role in the understanding of the function of cardiovascular components in health and disease. However, the computational effort to handle fine grids to resolve the geometries as well as sophisticated tissue models is very challenging. One possibility to derive a strongly scalable parallel solution algorithm is to consider finite element tearing and interconnecting (FETI) methods. In this study we propose and investigate the application of FETI methods to simulate the elastic behavior of biological soft tissues. As one particular example we choose the artery which is – as most other biological tissues – characterized by anisotropic and nonlinear material properties. We compare two specific approaches of FETI methods, classical and all-floating, and investigate the numerical behavior of different preconditioning techniques. In comparison to classical FETI, the all-floating approach has not only advantages concerning the implementation but in many cases also concerning the convergence of the global iterative solution method. This behavior is illustrated with numerical examples. We present results of linear elastic simulations to show convergence rates, as expected from the theory, and results from the more sophisticated nonlinear case where we apply a well-known anisotropic model to the realistic geometry of an artery. Although the FETI methods have a great applicability on artery simulations we will also discuss some limitations concerning the dependence on material parameters. PMID:26751957

  16. RSRE: RNA structural robustness evaluator

    PubMed Central

    Shu, Wenjie; Zheng, Zhiqiang; Wang, Shengqi

    2007-01-01

    Biological robustness, defined as the ability to maintain stable functioning in the face of various perturbations, is an important and fundamental topic in current biology, and has become a focus of numerous studies in recent years. Although structural robustness has been explored in several types of RNA molecules, the origins of robustness are still controversial. Computational analysis results are needed to make up for the lack of evidence of robustness in natural biological systems. The RNA structural robustness evaluator (RSRE) web server presented here provides a freely available online tool to quantitatively evaluate the structural robustness of RNA based on the widely accepted definition of neutrality. Several classical structure comparison methods are employed; five randomization methods are implemented to generate control sequences; sub-optimal predicted structures can be optionally utilized to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate analysis. The RSRE will be helpful in the wide exploration of RNA structural robustness and will catalyze our understanding of RNA evolution. The RSRE web server is freely available at http://biosrv1.bmi.ac.cn/RSRE/ or http://biotech.bmi.ac.cn/RSRE/. PMID:17567615

  17. Physical models of biological information and adaptation.

    PubMed

    Stuart, C I

    1985-04-07

    The bio-informational equivalence asserts that biological processes reduce to processes of information transfer. In this paper, that equivalence is treated as a metaphor with deeply anthropomorphic content of a sort that resists constitutive-analytical definition, including formulation within mathematical theories of information. It is argued that continuance of the metaphor, as a quasi-theoretical perspective in biology, must entail a methodological dislocation between biological and physical science. It is proposed that a general class of functions, drawn from classical physics, can serve to eliminate the anthropomorphism. Further considerations indicate that the concept of biological adaptation is central to the general applicability of the informational idea in biology; a non-anthropomorphic treatment of adaptive phenomena is suggested in terms of variational principles.

  18. Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution.

    PubMed

    Djordjevic, Ivan B

    2015-08-24

    Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually coupled.

  19. Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

    PubMed Central

    Djordjevic, Ivan B.

    2015-01-01

    Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually coupled. PMID:26305258

  20. Discrepant epidemiological patterns between classical and atypical scrapie in sheep flocks under French TSE control measures.

    PubMed

    Fediaevsky, Alexandre; Gasqui, Patrick; Calavas, Didier; Ducrot, Christian

    2010-09-01

    The occurrence of secondary cases of atypical and classical scrapie was examined in 340 outbreaks of atypical and 296 of classical sheep scrapie detected in France during active surveillance programmes between 2002 and 2007. The prevalence of atypical scrapie in these flocks was 0.05% under selective culling and 0.07% under intensified monitoring i.e. not significantly different from that detected during active surveillance of the general population (P>0.5), whereas these figures were much higher for classical scrapie (3.67% and 0.25%, respectively, P<10(-5)). In addition the number of atypical scrapie cases per outbreak did not indicate clustering. The results suggest that atypical scrapie occurs spontaneously or is not particularly contagious, and that the control measures in force allowed appropriate control of classical scrapie but were not more efficient than active surveillance in detecting cases of atypical scrapie. Copyright 2009 Elsevier Ltd. All rights reserved.

  1. Adrenal rest tissue in gonads of patients with classical congenital adrenal hyperplasia: multicenter study of 45 French male patients.

    PubMed

    Pierre, Peggy; Despert, François; Tranquart, François; Coutant, Régis; Tardy, Véronique; Kerlan, Véronique; Sonnet, Emmanuel; Baron, Sabine; Lorcy, Yannick; Emy, Philippe; Delavierre, Dominique; Monceaux, Françoise; Morel, Yves; Lecomte, Pierre

    2012-12-01

    Several cases of testicular adrenal rest tumours have been reported in men with congenital adrenal hyperplasia (CAH) due to the classical form of 21-hydroxylase deficiency but the prevalence has not been established. The aims of this report were to evaluate the frequency of testicular adrenal rest tissue in this population in a retrospective multicentre study involving eight endocrinology centres, and to determine whether treatment or genetic background had an impact on the occurrence of adrenal rest tissue. Testicular adrenal rest tissue (TART) was sought clinically and with ultrasound examination in forty-five males with CAH due to the classical form of 21-hydroxylase deficiency. When the diagnosis of testicular adrenal rest tumours was sought, good observance of treatment was judged on biological concentrations of 17-hydroxyprogesterone (17OHP), delta4-androstenedione, active renin and testosterone. The results of affected and non-affected subjects were compared. TART was detected in none of the 18 subjects aged 1 to 15years but was detected in 14 of the 27 subjects aged more than 15years. Five patients with an abnormal echography result had no clinical signs. Therapeutic control evaluated at diagnosis of TART seemed less effective when diagnosis was made in patients with adrenal rest tissue compared to TART-free subjects. Various genotypes were observed in patients with or without TART. Due to the high prevalence of TART in classical CAH and the delayed clinical diagnosis, testicular ultrasonography must be performed before puberty and thereafter regularly during adulthood even if the clinical examination is normal. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  2. Treatment of raw and ozonated oil sands process-affected water under decoupled denitrifying anoxic and nitrifying aerobic conditions: a comparative study.

    PubMed

    Xue, Jinkai; Zhang, Yanyan; Liu, Yang; Gamal El-Din, Mohamed

    2016-11-01

    Batch experiments were performed to evaluate biodegradation of raw and ozonated oil sands process-affected water (OSPW) under denitrifying anoxic and nitrifying aerobic conditions for 33 days. The results showed both the anoxic and aerobic conditions are effective in degrading OSPW classical and oxidized naphthenic acids (NAs) with the aerobic conditions demonstrating higher removal efficiency. The reactors under nitrifying aerobic condition reduced the total classical NAs of raw OSPW by 69.1 %, with better efficiency for species of higher hydrophobicity. Compared with conventional aerobic reactor, nitrifying aerobic condition substantially shortened the NA degradation half-life to 16 days. The mild-dose ozonation remarkably accelerated the subsequent aerobic biodegradation of classical NAs within the first 14 days, especially for those with long carbon chains. Moreover, the ozone pretreatment enhanced the biological removal of OSPW classical NAs by leaving a considerably lower final residual concentration of 10.4 mg/L under anoxic conditions, and 5.7 mg/L under aerobic conditions. The combination of ozonation and nitrifying aerobic biodegradation removed total classical NAs by 76.5 % and total oxy-NAs (O3-O6) by 23.6 %. 454 Pyrosequencing revealed that microbial species capable of degrading recalcitrant hydrocarbons were dominant in all reactors. The most abundant genus in the raw and ozonated anoxic reactors was Thauera (~56 % in the raw OSPW anoxic reactor, and ~65 % in the ozonated OSPW anoxic reactor); whereas Rhodanobacter (~40 %) and Pseudomonas (~40 %) dominated the raw and ozonated aerobic reactors, respectively. Therefore, the combination of mild-dose ozone pretreatment and subsequent biological process could be a competent choice for OSPW treatment.

  3. Force per cross-sectional area from molecules to muscles: a general property of biological motors

    PubMed Central

    Meyer-Vernet, Nicole

    2016-01-01

    We propose to formally extend the notion of specific tension, i.e. force per cross-sectional area—classically used for muscles, to quantify forces in molecular motors exerting various biological functions. In doing so, we review and compare the maximum tensions exerted by about 265 biological motors operated by about 150 species of different taxonomic groups. The motors considered range from single molecules and motile appendages of microorganisms to whole muscles of large animals. We show that specific tensions exerted by molecular and non-molecular motors follow similar statistical distributions, with in particular, similar medians and (logarithmic) means. Over the 1019 mass (M) range of the cell or body from which the motors are extracted, their specific tensions vary as Mα with α not significantly different from zero. The typical specific tension found in most motors is about 200 kPa, which generalizes to individual molecular motors and microorganisms a classical property of macroscopic muscles. We propose a basic order-of-magnitude interpretation of this result. PMID:27493785

  4. Anomalous resonance in a nanomechanical biosensor

    PubMed Central

    Gupta, Amit K.; Nair, Pradeep R.; Akin, Demir; Ladisch, Michael R.; Broyles, Steve; Alam, Muhammad A.; Bashir, Rashid

    2006-01-01

    The decrease in resonant frequency (−Δωr) of a classical cantilever provides a sensitive measure of the mass of entities attached on its surface. This elementary phenomenon has been the basis of a new class of bio-nanomechanical devices as sensing components of integrated microsystems that can perform rapid, sensitive, and selective detection of biological and biochemical entities. Based on classical analysis, there is a widespread perception that smaller sensors are more sensitive (sensitivity ≈ −0.5ωr/mC, where mC is the mass of the cantilever), and this notion has motivated scaling of biosensors to nanoscale dimensions. In this work, we show that the response of a nanomechanical biosensor is far more complex than previously anticipated. Indeed, in contrast to classical microscale sensors, the resonant frequencies of the nanosensor may actually decrease or increase after attachment of protein molecules. We demonstrate theoretically and experimentally that the direction of the frequency change arises from a size-specific modification of diffusion and attachment kinetics of biomolecules on the cantilevers. This work may have broad impact on microscale and nanoscale biosensor design, especially when predicting the characteristics of bio-nanoelectromechanical sensors functionalized with biological capture molecules. PMID:16938886

  5. Understanding viruses: Philosophical investigations.

    PubMed

    Pradeu, Thomas; Kostyrka, Gladys; Dupré, John

    2016-10-01

    Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues (the definition of viruses, the individuality and diachronic identity of a virus, the possibility to classify viruses into species, the question of whether viruses are living, the question of whether viruses are organisms, and finally the biological roles of viruses in ecology and evolution), and we show how they relate to classic questions of philosophy of biology and even general philosophy. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Biologically inspired rate control of chaos.

    PubMed

    Olde Scheper, Tjeerd V

    2017-10-01

    The overall intention of chaotic control is to eliminate chaos and to force the system to become stable in the classical sense. In this paper, I demonstrate a more subtle method that does not eliminate all traces of chaotic behaviour; yet it consistently, and reliably, can provide control as intended. The Rate Control of Chaos (RCC) method is derived from metabolic control processes and has several remarkable properties. RCC can control complex systems continuously, and unsupervised, it can also maintain control across bifurcations, and in the presence of significant systemic noise. Specifically, I show that RCC can control a typical set of chaotic models, including the 3 and 4 dimensional chaotic Lorenz systems, in all modes. Furthermore, it is capable of controlling spatiotemporal chaos without supervision and maintains control of the system across bifurcations. This property of RCC allows a dynamic system to operate in parameter spaces that are difficult to control otherwise. This may be particularly interesting for the control of forced systems or dynamic systems that are chaotically perturbed. These control properties of RCC are applicable to a range of dynamic systems, thereby appearing to have far-reaching effects beyond just controlling chaos. RCC may also point to the existence of a biochemical control function of an enzyme, to stabilise the dynamics of the reaction cascade.

  7. Reward value-based gain control: divisive normalization in parietal cortex.

    PubMed

    Louie, Kenway; Grattan, Lauren E; Glimcher, Paul W

    2011-07-20

    The representation of value is a critical component of decision making. Rational choice theory assumes that options are assigned absolute values, independent of the value or existence of other alternatives. However, context-dependent choice behavior in both animals and humans violates this assumption, suggesting that biological decision processes rely on comparative evaluation. Here we show that neurons in the monkey lateral intraparietal cortex encode a relative form of saccadic value, explicitly dependent on the values of the other available alternatives. Analogous to extra-classical receptive field effects in visual cortex, this relative representation incorporates target values outside the response field and is observed in both stimulus-driven activity and baseline firing rates. This context-dependent modulation is precisely described by divisive normalization, indicating that this standard form of sensory gain control may be a general mechanism of cortical computation. Such normalization in decision circuits effectively implements an adaptive gain control for value coding and provides a possible mechanistic basis for behavioral context-dependent violations of rationality.

  8. Study of Growth Kinetics in One Dimensional and Two Dimensional ZnO Nanostructures

    NASA Astrophysics Data System (ADS)

    Yin, Xin

    Because of the merits arising from the unique geometry, nanostructure materials have been an essential class of materials, which have shown great potentials in the fields of electronics, photonics, and biology. With various nanostructures being intensively investigated and successfully complemented into device applications, there has been one increasing demand to the investigation of the growth mechanism devoted to the controlled nanostructure synthesis. Motivated by this situation, this thesis is focused on the fundamental understanding of the nanostructure growth. Specifically, by taking zinc oxide as an example material, through controlling the basic driving force, that is, the supersaturation, I have rationally designed and synthesized various of nanostructures, and further applied the classical layer-by-layer growth mechanism to the understanding on the formation of these nanostructures, they are, the convex-plate-capped nanowires, the concave-plate-capped nanowires, the facet evolution at the tip of the nanowires, and the ultrathin 2D nanosheets.

  9. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations

    NASA Astrophysics Data System (ADS)

    Samoilov, Michael; Plyasunov, Sergey; Arkin, Adam P.

    2005-02-01

    Stochastic effects in biomolecular systems have now been recognized as a major physiologically and evolutionarily important factor in the development and function of many living organisms. Nevertheless, they are often thought of as providing only moderate refinements to the behaviors otherwise predicted by the classical deterministic system description. In this work we show by using both analytical and numerical investigation that at least in one ubiquitous class of (bio)chemical-reaction mechanisms, enzymatic futile cycles, the external noise may induce a bistable oscillatory (dynamic switching) behavior that is both quantitatively and qualitatively different from what is predicted or possible deterministically. We further demonstrate that the noise required to produce these distinct properties can itself be caused by a set of auxiliary chemical reactions, making it feasible for biological systems of sufficient complexity to generate such behavior internally. This new stochastic dynamics then serves to confer additional functional modalities on the enzymatic futile cycle mechanism that include stochastic amplification and signaling, the characteristics of which could be controlled by both the type and parameters of the driving noise. Hence, such noise-induced phenomena may, among other roles, potentially offer a novel type of control mechanism in pathways that contain these cycles and the like units. In particular, observations of endogenous or externally driven noise-induced dynamics in regulatory networks may thus provide additional insight into their topology, structure, and kinetics. network motif | signal transduction | chemical reaction | synthetic biology | systems biology

  10. Novel peptide-based platform for the dual presentation of biologically active peptide motifs on biomaterials.

    PubMed

    Mas-Moruno, Carlos; Fraioli, Roberta; Albericio, Fernando; Manero, José María; Gil, F Javier

    2014-05-14

    Biofunctionalization of metallic materials with cell adhesive molecules derived from the extracellular matrix is a feasible approach to improve cell-material interactions and enhance the biointegration of implant materials (e.g., osseointegration of bone implants). However, classical biomimetic strategies may prove insufficient to elicit complex and multiple biological signals required in the processes of tissue regeneration. Thus, newer strategies are focusing on installing multifunctionality on biomaterials. In this work, we introduce a novel peptide-based divalent platform with the capacity to simultaneously present distinct bioactive peptide motifs in a chemically controlled fashion. As a proof of concept, the integrin-binding sequences RGD and PHSRN were selected and introduced in the platform. The biofunctionalization of titanium with this platform showed a positive trend towards increased numbers of cell attachment, and statistically higher values of spreading and proliferation of osteoblast-like cells compared to control noncoated samples. Moreover, it displayed statistically comparable or improved cell responses compared to samples coated with the single peptides or with an equimolar mixture of the two motifs. Osteoblast-like cells produced higher levels of alkaline phosphatase on surfaces functionalized with the platform than on control titanium; however, these values were not statistically significant. This study demonstrates that these peptidic structures are versatile tools to convey multiple biofunctionality to biomaterials in a chemically defined manner.

  11. An assessment of interspecific competition between two introduced parasitoids of Diaphorina citri (Hemiptera: Liviidae) on caged citrus plants.

    PubMed

    Vankosky, Meghan A; Hoddle, Mark S

    2017-06-07

    Two parasitoids attacking nymphs of Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), Tamarixia radiata (Waterston) (Hymenoptera: Eulophidae) and Diaphorencyrtus aligarhensis (Shafee, Alam & Agarwal) (Hymenoptera: Encyrtidae) are being released in California, USA in a classical biological control program. To evaluate the effect of multiple parasitoid species on D. citri mortality, we conducted mesocosm experiments under controlled conditions using a complete block design with 6 treatments (D. citri nymphs exposed to: no parasitoids; D. aligarhensis or T. radiata alone; D. aligarhensis or T. radiata released first (by 48 h); and both species released simultaneously). Parasitism of D. citri nymphs by T. radiata exceeded 60% and was unchanged when D. aligarhensis were present. Parasitism by D. aligarhensis was greatest when T. radiata was absent (∼28%) and was reduced in all treatments with T. radiata present (<3%). D. citri mortality and parasitoid-related mortality of D. citri was consistent across parasitoid treatments. Laboratory results suggest that competition between D. aligarhensis and T. radiata is asymmetric and favors T. radiata. It may be difficult for D. aligarhensis to contribute significantly to D. citri biological control where T. radiata is present. However, results reported here suggest that competition between T. radiata and D. aligarhensis is not likely to reduce parasitism by T. radiata or reduce parasitoid-induced mortality of D. citri. © 2017 Institute of Zoology, Chinese Academy of Sciences.

  12. Linear Quantum Systems: Non-Classical States and Robust Stability

    DTIC Science & Technology

    2016-06-29

    quantum linear systems subject to non-classical quantum fields. The major outcomes of this project are (i) derivation of quantum filtering equations for...derivation of quantum filtering equations for systems non-classical input states including single photon states, (ii) determination of how linear...history going back some 50 years, to the birth of modern control theory with Kalman’s foundational work on filtering and LQG optimal control

  13. EWET: Data collection and interface for the genetic analysis of Echinococcus multilocularis based on EmsB microsatellite.

    PubMed

    Knapp, Jenny; Damy, Sylvie; Brillaud, Jonathan; Tissot, Jean-Daniel; Navion, Jérémy; Mélior, Raphael; Afonso, Eve; Hormaz, Vanessa; Gottstein, Bruno; Umhang, Gérald; Casulli, Adriano; Dadeau, Frédéric; Millon, Laurence; Raoul, Francis

    2017-01-01

    Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas), Asia (China, Japan and Kyrgyzstan), and North America (Canada and Alaska). Biological data on the isolates and metadata were also recorded (e.g. host, geographical location, EmsB analysis, citation in the literature). In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms) and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET) project. It allows researchers to access data collection, perform genetic analyses online (e.g. defining the genetic distance between their own samples and the samples in the database), consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed. The final aim of this project was to gather and arrange available data to permit to better understand the dispersion and transmission patterns of the parasite among definitive and intermediate hosts, in order to organize control strategies on the ground.

  14. EWET: Data collection and interface for the genetic analysis of Echinococcus multilocularis based on EmsB microsatellite

    PubMed Central

    Damy, Sylvie; Brillaud, Jonathan; Tissot, Jean-Daniel; Navion, Jérémy; Mélior, Raphael; Afonso, Eve; Hormaz, Vanessa; Gottstein, Bruno; Umhang, Gérald; Casulli, Adriano; Dadeau, Frédéric; Millon, Laurence; Raoul, Francis

    2017-01-01

    Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas), Asia (China, Japan and Kyrgyzstan), and North America (Canada and Alaska). Biological data on the isolates and metadata were also recorded (e.g. host, geographical location, EmsB analysis, citation in the literature). In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms) and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET) project. It allows researchers to access data collection, perform genetic analyses online (e.g. defining the genetic distance between their own samples and the samples in the database), consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed. The final aim of this project was to gather and arrange available data to permit to better understand the dispersion and transmission patterns of the parasite among definitive and intermediate hosts, in order to organize control strategies on the ground. PMID:28972978

  15. Quantum annealing versus classical machine learning applied to a simplified computational biology problem

    PubMed Central

    Li, Richard Y.; Di Felice, Rosa; Rohs, Remo; Lidar, Daniel A.

    2018-01-01

    Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the ability of a quantum machine learning approach to predict binding specificity. Using simplified datasets of a small number of DNA sequences derived from actual binding affinity experiments, we trained a commercially available quantum annealer to classify and rank transcription factor binding. The results were compared to state-of-the-art classical approaches for the same simplified datasets, including simulated annealing, simulated quantum annealing, multiple linear regression, LASSO, and extreme gradient boosting. Despite technological limitations, we find a slight advantage in classification performance and nearly equal ranking performance using the quantum annealer for these fairly small training data sets. Thus, we propose that quantum annealing might be an effective method to implement machine learning for certain computational biology problems. PMID:29652405

  16. Dispersion-cancelled biological imaging with quantum-inspired interferometry

    PubMed Central

    Mazurek, M. D.; Schreiter, K. M.; Prevedel, R.; Kaltenbaek, R.; Resch, K. J.

    2013-01-01

    Quantum information science promises transformative impact over a range of key technologies in computing, communication, and sensing. A prominent example uses entangled photons to overcome the resolution-degrading effects of dispersion in the medical-imaging technology, optical coherence tomography. The quantum solution introduces new challenges: inherently low signal and artifacts, additional unwanted signal features. It has recently been shown that entanglement is not a requirement for automatic dispersion cancellation. Such classical techniques could solve the low-signal problem, however they all still suffer from artifacts. Here, we introduce a method of chirped-pulse interferometry based on shaped laser pulses, and use it to produce artifact-free, high-resolution, dispersion-cancelled images of the internal structure of a biological sample. Our work fulfills one of the promises of quantum technologies: automatic-dispersion-cancellation interferometry in biomedical imaging. It also shows how subtle differences between a quantum technique and its classical analogue may have unforeseen, yet beneficial, consequences. PMID:23545597

  17. Web-based software tool for constraint-based design specification of synthetic biological systems.

    PubMed

    Oberortner, Ernst; Densmore, Douglas

    2015-06-19

    miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

  18. Establishment and abundance of Tetrastichus planipennisi (Hymenoptera: Eulophidae) in Michigan: potential for success in classical biocontrol of the invasive emerald ash borer (Coleoptera: Buprestidae).

    PubMed

    Duan, Jian J; Bauer, Leah S; Abell, Kristopher J; Lelito, Jonathan P; Van Driesche, Roy

    2013-06-01

    Tetrastichus planipennisi Yang is a gregarious larval endoparasitoid native to China and has been introduced to the United States since 2007 for classical biological control of the invasive emerald ash borer, Agrilus planipennis Fairmaire, an exotic beetle responsible for widespread ash mortality. Between 2007-2010, T. planipennisi adults (3,311-4,597 females and approximately 1,500 males per site) were released into each of six forest sites in three counties (Ingham, Gratiot, and Shiawassee) of southern Michigan. By the fall of 2012, the proportion of sampled trees with one or more broods of T. planipennisi increased to 92 and 83% in the parasitoid-release and control plots, respectively, from 33 and 4% in the first year after parasitoid releases (2009 fall for Ingham county sites and 2010 for other sites). Similarly, the mean number of T. planipennisi broods observed from sampled trees increased from less than one brood per tree in the first year after parasitoid releases to 2.46 (at control plots) to 3.08 (at release plots) broods by the fall of 2012. The rates of emerald ash borer larval parasitism by T. planipennisi also increased from 1.2% in the first year after parasitoid releases to 21.2% in the parasitoid-release plots, and from 0.2 to 12.8% for the control plots by the fall of 2012. These results demonstrate that T. planipennisi is established in southern Michigan and that its populations are increasing and expanding. This suggests that T. planipennisi will likely play a critical role in suppressing emerald ash borer populations in Michigan.

  19. Biomarker-driven phenotyping in Parkinson disease: a translational missing link in disease-modifying clinical trials

    PubMed Central

    Espay, Alberto J.; Schwarzschild, Michael A.; Tanner, Caroline M.; Fernandez, Hubert H; Simon, David K.; Leverenz, James B.; Merola, Aristide; Chen-Plotkin, Alice; Brundin, Patrik; Kauffman, Marcelo A.; Erro, Roberto; Kieburtz, Karl; Woo, Daniel; Macklin, Eric A.; Standaert, David G.; Lang, Anthony E.

    2016-01-01

    Past clinical trials of putative neuroprotective therapies have targeted Parkinson disease (PD) as a single pathogenic disease entity. From an Oslerian clinico-pathologic perspective, the wide complexity of PD converges into Lewy bodies and justifies a reductionist approach to PD: a single-mechanism therapy can affect most of those sharing the classic pathologic hallmark. From a systems-biology perspective, PD is a group of disorders that, while related by sharing the feature of nigral dopamine-neuron degeneration, exhibit unique genetic, biological and molecular abnormalities, which probably respond differentially to a given therapeutic approach, particularly for strategies aimed at neuroprotection. Under this model, only biomarker-defined, homogenous subtypes of PD are likely to respond optimally to therapies proven to affect the biological processes within each subtype. Therefore, we suggest that precision medicine applied to PD requires a reevaluation of the biomarker-discovery effort. This effort is currently centered on correlating biological measures to clinical features of PD and on identifying factors that predict whether various prodromal states will convert into the classical movement disorder. We suggest, instead, that subtyping of PD requires the reverse view, where abnormal biological signals (i.e., biomarkers) rather than clinical definitions are used to define disease phenotypes. Successful development of disease-modifying strategies will depend on how relevant the specific biological processes addressed by an intervention are to the pathogenetic mechanisms in the subgroup of targeted patients. This precision-medicine approach will likely yield smaller but well-defined subsets of PD amenable to successful neuroprotection. PMID:28233927

  20. Shielding in biology and biophysics: Methodology, dosimetry, interpretation

    NASA Astrophysics Data System (ADS)

    Vladimirsky, B. M.; Temuryants, N. A.

    2016-12-01

    An interdisciplinary review of the publications on the shielding of organisms by different materials is presented. The authors show that some discrepancies between the results of different researchers might be attributed to methodological reasons, including purely biological (neglect of rhythms) and technical (specific features of the design or material of the screen) ones. In some cases, an important factor is the instability of control indices due to the variations in space weather. According to the modern concept of biological exposure to microdoses, any isolation of a biological object by any material necessarily leads to several simultaneous changes in environmental parameters, and this undermines the principle of "all other conditions being equal" in the classical differential scheme of an experiment. The shielding effects of water solution are universally recognized and their influence is to be observed for all organisms. Data on the exposure of living organisms to weak combined magnetic fields and on the influence of space weather enabled the development of theoretical models generally explaining the effect of shielding for bioorganisms. Ferromagnetic shielding results in changes of both the static magnetic field and the field of radio waves within the area protected by the screen. When screens are nonmagnetic, changes are due to the isolation from the radio waves. In both cases, some contribution to the fluctuations of measured parameters can be made by variations in the level of ionizing radiation.

  1. Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? What Really Constitutes the Study of "Systems Biology" and How Might Such an Approach Facilitate Vaccine Design.

    PubMed

    Germain, Ronald N

    2017-10-16

    A dichotomy exists in the field of vaccinology about the promise versus the hype associated with application of "systems biology" approaches to rational vaccine design. Some feel it is the only way to efficiently uncover currently unknown parameters controlling desired immune responses or discover what elements actually mediate these responses. Others feel that traditional experimental, often reductionist, methods for incrementally unraveling complex biology provide a more solid way forward, and that "systems" approaches are costly ways to collect data without gaining true insight. Here I argue that both views are inaccurate. This is largely because of confusion about what can be gained from classical experimentation versus statistical analysis of large data sets (bioinformatics) versus methods that quantitatively explain emergent properties of complex assemblies of biological components, with the latter reflecting what was previously called "physiology." Reductionist studies will remain essential for generating detailed insight into the functional attributes of specific elements of biological systems, but such analyses lack the power to provide a quantitative and predictive understanding of global system behavior. But by employing (1) large-scale screening methods for discovery of unknown components and connections in the immune system ( omics ), (2) statistical analysis of large data sets ( bioinformatics ), and (3) the capacity of quantitative computational methods to translate these individual components and connections into models of emergent behavior ( systems biology ), we will be able to better understand how the overall immune system functions and to determine with greater precision how to manipulate it to produce desired protective responses. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  2. Modifiers of ovarian function in girls and women with classic galactosemia.

    PubMed

    Spencer, Jessica B; Badik, Jennifer R; Ryan, Emily L; Gleason, Tyler J; Broadaway, K Alaine; Epstein, Michael P; Fridovich-Keil, Judith L

    2013-07-01

    Classic galactosemia is a potentially lethal genetic disorder resulting from profound impairment of galactose-1P uridylyltransferase (GALT). More than 80% of girls and women with classic galactosemia experience primary or premature ovarian insufficiency despite neonatal diagnosis and rigorous lifelong dietary galactose restriction. The goal of this study was to test the relationship between markers of ovarian reserve, cryptic residual GALT activity, and spontaneous pubertal development in girls with classic galactosemia. This was a cross-sectional study with some longitudinal follow-up in a university research environment. Patients included girls and women with classic galactosemia and unaffected controls, <1 month to 30 years old. We evaluated plasma anti-Müllerian hormone (AMH) and FSH levels, antral follicle counts ascertained by ultrasound, and ovarian function as indicated by spontaneous vs assisted menarche. More than 73% of the pre- and postpubertal girls and women with classic galactosemia in this study, ages >3 months to 30 years, demonstrated AMH levels below the 95% confidence interval for AMH among controls of the same age, and both pre- and postpubertal girls and women with classic galactosemia also demonstrated abnormally low antral follicle counts relative to age-matched controls. Predicted residual GALT activity ≥ 0.4% significantly increased the likelihood that a girl with classic galactosemia would demonstrate an AMH level ≥ 0.1 ng/mL. A majority of girls with classic galactosemia demonstrate evidence of diminished ovarian reserve by 3 months of age, and predicted cryptic residual GALT activity is a modifier of ovarian function in galactosemic girls and women.

  3. Introducing the Classics to Reluctant Readers.

    ERIC Educational Resources Information Center

    Lazarus, Lissa J.

    Using the pocket classics can be a painless way to introduce the classics to eighth-grade students. Condensed versions of the classics can take the sting out of the reading, stimulate students' interest, and help prepare them for high school. To offer students in one eighth-grade class some control over their own learning, a contract system was…

  4. Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory?

    PubMed Central

    Brezinski, Mark E; Rupnick, Maria

    2016-01-01

    Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems. PMID:29200743

  5. Can We Advance Macroscopic Quantum Systems Outside the Framework of Complex Decoherence Theory?

    PubMed

    Brezinski, Mark E; Rupnick, Maria

    2014-07-01

    Macroscopic quantum systems (MQS) are macroscopic systems driven by quantum rather than classical mechanics, a long studied area with minimal success till recently. Harnessing the benefits of quantum mechanics on a macroscopic level would revolutionize fields ranging from telecommunication to biology, the latter focused on here for reasons discussed. Contrary to misconceptions, there are no known physical laws that prevent the development of MQS. Instead, they are generally believed universally lost in complex systems from environmental entanglements (decoherence). But we argue success is achievable MQS with decoherence compensation developed, naturally or artificially, from top-down rather current reductionist approaches. This paper advances the MQS field by a complex systems approach to decoherence. First, why complex system decoherence approaches (top-down) are needed is discussed. Specifically, complex adaptive systems (CAS) are not amenable to reductionist models (and their master equations) because of emergent behaviour, approximation failures, not accounting for quantum compensatory mechanisms, ignoring path integrals, and the subentity problem. In addition, since MQS must exist within the context of the classical world, where rapid decoherence and prolonged coherence are both needed. Nature has already demonstrated this for quantum subsystems such as photosynthesis and magnetoreception. Second, we perform a preliminary study that illustrates a top-down approach to potential MQS. In summary, reductionist arguments against MQS are not justifiable. It is more likely they are not easily detectable in large intact classical systems or have been destroyed by reductionist experimental set-ups. This complex systems decoherence approach, using top down investigations, is critical to paradigm shifts in MQS research both in biological and non-biological systems.

  6. Species-Specific Detection of Mycosphaerella polygoni-cuspidati as a Biological Control Agent for Fallopia japonica by PCR Assay.

    PubMed

    Kurose, Daisuke; Furuya, Naruto; Saeki, Tetsuya; Tsuchiya, Kenichi; Tsushima, Seiya; Seier, Marion K

    2016-10-01

    The ascomycete fungus Mycosphaerella polygoni-cuspidati has been undergoing evaluation as a potential classical biological control agent for the invasive weed Fallopia japonica (Japanese knotweed), which has become troublesome in Europe and North America. In advance of the potential release of a biocontrol agent into a new environment, it is crucial to develop an effective monitoring system to enable the evaluation of agent establishment and dispersal within the target host population, as well as any potential attacks on non-target species. Therefore, a primer pair was designed for direct, rapid, and specific detection of the Japanese knotweed pathogen M. polygoni-cuspidati based on the sequences of the internal transcribed spacer regions including the 5.8S rDNA. A PCR product of approximately 298 bp was obtained only when the DNA extracted from mycelial fragments of M. polygoni-cuspidati was used. The lower limit of detection of the PCR method was 100 fg of genomic DNA. Using the specific primer pair, M. polygoni-cuspidati could be detected from both naturally and artificially infected Japanese knotweed plants. No amplification was observed for other Mycosphaerella spp. or fungal endophytes isolated from F. japonica. The designed primer pair is thus effective for the specific detection of M. polygoni-cuspidati in planta.

  7. Ensemble transcript interaction networks: a case study on Alzheimer's disease.

    PubMed

    Armañanzas, Rubén; Larrañaga, Pedro; Bielza, Concha

    2012-10-01

    Systems biology techniques are a topic of recent interest within the neurological field. Computational intelligence (CI) addresses this holistic perspective by means of consensus or ensemble techniques ultimately capable of uncovering new and relevant findings. In this paper, we propose the application of a CI approach based on ensemble Bayesian network classifiers and multivariate feature subset selection to induce probabilistic dependences that could match or unveil biological relationships. The research focuses on the analysis of high-throughput Alzheimer's disease (AD) transcript profiling. The analysis is conducted from two perspectives. First, we compare the expression profiles of hippocampus subregion entorhinal cortex (EC) samples of AD patients and controls. Second, we use the ensemble approach to study four types of samples: EC and dentate gyrus (DG) samples from both patients and controls. Results disclose transcript interaction networks with remarkable structures and genes not directly related to AD by previous studies. The ensemble is able to identify a variety of transcripts that play key roles in other neurological pathologies. Classical statistical assessment by means of non-parametric tests confirms the relevance of the majority of the transcripts. The ensemble approach pinpoints key metabolic mechanisms that could lead to new findings in the pathogenesis and development of AD. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  8. Host tracking or cryptic adaptation? Phylogeography of Pediobius saulius (Hymenoptera, Eulophidae), a parasitoid of the highly invasive horse-chestnut leafminer

    PubMed Central

    Hernández-López, Antonio; Rougerie, Rodolphe; Augustin, Sylvie; Lees, David C; Tomov, Rumen; Kenis, Marc; Çota, Ejup; Kullaj, Endrit; Hansson, Christer; Grabenweger, Giselher; Roques, Alain; López-Vaamonde, Carlos

    2012-01-01

    Classical biological control is often advocated as a tool for managing invasive species. However, accurate evaluations of parasitoid species complexes and assessment of host specificity are impeded by the lack of morphological variation. Here, we study the possibility of host races/species within the eulophid wasp Pediobius saulius, a pupal generalist parasitoid that parasitize the highly invasive horse-chestnut leaf-mining moth Cameraria ohridella. We analysed the population genetic structure, host associations and phylogeographic patterns of P. saulius in Europe using the COI mitochondrial gene. This marker strongly supports a division into at least five highly differentiated parasitoid complexes, within two of which clades with differing degrees of host specialization were found: a Balkan clade that mainly (but not only) attacks C. ohridella and a more generalist European group that attacks many hosts, including C. ohridella. The divergence in COI (up to 7.6%) suggests the existence of cryptic species, although this is neither confirmed by nuclear divergence nor morphology. We do not find evidence of host tracking. The higher parasitism rates observed in the Balkans and the scarcity of the Balkan–Cameraria haplotypes out of the Balkans open the possibility of using these Balkan haplotypes as biological control agents of C. ohridella elsewhere in Europe. PMID:25568046

  9. Quantum-classical interface based on single flux quantum digital logic

    NASA Astrophysics Data System (ADS)

    McDermott, R.; Vavilov, M. G.; Plourde, B. L. T.; Wilhelm, F. K.; Liebermann, P. J.; Mukhanov, O. A.; Ohki, T. A.

    2018-04-01

    We describe an approach to the integrated control and measurement of a large-scale superconducting multiqubit array comprising up to 108 physical qubits using a proximal coprocessor based on the Single Flux Quantum (SFQ) digital logic family. Coherent control is realized by irradiating the qubits directly with classical bitstreams derived from optimal control theory. Qubit measurement is performed by a Josephson photon counter, which provides access to the classical result of projective quantum measurement at the millikelvin stage. We analyze the power budget and physical footprint of the SFQ coprocessor and discuss challenges and opportunities associated with this approach.

  10. Travellers' diarrhoea: Impact of TD definition and control group design on study results.

    PubMed

    Lääveri, Tinja; Pakkanen, Sari H; Kirveskari, Juha; Kantele, Anu

    2018-02-02

    Travellers' diarrhoea (TD) is a common health problem among visitors to the (sub)tropics. Much research deals with aetiology, prevention, and post-infection sequalae, yet the data may not allow comparisons due to incompatible definitions of TD and No TD control groups. The impact of defining TD and No TD control groups was explored by revisiting our recent data. We set up two TD groups: classical TD i.e. ≥3 loose or liquid stools/day and WHO TD (diarrhoea as defined by the WHO) i.e. any diarrhoea, and four No TD groups by TD definition and timing (no classical/WHO TD during travel, no ongoing classical/WHO TD). TD was recorded for 37% versus 65% of subjects when using classical versus WHO definitions, respectively; the proportions of the various pathogens proved similar. The strictest criterion for the No TD control group (no WHO TD during travel) yielded pathogens among 61% and the least strict (no ongoing classical TD) among 73% of the travellers; the differences were greatest for enteroaggregative Escherichia coli and Campylobacter. Definition of TD and control group design substantially impact on TD study results. The WHO definition yields more cases, but the pathogen selection is similar by both definitions. Design of the No TD control group was found critical: only those remaining asymptomatic throughout the journey should be included. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. A biomolecular proportional integral controller based on feedback regulations of protein level and activity.

    PubMed

    Mairet, Francis

    2018-02-01

    Homeostasis is the capacity of living organisms to keep internal conditions regulated at a constant level, despite environmental fluctuations. Integral feedback control is known to play a key role in this behaviour. Here, I show that a feedback system involving transcriptional and post-translational regulations of the same executor protein acts as a proportional integral (PI) controller, leading to enhanced transient performances in comparison with a classical integral loop. Such a biomolecular controller-which I call a level and activity-PI controller (LA-PI)-is involved in the regulation of ammonium uptake by Escherichia coli through the transporter AmtB. The P II molecules, which reflect the nitrogen status of the cell, inhibit both the production of AmtB and its activity (via the NtrB-NtrC system and the formation of a complex with GlnK, respectively). Other examples of LA-PI controller include copper and zinc transporters, and the redox regulation in photosynthesis. This scheme has thus emerged through evolution in many biological systems, surely because of the benefits it offers in terms of performances (rapid and perfect adaptation) and economy (protein production according to needs).

  12. Microbial control of arthropod pests of tropical tree fruits.

    PubMed

    Dolinski, Claudia; Lacey, Lawrence A

    2007-01-01

    A multitude of insects and mites attack fruit crops throughout the tropics. The traditional method for controlling most of these pests is the application of chemical pesticides. Growing concern on the negative environmental effects has encouraged the development of alternatives. Inundatively and inoculatively applied microbial control agents (virus, bacteria, fungi, and entomopathogenic nematodes) have been developed as alternative control methods of a wide variety of arthropods including tropical fruit pests. The majority of the research and applications in tropical fruit agroecosystems has been conducted in citrus, banana, coconut, and mango. Successful microbial control initiatives of citrus pests and mites have been reported. Microbial control of arthropod pests of banana includes banana weevil, Cosmopolites sordidus Germar (Coleoptera: Curculionidae) (with EPNs and fungi) among others Oryctes rhinoceros (L.) is one of the most important pests of coconut and one of the most successful uses of non-occluded virus for classical biological control. Key pests of mango that have been controlled with microbial control agents include fruit flies (Diptera: Tephritidae) (with EPNs and fungi), and other pests. Also successful is the microbial control of arthropod pests of guava, papaya and pineapple. The challenge towards a broader application of entomopathogens is the development of successful combinations of entomopathogens, predators, and parasitoids along with other interventions to produce effective and sustainable pest management.

  13. An intermediate-level course on Biological Physics

    NASA Astrophysics Data System (ADS)

    Nelson, Phil

    2004-03-01

    I describe both undergraduate and graduate 1-semester courses designed to give a survey of Biological Physics. The courses cover classical as well as recent topics. The undergraduate version requires calculus-based first-year physics as its prerequisite. With this level of assumed background, we can arrive at topics such as molecular motors, manipulation of single molecules, and the propagation of nerve impulses. Students majoring in physics, chemistry, biochemistry, and every engineering major (as well as a few in biology), end up taking this course. The graduate course covers the same material but includes exercises with symbolic mathematics packages and data modeling.

  14. The near demise and subsequent revival of classical genetics for investigating Caenorhabditis elegans embryogenesis: RNAi meets next-generation DNA sequencing.

    PubMed

    Bowerman, Bruce

    2011-10-01

    Molecular genetic investigation of the early Caenorhabditis elegans embryo has contributed substantially to the discovery and general understanding of the genes, pathways, and mechanisms that regulate and execute developmental and cell biological processes. Initially, worm geneticists relied exclusively on a classical genetics approach, isolating mutants with interesting phenotypes after mutagenesis and then determining the identity of the affected genes. Subsequently, the discovery of RNA interference (RNAi) led to a much greater reliance on a reverse genetics approach: reducing the function of known genes with RNAi and then observing the phenotypic consequences. Now the advent of next-generation DNA sequencing technologies and the ensuing ease and affordability of whole-genome sequencing are reviving the use of classical genetics to investigate early C. elegans embryogenesis.

  15. Comparison of Balance Performance Between Thai Classical Dancers and Non-Dancers.

    PubMed

    Krityakiarana, Warin; Jongkamonwiwat, Nopporn

    2016-01-01

    Thai classical dance is a traditional dramatic art, the technique of which has many features in common with South East Asian performing art. The choreographic patterns consist of various forms of balance control together with limb movements in slow rhythm. The grace and beauty of the dancer are dependent on how well the limb movements curve and angle. The relationship of whole body proportion and balance control in various patterns of support base is also important. The purpose of this study was to compare balance abilities between Thai classical dancers and non-dancers in different balance conditions. Twenty-five Thai classical dancers and 25 non-dancers performed the modified Sensory Organization Test (mSOT) and were further challenged by adding dynamic head tilts (DHTs) in four different directions during mSOT. Mixed model ANOVA was applied to determine the equilibrium score in each balance condition and also the interaction between dancer and non-dancer groups. It was found that Thai classical dancers achieved better equilibrium scores in all mSOT conditions except the least challenging one. Moreover, additional multitask conditions (mSOT+DHT) were revealed to profoundly affect differences between dancers and controls. In conclusion, Thai classical dancers demonstrated a better ability to maintain postural stability during different challenging postural tests. This information suggests various ways of putting the practice of Thai classical dance to use in the future.

  16. Dynamic facial expressions of emotion transmit an evolving hierarchy of signals over time.

    PubMed

    Jack, Rachael E; Garrod, Oliver G B; Schyns, Philippe G

    2014-01-20

    Designed by biological and social evolutionary pressures, facial expressions of emotion comprise specific facial movements to support a near-optimal system of signaling and decoding. Although highly dynamical, little is known about the form and function of facial expression temporal dynamics. Do facial expressions transmit diagnostic signals simultaneously to optimize categorization of the six classic emotions, or sequentially to support a more complex communication system of successive categorizations over time? Our data support the latter. Using a combination of perceptual expectation modeling, information theory, and Bayesian classifiers, we show that dynamic facial expressions of emotion transmit an evolving hierarchy of "biologically basic to socially specific" information over time. Early in the signaling dynamics, facial expressions systematically transmit few, biologically rooted face signals supporting the categorization of fewer elementary categories (e.g., approach/avoidance). Later transmissions comprise more complex signals that support categorization of a larger number of socially specific categories (i.e., the six classic emotions). Here, we show that dynamic facial expressions of emotion provide a sophisticated signaling system, questioning the widely accepted notion that emotion communication is comprised of six basic (i.e., psychologically irreducible) categories, and instead suggesting four. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Analysis of classical Fourier, SPL and DPL heat transfer model in biological tissues in presence of metabolic and external heat source

    NASA Astrophysics Data System (ADS)

    Kumar, Dinesh; Singh, Surjan; Rai, K. N.

    2016-06-01

    In this paper, the temperature distribution in a finite biological tissue in presence of metabolic and external heat source when the surface subjected to different type of boundary conditions is studied. Classical Fourier, single-phase-lag (SPL) and dual-phase-lag (DPL) models were developed for bio-heat transfer in biological tissues. The analytical solution obtained for all the three models using Laplace transform technique and results are compared. The effect of the variability of different parameters such as relaxation time, metabolic heat source, spatial heat source, different type boundary conditions on temperature distribution in different type of the tissues like muscle, tumor, fat, dermis and subcutaneous based on three models are analyzed and discussed in detail. The result obtained in three models is compared with experimental observation of Stolwijk and Hardy (Pflug Arch 291:129-162, 1966). It has been observe that the DPL bio-heat transfer model provides better result in comparison of other two models. The value of metabolic and spatial heat source in boundary condition of first, second and third kind for different type of thermal therapies are evaluated.

  18. SAW Synthesis With IDTs Array and the Inverse Filter: Toward a Versatile SAW Toolbox for Microfluidics and Biological Applications.

    PubMed

    Riaud, Antoine; Baudoin, Michael; Thomas, Jean-Louis; Bou Matar, Olivier

    2016-10-01

    Surface acoustic waves (SAWs) are versatile tools to manipulate fluids at small scales for microfluidics and biological applications. A nonexhaustive list of operations that can be performed with SAW includes sessile droplet displacement, atomization, division, and merging but also the actuation of fluids embedded in microchannels or the manipulation of suspended particles. However, each of these operations requires a specific design of the wave generation system, the so-called interdigitated transducers (IDTs). Depending on the application, it might indeed be necessary to generate focused or plane, propagating or standing, and aligned or shifted waves. Furthermore, the possibilities offered by more complex wave fields such as acoustical vortices for particle tweezing and liquid twisting cannot be explored with classical IDTs. In this paper, we show that the inverse filter technique coupled with an IDTs array enables us to synthesize all classical wave fields used in microfluidics and biological applications with a single multifunctional platform. It also enables us to generate swirling SAWs, whose potential for the on-chip synthesis of tailored acoustical vortices has been demonstrated lately. The possibilities offered by this platform are illustrated by performing many operations successively on sessile droplets with the same system.

  19. Modifiers of Ovarian Function in Girls and Women With Classic Galactosemia

    PubMed Central

    Spencer, Jessica B.; Badik, Jennifer R.; Ryan, Emily L.; Gleason, Tyler J.; Broadaway, K. Alaine; Epstein, Michael P.

    2013-01-01

    Context: Classic galactosemia is a potentially lethal genetic disorder resulting from profound impairment of galactose-1P uridylyltransferase (GALT). More than 80% of girls and women with classic galactosemia experience primary or premature ovarian insufficiency despite neonatal diagnosis and rigorous lifelong dietary galactose restriction. Objective: The goal of this study was to test the relationship between markers of ovarian reserve, cryptic residual GALT activity, and spontaneous pubertal development in girls with classic galactosemia. Design and Setting: This was a cross-sectional study with some longitudinal follow-up in a university research environment. Patients: Patients included girls and women with classic galactosemia and unaffected controls, <1 month to 30 years old. Main Outcome Measures: We evaluated plasma anti-Müllerian hormone (AMH) and FSH levels, antral follicle counts ascertained by ultrasound, and ovarian function as indicated by spontaneous vs assisted menarche. Results: More than 73% of the pre- and postpubertal girls and women with classic galactosemia in this study, ages >3 months to 30 years, demonstrated AMH levels below the 95% confidence interval for AMH among controls of the same age, and both pre- and postpubertal girls and women with classic galactosemia also demonstrated abnormally low antral follicle counts relative to age-matched controls. Predicted residual GALT activity ≥0.4% significantly increased the likelihood that a girl with classic galactosemia would demonstrate an AMH level ≥0.1 ng/mL. Conclusions: A majority of girls with classic galactosemia demonstrate evidence of diminished ovarian reserve by 3 months of age, and predicted cryptic residual GALT activity is a modifier of ovarian function in galactosemic girls and women. PMID:23690308

  20. A two-agent model applied to the biological control of the sugarcane borer (Diatraea saccharalis) by the egg parasitoid Trichogramma galloi and the larvae parasitoid Cotesia flavipes.

    PubMed

    Molnár, Sándor; López, Inmaculada; Gámez, Manuel; Garay, József

    2016-03-01

    The paper is aimed at a methodological development in biological pest control. The considered one pest two-agent system is modelled as a verticum-type system. Originally, linear verticum-type systems were introduced by one of the authors for modelling certain industrial systems. These systems are hierarchically composed of linear subsystems such that a part of the state variables of each subsystem affect the dynamics of the next subsystem. Recently, verticum-type system models have been applied to population ecology as well, which required the extension of the concept a verticum-type system to the nonlinear case. In the present paper the general concepts and technics of nonlinear verticum-type control systems are used to obtain biological control strategies in a two-agent system. For the illustration of this verticum-type control, these tools of mathematical systems theory are applied to a dynamic model of interactions between the egg and larvae populations of the sugarcane borer (Diatraea saccharalis) and its parasitoids: the egg parasitoid Trichogramma galloi and the larvae parasitoid Cotesia flavipes. In this application a key role is played by the concept of controllability, which means that it is possible to steer the system to an equilibrium in given time. In addition to a usual linearization, the basic idea is a decomposition of the control of the whole system into the control of the subsystems, making use of the verticum structure of the population system. The main aim of this study is to show several advantages of the verticum (or decomposition) approach over the classical control theoretical model (without decomposition). For example, in the case of verticum control the pest larval density decreases below the critical threshold value much quicker than without decomposition. Furthermore, it is also shown that the verticum approach may be better even in terms of cost effectiveness. The presented optimal control methodology also turned out to be an efficient tool for the "in silico" analysis of the cost-effectiveness of different biocontrol strategies, e.g. by answering the question how far it is cost-effective to speed up the reduction of the pest larvae density, or along which trajectory this reduction should be carried out. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

    Zhang, Ying-Jie, E-mail: yingjiezhang@qfnu.edu.cn; Han, Wei; Xia, Yun-Jie, E-mail: yjxia@qfnu.edu.cn

    We propose a scheme of controlling entanglement dynamics of a quantum system by applying the external classical driving field for two atoms separately located in a single-mode photon cavity. It is shown that, with a judicious choice of the classical-driving strength and the atom–photon detuning, the effective atom–photon interaction Hamiltonian can be switched from Jaynes–Cummings model to anti-Jaynes–Cummings model. By tuning the controllable atom–photon interaction induced by the classical field, we illustrate that the evolution trajectory of the Bell-like entanglement states can be manipulated from entanglement-sudden-death to no-entanglement-sudden-death, from no-entanglement-invariant to entanglement-invariant. Furthermore, the robustness of the initial Bell-like entanglementmore » can be improved by the classical driving field in the leaky cavities. This classical-driving-assisted architecture can be easily extensible to multi-atom quantum system for scalability.« less

  2. Integrating Multiscale Modeling with Drug Effects for Cancer Treatment.

    PubMed

    Li, Xiangfang L; Oduola, Wasiu O; Qian, Lijun; Dougherty, Edward R

    2015-01-01

    In this paper, we review multiscale modeling for cancer treatment with the incorporation of drug effects from an applied system's pharmacology perspective. Both the classical pharmacology and systems biology are inherently quantitative; however, systems biology focuses more on networks and multi factorial controls over biological processes rather than on drugs and targets in isolation, whereas systems pharmacology has a strong focus on studying drugs with regard to the pharmacokinetic (PK) and pharmacodynamic (PD) relations accompanying drug interactions with multiscale physiology as well as the prediction of dosage-exposure responses and economic potentials of drugs. Thus, it requires multiscale methods to address the need for integrating models from the molecular levels to the cellular, tissue, and organism levels. It is a common belief that tumorigenesis and tumor growth can be best understood and tackled by employing and integrating a multifaceted approach that includes in vivo and in vitro experiments, in silico models, multiscale tumor modeling, continuous/discrete modeling, agent-based modeling, and multiscale modeling with PK/PD drug effect inputs. We provide an example application of multiscale modeling employing stochastic hybrid system for a colon cancer cell line HCT-116 with the application of Lapatinib drug. It is observed that the simulation results are similar to those observed from the setup of the wet-lab experiments at the Translational Genomics Research Institute.

  3. Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells.

    PubMed

    Chang, Ting-Yu; Wu, Yu-Hsuan; Cheng, Cheng-Chung; Wang, Hsei-Wei

    2011-09-01

    Alternative RNA splicing greatly increases proteome diversity, and the possibility of studying genome-wide alternative splicing (AS) events becomes available with the advent of high-throughput genomics tools devoted to this issue. Kaposi's sarcoma associated herpesvirus (KSHV) is the etiological agent of KS, a tumor of lymphatic endothelial cell (LEC) lineage, but little is known about the AS variations induced by KSHV. We analyzed KSHV-controlled AS using high-density microarrays capable of detecting all exons in the human genome. Splicing variants and altered exon-intron usage in infected LEC were found, and these correlated with protein domain modification. The different 3'-UTR used in new transcripts also help isoforms to escape microRNA-mediated surveillance. Exome-level analysis further revealed information that cannot be disclosed using classical gene-level profiling: a significant exon usage difference existed between LEC and CD34(+) precursor cells, and KSHV infection resulted in LEC-to-precursor, dedifferentiation-like exon level reprogramming. Our results demonstrate the application of exon arrays in systems biology research, and suggest the regulatory effects of AS in endothelial cells are far more complex than previously observed. This extra layer of molecular diversity helps to account for various aspects of endothelial biology, KSHV life cycle and disease pathogenesis that until now have been unexplored.

  4. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

    PubMed Central

    Rialle, Stéphanie; Felicori, Liza; Dias-Lopes, Camila; Pérès, Sabine; El Atia, Sanaâ; Thierry, Alain R.; Amar, Patrick; Molina, Franck

    2010-01-01

    Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks. Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/ Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20628073

  5. Generation of entanglement in quantum parametric oscillators using phase control.

    PubMed

    Gonzalez-Henao, J C; Pugliese, E; Euzzor, S; Abdalah, S F; Meucci, R; Roversi, J A

    2015-08-19

    The control of quantum entanglement in systems in contact with environment plays an important role in information processing, cryptography and quantum computing. However, interactions with the environment, even when very weak, entail decoherence in the system with consequent loss of entanglement. Here we consider a system of two coupled oscillators in contact with a common heat bath and with a time dependent oscillation frequency. The possibility to control the entanglement of the oscillators by means of an external sinusoidal perturbation applied to the oscillation frequency has been theoretically explored. We demonstrate that the oscillators become entangled exactly in the region where the classical counterpart is unstable, otherwise when the classical system is stable, entanglement is not possible. Therefore, we can control the entanglement swapping from stable to unstable regions by adjusting amplitude and phase of our external controller. We also show that the entanglement rate is approximately proportional to the real part of the Floquet coefficient of the classical counterpart of the oscillators. Our results have the intriguing peculiarity of manipulating quantum information operating on a classical system.

  6. Functional Basis for Efficient Physical Layer Classical Control in Quantum Processors

    NASA Astrophysics Data System (ADS)

    Ball, Harrison; Nguyen, Trung; Leong, Philip H. W.; Biercuk, Michael J.

    2016-12-01

    The rapid progress seen in the development of quantum-coherent devices for information processing has motivated serious consideration of quantum computer architecture and organization. One topic which remains open for investigation and optimization relates to the design of the classical-quantum interface, where control operations on individual qubits are applied according to higher-level algorithms; accommodating competing demands on performance and scalability remains a major outstanding challenge. In this work, we present a resource-efficient, scalable framework for the implementation of embedded physical layer classical controllers for quantum-information systems. Design drivers and key functionalities are introduced, leading to the selection of Walsh functions as an effective functional basis for both programing and controller hardware implementation. This approach leverages the simplicity of real-time Walsh-function generation in classical digital hardware, and the fact that a wide variety of physical layer controls, such as dynamic error suppression, are known to fall within the Walsh family. We experimentally implement a real-time field-programmable-gate-array-based Walsh controller producing Walsh timing signals and Walsh-synthesized analog waveforms appropriate for critical tasks in error-resistant quantum control and noise characterization. These demonstrations represent the first step towards a unified framework for the realization of physical layer controls compatible with large-scale quantum-information processing.

  7. Impact of Field Densities of the Naturalized Defoliator Caloptilia triadicae (Lepidoptera: Gracillariidae) on the Invasive Weed Chinese Tallowtree.

    PubMed

    Wheeler, G S; Hight, S D; Wright, S A

    2017-12-08

    Chinese tallowtree, Triadica sebifera (L.) Small (Euphoriaceae), is one of the most aggressive weeds of coastal wetlands and forests of the southeastern United States. The lack of specialist herbivores in the invaded range may be one of the factors that contribute to the invasive nature of this weed. Chinese tallowtree has been the target of a classical biological control project since 2006. Several herbivore species are being tested for biological control of Chinese tallowtree. Concurrently, an adventive herbivore, Caloptilia triadicae Davis (Lepidoptera: Gracillariidae), was found feeding on Chinese tallowtree in the southeastern United States in 2004 and now occurs throughout the invaded range. Field populations of C. triadicae from two sites caused extensive mining damage to the Chinese tallowtree leaves. The greatest damage occurred after 30 d of exposure to C. triadicae in the herbivory treatment and amounted to about 25-30 leaf mines (early instars) and leaf rolls (late instars) per plant. Insecticide-treated plants had atmost 5-10 leaf mines and rolls per plant. Despite this difference, plant growth in height, number of new branches, and leaves did not differ significantly from plants protected from herbivory. Analysis of harvested plant results suggested that, in general, herbivory had little impact on biomass. However, there was a slight reduction in trunk weights in the unrestriced herbivory treatment compared with the insecticide-treated plants. Although this study exposed experimental plants to only 60 d of herbivory, these results suggested that C. triadicae alone will not exert sufficient control of invasive populations of Chinese tallowtree. Furthermore, they indicated that continued development of biological control agents that target Chinese tallowtree are needed. Published by Oxford University Press on behalf of Entomological Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  8. Linear Quantum Systems: Non-Classical States and Robust Stability

    DTIC Science & Technology

    2016-06-29

    has a history going back some 50 years, to the birth of modern control theory with Kalman’s foundational work on filtering and LQG optimal control ...information   if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ORGANIZATION. 1. REPORT DATE (DD...analysis and control of quantum linear systems and their interactions with non-classical quantum fields by developing control theoretic concepts exploiting

  9. [Consideration about chemistry, manufacture and control (CMC) key problems in simplified registration of classical traditional Chinese medicine excellent prescriptions].

    PubMed

    Wang, Zhi-Min; Liu, Ju-Yan; Liu, Xiao-Qian; Wang, De-Qin; Yan, Li-Hua; Zhu, Jin-Jin; Gao, Hui-Min; Li, Chun; Wang, Jin-Yu; Li, Chu-Yuan; Ni, Qing-Chun; Huang, Ji-Sheng; Lin, Juan

    2017-05-01

    As an outstanding representative of traditional Chinese medicine(TCM) prescriptions accumulated from famous TCM doctors' clinical experiences in past dynasties, classical TCM excellent prescriptions (cTCMeP) are the most valuable part of TCM system. To support the research and development of cTCMeP, a series of regulations and measures were issued to encourage its simplified registration. There is still a long-way to go because many key problems and puzzles about technology, registration and administration in cTCMeP R&D process are not resolved. Based on the analysis of registration and management regulations of botanical drug products in FDA of USA and Japan, and EMA of Europe, the possible key problems and countermeasures in chemistry, manufacture and control (CMC) of simplified registration of cTCMeP were analyzed on the consideration of its actual situation. The method of "reference decoction extract by traditional prescription" (RDETP) was firstly proposed as standard to evaluate the quality and preparation uniformity between the new developing product under simplified registration and traditional original usages of cTCMeP, instead of Standard Decoction method in Japan. "Totality of the evidence" approach, mass balance and bioassay/biological assay of cTCMeP were emphatically suggested to introduce to the quality uniformity evaluation system in the raw drug material, drug substance and final product between the modern product and traditional decoction. Copyright© by the Chinese Pharmaceutical Association.

  10. Controlled quantum secure direct communication by entanglement distillation or generalized measurement

    NASA Astrophysics Data System (ADS)

    Tan, Xiaoqing; Zhang, Xiaoqian

    2016-05-01

    We propose two controlled quantum secure communication schemes by entanglement distillation or generalized measurement. The sender Alice, the receiver Bob and the controllers David and Cliff take part in the whole schemes. The supervisors David and Cliff can control the information transmitted from Alice to Bob by adjusting the local measurement angles θ _4 and θ _3. Bob can verify his secret information by classical one-way function after communication. The average amount of information is analyzed and compared for these two methods by MATLAB. The generalized measurement is a better scheme. Our schemes are secure against some well-known attacks because classical encryption and decoy states are used to ensure the security of the classical channel and the quantum channel.

  11. Cell and molecular biology of the spiny dogfish Squalus acanthias and little skate Leucoraja erinacea: insights from in vitro cultured cells.

    PubMed

    Barnes, D W

    2012-04-01

    Two of the most commonly used elasmobranch experimental model species are the spiny dogfish Squalus acanthias and the little skate Leucoraja erinacea. Comparative biology and genomics with these species have provided useful information in physiology, pharmacology, toxicology, immunology, evolutionary developmental biology and genetics. A wealth of information has been obtained using in vitro approaches to study isolated cells and tissues from these organisms under circumstances in which the extracellular environment can be controlled. In addition to classical work with primary cell cultures, continuously proliferating cell lines have been derived recently, representing the first cell lines from cartilaginous fishes. These lines have proved to be valuable tools with which to explore functional genomic and biological questions and to test hypotheses at the molecular level. In genomic experiments, complementary (c)DNA libraries have been constructed, and c. 8000 unique transcripts identified, with over 3000 representing previously unknown gene sequences. A sub-set of messenger (m)RNAs has been detected for which the 3' untranslated regions show elements that are remarkably well conserved evolutionarily, representing novel, potentially regulatory gene sequences. The cell culture systems provide physiologically valid tools to study functional roles of these sequences and other aspects of elasmobranch molecular cell biology and physiology. Information derived from the use of in vitro cell cultures is valuable in revealing gene diversity and information for genomic sequence assembly, as well as for identification of new genes and molecular markers, construction of gene-array probes and acquisition of full-length cDNA sequences. © 2012 The Author. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  12. A biomolecular proportional integral controller based on feedback regulations of protein level and activity

    PubMed Central

    2018-01-01

    Homeostasis is the capacity of living organisms to keep internal conditions regulated at a constant level, despite environmental fluctuations. Integral feedback control is known to play a key role in this behaviour. Here, I show that a feedback system involving transcriptional and post-translational regulations of the same executor protein acts as a proportional integral (PI) controller, leading to enhanced transient performances in comparison with a classical integral loop. Such a biomolecular controller—which I call a level and activity-PI controller (LA-PI)—is involved in the regulation of ammonium uptake by Escherichia coli through the transporter AmtB. The PII molecules, which reflect the nitrogen status of the cell, inhibit both the production of AmtB and its activity (via the NtrB-NtrC system and the formation of a complex with GlnK, respectively). Other examples of LA-PI controller include copper and zinc transporters, and the redox regulation in photosynthesis. This scheme has thus emerged through evolution in many biological systems, surely because of the benefits it offers in terms of performances (rapid and perfect adaptation) and economy (protein production according to needs). PMID:29515895

  13. ASSESSING THE IMPACTS OF ANTHROPOGENIC STRESSORS ON MACROINVERTEBRATE INDICATORS IN OHIO

    EPA Science Inventory

    In the past few years, there has been increasing interest in using biological community data to provide information about specific anthropogenic factors impacting streams. Previous studies have used statistical approaches that are variants of classical and modern multiple regres...

  14. Marijuana smoking: effects of varying puff volume and breathhold duration.

    PubMed

    Azorlosa, J L; Greenwald, M K; Stitzer, M L

    1995-02-01

    Two studies were conducted to quantify biological and behavioral effects resulting from exposure to controlled doses of marijuana smoke. In one study, puff volume (30, 60 and 90 ml) and in a second study, breathhold duration (0, 10 and 20 sec) were systematically varied while holding constant other smoking topography parameters (number of puffs = 10, interpuff interval = 60 sec and inhalation volume = 25% of vital capacity). Each study also varied levels of delta 9-tetrahydro-cannabinol marijuana cigarette content (1.75% and 3.55%). Regular marijuana users served as subjects (n = 7 in each experiment). Subjects smoked 10 puffs in each of six sessions; a seventh, nonsmoking session (all measures recorded at the same times as in active smoking sessions) served as a control. Variations in puff volume produced significant dose-related changes in postsmoking plasma delta 9-tetrahydro-cannabinol levels, carbon monoxide boost and subjective effects (e.g., "high"). In contrast, breathholding for 10 or 20 sec versus 0 sec increased plasma delta 9-tetrahydro-cannabinol levels but not CO boost or subjective effects. Task performance measures were not reliably influenced by marijuana smoke exposure within the dosing ranges examined. These findings confirm the utility of the controlled smoking technology, support the notion that cumulative puff volume systematically influences biological exposure and subjective effects, but cast doubt on the common belief that prolonged breathholding of marijuana smoke enhances classical subjective effects associated with its reinforcing value in humans.

  15. Quantum synchronization of quantum van der Pol oscillators with trapped ions.

    PubMed

    Lee, Tony E; Sadeghpour, H R

    2013-12-06

    The van der Pol oscillator is the prototypical self-sustained oscillator and has been used to model nonlinear behavior in biological and other classical processes. We investigate how quantum fluctuations affect phase locking of one or many van der Pol oscillators. We find that phase locking is much more robust in the quantum model than in the equivalent classical model. Trapped-ion experiments are ideally suited to simulate van der Pol oscillators in the quantum regime via sideband heating and cooling of motional modes. We provide realistic experimental parameters for 171Yb+ achievable with current technology.

  16. Theory of long-range diffusion of proteins on a spherical biological membrane: application to protein cluster formation and actin-comet tail growth.

    PubMed

    Amatore, Christian; Oleinick, Alexander I; Klymenko, Oleksiy V; Svir, Irina

    2009-07-13

    Breaking of symmetry is often required in biology in order to produce a specific function. In this work we address the problem of protein diffusion over a spherical vesicle surface towards one pole of the vesicle in order to produce ultimately an active protein cluster performing a specific biological function. Such a process is, for example, prerequisite for the assembling of proteins which then cooperatively catalyze the polymerization of actin monomers to sustain the growth of actin tails as occurs in natural vesicles such as those contained in Xenopus eggs. By this process such vesicles may propel themselves within the cell by the principle of action-reaction. In this work the physicochemical treatment of diffusion of large biomolecules within a cellular membrane is extended to encompass the case when proteins may be transiently poised by corral-like structures partitioning the membrane as has been recently documented in the literature. In such case the exchange of proteins between adjacent corrals occurs by energy-gated transitions instead of classical Brownian motion, yet the present analysis shows that long-range movements of the biomolecules may still be described by a classical diffusion law though the diffusion coefficient has then a different physical meaning. Such a model explains why otherwise classical diffusion of proteins may give rise to too small diffusion coefficients compared to predictions based on the protein dimension. This model is implemented to examine the rate of proteins clustering at one pole of a spherical vesicle and its outcome is discussed in relevance to the mechanism of actin comet tails growth.

  17. Integrative mental health care: from theory to practice, Part 2.

    PubMed

    Lake, James

    2008-01-01

    Integrative approaches will lead to more accurate and different understandings of mental illness. Beneficial responses to complementary and alternative therapies provide important clues about the phenomenal nature of the human body in space-time and disparate biological, informational, and energetic factors associated with normal and abnormal psychological functioning. The conceptual framework of contemporary Western psychiatry includes multiple theoretical viewpoints, and there is no single best explanatory model of mental illness. Future theories of mental illness causation will not depend exclusively on empirical verification of strictly biological processes but will take into account both classically described biological processes and non-classical models, including complexity theory, resulting in more complete explanations of the characteristics and causes of symptoms and mechanisms of action that result in beneficial responses to treatments. Part 1 of this article examined the limitations of the theory and contemporary clinical methods employed in Western psychiatry and discussed implications of emerging paradigms in physics and the biological sciences for the future of psychiatry. In part 2, a practical methodology, for planning integrative assessment and treatment strategies in mental health care is proposed. Using this methodology the integrative management of moderate and severe psychiatric symptoms is reviewed in detail. As the conceptual framework of Western medicine evolves toward an increasingly integrative perspective, novel understanding of complex relationships between biological, informational, and energetic processes associated with normal psychological functioning and mental illness will lead to more effective integrative assessment and treatment strategies addressing the causes or meanings of symptoms at multiple hierarchic levels of body-brain-mind.

  18. Integrative mental health care: from theory to practice, part 1.

    PubMed

    Lake, James

    2007-01-01

    Integrative approaches will lead to more accurate and different understandings of mental illness. Beneficial responses to complementary and alternative therapies provide important clues about the phenomenal nature of the human body in space-time and disparate biological, informational, and energetic factors associated with normal and abnormal psychological functioning. The conceptual framework of contemporary Western psychiatry includes multiple theoretical viewpoints, and there is no single best explanatory model of mental illness. Future theories of mental illness causation will not depend exclusively on empirical verification of strictly biological processes but will take into account both classically described biological processes and non-classical models, including complexity theory, resulting in more complete explanations of the characteristics and causes of symptoms and mechanisms of action that result in beneficial responses to treatments. Part 1 of this article examines the limitations of the theory and contemporary clinical methods employed in Western psychiatry and discusses implications of emerging paradigms in physics and the biological sciences for the future of psychiatry. In part 2, a practical methodology for planning integrative assessment and treatment strategies in mental health care is proposed. Using this methodology the integrative management of moderate and severe psychiatric symptoms is reviewed in detail. As the conceptual framework of Western medicine evolves toward an increasingly integrative perspective, novel understandings of complex relationships between biological, informational, and energetic processes associated with normal psychological functioning and mental illness will lead to more effective integrative assessment and treatment strategies addressing the causes or meanings of symptoms at multiple hierarchic levels of body-brain-mind.

  19. Quantum Barro-Gordon game in monetary economics

    NASA Astrophysics Data System (ADS)

    Samadi, Ali Hussein; Montakhab, Afshin; Marzban, Hussein; Owjimehr, Sakine

    2018-01-01

    Classical game theory addresses decision problems in multi-agent environment where one rational agent's decision affects other agents' payoffs. Game theory has widespread application in economic, social and biological sciences. In recent years quantum versions of classical games have been proposed and studied. In this paper, we consider a quantum version of the classical Barro-Gordon game which captures the problem of time inconsistency in monetary economics. Such time inconsistency refers to the temptation of weak policy maker to implement high inflation when the public expects low inflation. The inconsistency arises when the public punishes the weak policy maker in the next cycle. We first present a quantum version of the Barro-Gordon game. Next, we show that in a particular case of the quantum game, time-consistent Nash equilibrium could be achieved when public expects low inflation, thus resolving the game.

  20. Note: Wide-operating-range control for thermoelectric coolers.

    PubMed

    Peronio, P; Labanca, I; Ghioni, M; Rech, I

    2017-11-01

    A new algorithm for controlling the temperature of a thermoelectric cooler is proposed. Unlike a classic proportional-integral-derivative (PID) control, which computes the bias voltage from the temperature error, the proposed algorithm exploits the linear relation that exists between the cold side's temperature and the amount of heat that is removed per unit time. Since this control is based on an existing linear relation, it is insensitive to changes in the operating point that are instead crucial in classic PID control of a non-linear system.

  1. Note: Wide-operating-range control for thermoelectric coolers

    NASA Astrophysics Data System (ADS)

    Peronio, P.; Labanca, I.; Ghioni, M.; Rech, I.

    2017-11-01

    A new algorithm for controlling the temperature of a thermoelectric cooler is proposed. Unlike a classic proportional-integral-derivative (PID) control, which computes the bias voltage from the temperature error, the proposed algorithm exploits the linear relation that exists between the cold side's temperature and the amount of heat that is removed per unit time. Since this control is based on an existing linear relation, it is insensitive to changes in the operating point that are instead crucial in classic PID control of a non-linear system.

  2. γ/δ T cell subsets in human aging using the classical α/β T cell model.

    PubMed

    Vasudev, Anusha; Ying, Crystal Tan Tze; Ayyadhury, Shamini; Puan, Kia Joo; Andiappan, Anand Kumar; Nyunt, Ma Shwe Zin; Shadan, Nurhidaya Binte; Mustafa, Seri; Low, Ivy; Rotzschke, Olaf; Fulop, Tamas; Ng, Tze Pin; Larbi, Anis

    2014-10-01

    Aging is associated with an increased susceptibility to infections and diseases. It has also been associated with reduced functionality and altered distribution of immune cells, especially T cells. Whereas classical α/β T cells, especially CD8(+) T cells, were shown to be highly susceptible to aging, the effects of viral persistent stimulations on the fate of γ/δ T cells are much less documented. Healthy, elderly individuals of Chinese ethnical background were recruited under the aegis of SLAS-II. In this observational study, γ/δ T cell populations were characterized by flow cytometry and compared with the α/β CD4(+) and CD8(+) T cells in elderly and young controls. In our study, we identified a reduced frequency of γ/δ T cells but not α/β T cells with aging. The classical markers of α/β T cell aging, including CD28, CD27, and CD57, did not prove significant for γ/δ T cells. The extreme range of expression of these markers in γ/δ T cells was responsible for the lack of relationship between γ/δ T cell subsets, CD4/CD8 ratio, and anti-CMV titers that was significant for α/β T cells and, especially, CD8(+) T cells. Although markers of aging for γ/δ T cells are not clearly identified, our data collectively suggest that the presence of CD27 γ/δ T cells is associated with markers of α/β T cell aging. © 2014 Society for Leukocyte Biology.

  3. Exploiting evanescent-wave amplification for subwavelength low-contrast particle detection

    NASA Astrophysics Data System (ADS)

    Roy, S.; Pereira, S. F.; Urbach, H. P.; Wei, Xukang; El Gawhary, O.

    2017-07-01

    The classical problem of subwavelength particle detection on a flat surface is especially challenging when the refractive index of the particle is close to that of the substrate. We demonstrate a method to improve the detection ability several times for such a situation, by enhancing the "forbidden" evanescent waves in the substrate using the principle of super-resolution with evanescent waves amplification. The working mechanism of the system and experimental validation from a design with a thin single dielectric layer is presented. The resulting system is a simple but complete example of evanescent-wave generation, amplification, and the consequent modulation of the far field. This principle can have far reaching impact in the field of particle detection in several applications ranging from contamination control to interferometric scattering microscopy for biological samples.

  4. Novel perspectives for the engineering of abiotic stress tolerance in plants.

    PubMed

    Cabello, Julieta V; Lodeyro, Anabella F; Zurbriggen, Matias D

    2014-04-01

    Adverse environmental conditions pose serious limitations to agricultural production. Classical biotechnological approaches towards increasing abiotic stress tolerance focus on boosting plant endogenous defence mechanisms. However, overexpression of regulatory elements or effectors is usually accompanied by growth handicap and yield penalties due to crosstalk between developmental and stress-response networks. Herein we offer an overview on novel strategies with the potential to overcome these limitations based on the engineering of regulatory systems involved in the fine-tuning of the plant response to environmental hardships, including post-translational modifications, small RNAs, epigenetic control of gene expression and hormonal networks. The development and application of plant synthetic biology tools and approaches will add new functionalities and perspectives to genetic engineering programs for enhancing abiotic stress tolerance. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Genetic and Genomic Toolbox of Zea mays

    PubMed Central

    Nannas, Natalie J.; Dawe, R. Kelly

    2015-01-01

    Maize has a long history of genetic and genomic tool development and is considered one of the most accessible higher plant systems. With a fully sequenced genome, a suite of cytogenetic tools, methods for both forward and reverse genetics, and characterized phenotype markers, maize is amenable to studying questions beyond plant biology. Major discoveries in the areas of transposons, imprinting, and chromosome biology came from work in maize. Moving forward in the post-genomic era, this classic model system will continue to be at the forefront of basic biological study. In this review, we outline the basics of working with maize and describe its rich genetic toolbox. PMID:25740912

  6. Quorum sensing: a quantum perspective.

    PubMed

    Majumdar, Sarangam; Pal, Sukla

    2016-09-01

    Quorum sensing is the efficient mode of communication in the bacterial world. After a lot of advancements in the classical theory of quorum sensing few basic questions of quorum sensing still remain unanswered. The sufficient progresses in quantum biology demands to explain these questions from the quantum perspective as non trivial quantum effects already have manifested in various biological processes like photosynthesis, magneto-reception etc. Therefore, it's the time to review the bacterial communications from the quantum view point. In this article we carefully accumulate the latest results and arguments to strengthen quantum biology through the addition of quorum sensing mechanism in the light of quantum mechanics.

  7. ECOTOXICOGENOMICS: LINKAGES BETWEEN EXPOSURE AND EFFECTS IN ASSESSING RISKS OF AQUATIC CONTAMINANTS TO FISH

    EPA Science Inventory

    Understanding the biological effects of exposures to chemicals in the environment relies on classical and emerging technologies in the areas of genomics, proteomics, and metabonomics. Linkages between the historical and newer toxicological tools are currently being developed in o...

  8. Modeling the Classic Meselson and Stahl Experiment.

    ERIC Educational Resources Information Center

    D'Agostino, JoBeth

    2001-01-01

    Points out the importance of molecular models in biology and chemistry. Presents a laboratory activity on DNA. Uses different colored wax strips to represent "heavy" and "light" DNA, cesium chloride for identification of small density differences, and three different liquids with varying densities to model gradient…

  9. The unconventional antimicrobial peptides of the classical propionibacteria.

    PubMed

    Faye, Therese; Holo, Helge; Langsrud, Thor; Nes, Ingolf F; Brede, Dag A

    2011-02-01

    The classical propionibacteria produce genetically unique antimicrobial peptides, whose biological activities are without equivalents, and to which there are no homologous sequences in public databases. In this review, we summarize the genetics, biochemistry, biosynthesis, and biological activities of three extensively studied antimicrobial peptides from propionibacteria. The propionicin T1 peptide constitutes a bona fide example of an unmodified general secretory pathway (sec)-dependent bacteriocin, which is bactericidal towards all tested species of propionibacteria except Propionibacterium freudenreichii. The PAMP antimicrobial peptide represents a novel concept within bacterial antagonism, where an inactive precursor protein is secreted in large amounts, and which activation appears to rely on subsequent processing by proteases in its resident milieu. Propionicin F is a negatively charged bacteriocin that displays an intraspecies bactericidal inhibition spectrum. The biosynthesis of propionicin F appears to proceed through a series of unusual events requiring both N- and C-terminal processing of a precursor protein, which probably requires the radical SAM superfamily enzyme PcfB.

  10. Modalities of gene action predicted by the classical evolutionary biological theory of aging.

    PubMed

    Martin, George M

    2007-04-01

    What might now be referred to as the "classical" evolutionary biological theory of why we age has had a number of serious challenges in recent years. While the theory might therefore have to be modified under certain circumstances, in the author's opinion, it still provides the soundest theoretical basis for thinking about how we age. Nine modalities of gene action that have the potential to modulate processes of aging are reviewed, including the two most widely reviewed and accepted concepts ("antagonistic pleiotropy" and "mutation accumulation"). While several of these nine mechanisms can be regarded as derivatives of the antagonistic pleiotropic concept, they frame more specific questions for future research. Such research should pursue what appears to be the dominant factor in the determination of intraspecific variations in longevity-stochastic mechanisms, most likely based upon epigenetics. This contrasts with the dominant factor in the determination of interspecific variations in longevity-the constitutional genome, most likely based upon variations in regulatory loci.

  11. Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives

    DOE PAGES

    Jagiello, Karolina; Grzonkowska, Monika; Swirog, Marta; ...

    2016-08-29

    In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure–Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure–Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide themore » recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner.« less

  12. Quantum annealing versus classical machine learning applied to a simplified computational biology problem

    NASA Astrophysics Data System (ADS)

    Li, Richard Y.; Di Felice, Rosa; Rohs, Remo; Lidar, Daniel A.

    2018-03-01

    Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the ability of a quantum machine learning approach to classify and rank binding affinities. Using simplified data sets of a small number of DNA sequences derived from actual binding affinity experiments, we trained a commercially available quantum annealer to classify and rank transcription factor binding. The results were compared to state-of-the-art classical approaches for the same simplified data sets, including simulated annealing, simulated quantum annealing, multiple linear regression, LASSO, and extreme gradient boosting. Despite technological limitations, we find a slight advantage in classification performance and nearly equal ranking performance using the quantum annealer for these fairly small training data sets. Thus, we propose that quantum annealing might be an effective method to implement machine learning for certain computational biology problems.

  13. [Psychosomatics is "expensive"].

    PubMed

    Hnízdil, J; Savlík, J

    2005-01-01

    Experience shoves that number of diseases where recognition and treatment is without limits of classical medicine is rising, however it is fully within the competence of psychosomatic approach. It does not concern the classical classification into organic and functional defects, but it concerns the possibility of complex approach. The theorem of "diagnosis per exclusionem" is still valid, as well as it is true that the means of medicine end at its biological limitations. We consider stressing in our article that psychosomatic diseases or psychosomatic patients do not exist and psychosomatics is not and independent specialization. Psychosomatics is, as inseparable unity of psychic and somatic activities, each human being. Complex biopsychosocial (psychosomatic) approach is the way of thinking and work, which considers human in unrepeatable oneness and context of his life. It does not mean to underestimate objective biological findings and results of instrumentally investigation, but their implanting into the complex network of consequences of the patient's life in order to choose the most appropriate methods of the care of the individual in healthiness and disease.

  14. Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives

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

    Jagiello, Karolina; Grzonkowska, Monika; Swirog, Marta

    In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure–Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure–Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide themore » recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner.« less

  15. Prelude to corneal tissue engineering – Gaining control of collagen organization

    PubMed Central

    Ruberti, Jeffrey W.; Zieske, James D.

    2012-01-01

    By most standard engineering practice principles, it is premature to credibly discuss the “engineering” of a human cornea. A professional design engineer would assert that we still do not know what a cornea is (and correctly so), therefore we cannot possibly build one. The proof resides in the fact that there are no clinically viable corneas based on classical tissue engineering methods available. This is possibly because tissue engineering in the classical sense (seeding a degradable scaffolding with a population synthetically active cells) does not produce conditions which support the generation of organized tissue. Alternative approaches to the problem are in their infancy and include the methods which attempt to recapitulate development or to produce corneal stromal analogs de novo which require minimal remodeling. Nonetheless, tissue engineering efforts, which have been focused on producing the fundamental functional component of a cornea (organized alternating arrays of collagen or “lamellae”) may have already provided valuable new insights and tools relevant to development, growth, remodeling and pathologies associated with connective tissue in general. This is because engineers ask a fundamentally different question (How can that be done?) than do biological scientists (How is that done?). The difference in inquiry has prompted us to closely examine (and to mimic) development as well as investigate collagen physicochemical behavior so that we may exert control over organization both in cell-culture (in vitro) and on the benchtop (de novo). Our initial results indicate that reproducing corneal stroma-like local and long-range organization of collagen may be simpler than we anticipated while controlling spacing and fibril morphology remains difficult, but perhaps not impossible in the (reasonably) near term. PMID:18775789

  16. Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation

    PubMed Central

    Zahn, Dirk

    2015-01-01

    Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation. PMID:25914369

  17. Sensing in tissue bioreactors

    NASA Astrophysics Data System (ADS)

    Rolfe, P.

    2006-03-01

    Specialized sensing and measurement instruments are under development to aid the controlled culture of cells in bioreactors for the fabrication of biological tissues. Precisely defined physical and chemical conditions are needed for the correct culture of the many cell-tissue types now being studied, including chondrocytes (cartilage), vascular endothelial cells and smooth muscle cells (blood vessels), fibroblasts, hepatocytes (liver) and receptor neurones. Cell and tissue culture processes are dynamic and therefore, optimal control requires monitoring of the key process variables. Chemical and physical sensing is approached in this paper with the aim of enabling automatic optimal control, based on classical cell growth models, to be achieved. Non-invasive sensing is performed via the bioreactor wall, invasive sensing with probes placed inside the cell culture chamber and indirect monitoring using analysis within a shunt or a sampling chamber. Electroanalytical and photonics-based systems are described. Chemical sensing for gases, ions, metabolites, certain hormones and proteins, is under development. Spectroscopic analysis of the culture medium is used for measurement of glucose and for proteins that are markers of cell biosynthetic behaviour. Optical interrogation of cells and tissues is also investigated for structural analysis based on scatter.

  18. DNA - peptide polyelectrolyte complexes: Phase control by hybridization

    NASA Astrophysics Data System (ADS)

    Vieregg, Jeffrey; Lueckheide, Michael; Marciel, Amanda; Leon, Lorraine; Tirrell, Matthew

    DNA is one of the most highly-charged molecules known, and interacts strongly with charged molecules in the cell. Condensation of long double-stranded DNA is one of the classic problems of biophysics, but the polyelectrolyte behavior of short and/or single-stranded nucleic acids has attracted far less study despite its importance for both biological and engineered systems. We report here studies of DNA oligonucleotides complexed with cationic peptides and polyamines. As seen previously for longer sequences, double-stranded oligonucleotides form solid precipitates, but single-stranded oligonucleotides instead undergo liquid-liquid phase separation to form coacervate droplets. Complexed oligonucleotides remain competent for hybridization, and display sequence-dependent environmental response. We observe similar behavior for RNA oligonucleotides, and methylphosphonate substitution of the DNA backbone indicates that nucleic acid charge density controls whether liquid or solid complexes are formed. Liquid-liquid phase separations of this type have been implicated in formation of membraneless organelles in vivo, and have been suggested as protocells in early life scenarios; oligonucleotides offer an excellent method to probe the physics controlling these phenomena.

  19. The concept of "buffering" in systems and control theory: from metaphor to math.

    PubMed

    Schmitt, Bernhard M

    2004-10-04

    The paradigm of "buffering" is used increasingly for the description of diverse "systemic" phenomena encountered in evolutionary genetics, ecology, integrative physiology, and other areas. However, in this new context, the paradigm has not yet matured into a truly quantitative concept inasmuch as it lacks a corresponding quantitative measure of "systems-level buffering strength". Here, I develop such measures on the basis of a formal and general approach to the quantitation of buffering action. "Systems-level buffering" is shown to be synonymous with "disturbance rejection" in feedback-control systems, and can be quantitated by means of dimensionless proportions between partial flows in two-partitioned systems. The units allow either the time-independent, "static" buffering properties or the time-dependent, "dynamic" ones to be measured. Analogous to this "resistance to change", one can define and measure the "conductance to change"; this quantity corresponds to "set-point tracking" in feedback-control systems. Together, these units provide a systematic framework for the quantitation of buffering action in systems biology, and reveal the common principle behind systems-level buffering, classical acid-base buffering, and multiple other manifestations of buffering.

  20. Student Support for Research in Hierarchical Control and Trajectory Planning

    NASA Technical Reports Server (NTRS)

    Martin, Clyde F.

    1999-01-01

    Generally, classical polynomial splines tend to exhibit unwanted undulations. In this work, we discuss a technique, based on control principles, for eliminating these undulations and increasing the smoothness properties of the spline interpolants. We give a generalization of the classical polynomial splines and show that this generalization is, in fact, a family of splines that covers the broad spectrum of polynomial, trigonometric and exponential splines. A particular element in this family is determined by the appropriate control data. It is shown that this technique is easy to implement. Several numerical and curve-fitting examples are given to illustrate the advantages of this technique over the classical approach. Finally, we discuss the convergence properties of the interpolant.

  1. Evolutionary Effect on the Embodied Beauty of Landscape Architectures.

    PubMed

    Zhang, Wei; Tang, Xiaoxiang; He, Xianyou; Chen, Guangyao

    2018-01-01

    According to the framework of evolutionary aesthetics, a sense of beauty is related to environmental adaptation and plasticity of human beings, which has adaptive value and biological foundations. Prior studies have demonstrated that organisms derive benefits from the landscape. In this study, we investigated whether the benefits of landscape might elicit a stronger sense of beauty and what the nature of this sense of beauty is. In two experiments, when viewing classical landscape and nonlandscape architectures photographs, participants rated the aesthetic scores (Experiment 1) and had a two-alternative forced choice aesthetic judgment by pressing the reaction button located near to (15 cm) or far from (45 cm) the presenting stimuli (Experiment 2). The results showed that reaction of aesthetic ratings for classical landscape architectures was faster than those of classical nonlandscape architectures. Furthermore, only the reaction of beautiful judgment of classical landscape architecture photograph was significantly faster when the reaction button was in the near position to the presenting photograph than those in the position of far away from the presenting photograph. This finding suggests a facilitated effect for the aesthetic perception of classical landscape architectures due to their corresponding components including water and green plants with strong evolutionary implications. Furthermore, this sense of beauty for classical landscape architectures might be the embodied approach to beauty based on the viewpoint of evolutionary aesthetics and embodied cognition.

  2. Recoding structural glycoprotein E2 in classical swine fever virus (CSFV) produces complete virus attenuation in swine and protects infected animals against disease

    USDA-ARS?s Scientific Manuscript database

    Controlling classical swine fever (CSF) involves vaccination in endemic regions and preemptive slaughter of infected swine herds during epidemics. Generally, live attenuated vaccines induce solid immunity. Using diverse approaches, reverse genetics has been useful in developing classical swine fever...

  3. A model for one-dimensional morphoelasticity and its application to fibroblast-populated collagen lattices.

    PubMed

    Menon, Shakti N; Hall, Cameron L; McCue, Scott W; McElwain, D L Sean

    2017-10-01

    The mechanical behaviour of solid biological tissues has long been described using models based on classical continuum mechanics. However, the classical continuum theories of elasticity and viscoelasticity cannot easily capture the continual remodelling and associated structural changes in biological tissues. Furthermore, models drawn from plasticity theory are difficult to apply and interpret in this context, where there is no equivalent of a yield stress or flow rule. In this work, we describe a novel one-dimensional mathematical model of tissue remodelling based on the multiplicative decomposition of the deformation gradient. We express the mechanical effects of remodelling as an evolution equation for the effective strain, a measure of the difference between the current state and a hypothetical mechanically relaxed state of the tissue. This morphoelastic model combines the simplicity and interpretability of classical viscoelastic models with the versatility of plasticity theory. A novel feature of our model is that while most models describe growth as a continuous quantity, here we begin with discrete cells and develop a continuum representation of lattice remodelling based on an appropriate limit of the behaviour of discrete cells. To demonstrate the utility of our approach, we use this framework to capture qualitative aspects of the continual remodelling observed in fibroblast-populated collagen lattices, in particular its contraction and its subsequent sudden re-expansion when remodelling is interrupted.

  4. Personality Theories for the 21st Century

    ERIC Educational Resources Information Center

    McCrae, Robert R.

    2011-01-01

    Classic personality theories, although intriguing, are outdated. The five-factor model of personality traits reinvigorated personality research, and the resulting findings spurred a new generation of personality theories. These theories assign a central place to traits and acknowledge the crucial role of evolved biology in shaping human…

  5. ECOTOXICOGENOMICS: LINKAGES BETWEEN EXPOSURE AND EFFECTS IN ASSESSING RISKS OF AQUATIC CONTAMINANTS TO FISH (JOURNAL ARTICLE)

    EPA Science Inventory

    Understanding the biological effects of exposures to chemicals in the environment relies on classical methods and emerging technologies in the areas of genomics, proteomics, and metabonomics. Linkages between the historical and newer toxicological tools are currently being devel...

  6. Substance P-immunoreactive nerves in endobronchial biopsies in cough-variant asthma and classic asthma.

    PubMed

    Lee, Sang Yeub; Kim, Min Kyung; Shin, Chol; Shim, Jae Jeong; Kim, Han Kyeom; Kang, Kyung Ho; Yoo, Se Hwa; In, Kwang Ho

    2003-01-01

    Unlike classic asthma, cough-variant asthma does not show any evidence of airway obstruction. The main symptom is a dry cough with little known pathophysiology. Hypersensitivity of the cough receptors in cough-variant asthma and an increase in the sensory nerve density of the airway epithelium in persistent dry cough patients have been reported. Therefore, it is possible that there is a higher sensory nerve density in cough-variant asthma patients than in classic asthma patients. This study was undertaken to compare the substance P (SP)-immunoreactive nerve density in mucosal biopsies of cough-variant asthma patients, classic asthma patients, and in control subjects. Bronchoscopic biopsies were performed in 6 cough-variant asthma patients, 14 classic asthma patients, and 5 normal controls. The tissues obtained were stained immunohistochemically. The SP-immunoreactive nerve density was measured in the bronchial epithelium using a light microscope at 400 x magnification. SP- immunoreactive nerve density for the cough-variant asthma group was significantly higher than that of the classic asthma group (p = 0.001), and of the normal control group (p = 0.006). It is possible that a sensory nerve abnormality within the airway may be related to hypersensitivity of the cough receptor, and that this may be one of the pathophysiologies of cough-variant asthma. Copyright 2003 S. Karger AG, Basel

  7. Synthetic biology: new engineering rules for an emerging discipline

    PubMed Central

    Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

    2006-01-01

    Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development. PMID:16738572

  8. Synthetic biology: new engineering rules for an emerging discipline.

    PubMed

    Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

    2006-01-01

    Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

  9. Biologically sensitive field-effect transistors: from ISFETs to NanoFETs.

    PubMed

    Pachauri, Vivek; Ingebrandt, Sven

    2016-06-30

    Biologically sensitive field-effect transistors (BioFETs) are one of the most abundant classes of electronic sensors for biomolecular detection. Most of the time these sensors are realized as classical ion-sensitive field-effect transistors (ISFETs) having non-metallized gate dielectrics facing an electrolyte solution. In ISFETs, a semiconductor material is used as the active transducer element covered by a gate dielectric layer which is electronically sensitive to the (bio-)chemical changes that occur on its surface. This review will provide a brief overview of the history of ISFET biosensors with general operation concepts and sensing mechanisms. We also discuss silicon nanowire-based ISFETs (SiNW FETs) as the modern nanoscale version of classical ISFETs, as well as strategies to functionalize them with biologically sensitive layers. We include in our discussion other ISFET types based on nanomaterials such as carbon nanotubes, metal oxides and so on. The latest examples of highly sensitive label-free detection of deoxyribonucleic acid (DNA) molecules using SiNW FETs and single-cell recordings for drug screening and other applications of ISFETs will be highlighted. Finally, we suggest new device platforms and newly developed, miniaturized read-out tools with multichannel potentiometric and impedimetric measurement capabilities for future biomedical applications. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  10. Biologically sensitive field-effect transistors: from ISFETs to NanoFETs

    PubMed Central

    Pachauri, Vivek

    2016-01-01

    Biologically sensitive field-effect transistors (BioFETs) are one of the most abundant classes of electronic sensors for biomolecular detection. Most of the time these sensors are realized as classical ion-sensitive field-effect transistors (ISFETs) having non-metallized gate dielectrics facing an electrolyte solution. In ISFETs, a semiconductor material is used as the active transducer element covered by a gate dielectric layer which is electronically sensitive to the (bio-)chemical changes that occur on its surface. This review will provide a brief overview of the history of ISFET biosensors with general operation concepts and sensing mechanisms. We also discuss silicon nanowire-based ISFETs (SiNW FETs) as the modern nanoscale version of classical ISFETs, as well as strategies to functionalize them with biologically sensitive layers. We include in our discussion other ISFET types based on nanomaterials such as carbon nanotubes, metal oxides and so on. The latest examples of highly sensitive label-free detection of deoxyribonucleic acid (DNA) molecules using SiNW FETs and single-cell recordings for drug screening and other applications of ISFETs will be highlighted. Finally, we suggest new device platforms and newly developed, miniaturized read-out tools with multichannel potentiometric and impedimetric measurement capabilities for future biomedical applications. PMID:27365038

  11. Host Range Testing of Diaphorencyrtus aligarhensis (Hymenoptera: Encyrtidae) for Use in Classical Biological Control of Diaphorina citri (Hemiptera: Liviidae) in California.

    PubMed

    Bistline-East, Allison; Pandey, Raju; Kececi, Mehmet; Hoddle, Mark S

    2015-06-01

    Host range tests for Diaphorencyrtus aligarhensis (Shafee, Alam, & Agarwal) (Hymenoptera: Encyrtidae), an endoparasitoid of Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), sourced from Punjab Pakistan, were conducted in quarantine at the University of California, Riverside, CA. Seven nontarget psyllid species representing four psyllid families were exposed to mated D. aligarhensis females in four different treatment types: 1) short sequential no-choice treatments, 2) prolonged sequential no-choice treatments, 3) prolonged no-choice static treatments, and 4) choice treatments. Selection of nontarget psyllid species was based on phylogenetic proximity to D. citri, likelihood of being encountered by D. aligarhensis in the prospective release areas in California, and psyllid species in biological control of invasive weeds. D. aligarhensis exhibited high host affinity to D. citri, and only parasitized one nontarget species, the pestiferous potato psyllid, Bactericera cockerelli (Sulc), at low levels (<14%). Based on the results of this study, we conclude that D. aligarhensis has a narrow host range and exhibits a high level of host specificity, as it shows a significant attack preference for the target pest, D. citri. Results presented here suggest D. aligarhensis poses minimal risk to nontarget psyllid species in California. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions.

    PubMed

    Beckmann, Benedikt M; Castello, Alfredo; Medenbach, Jan

    2016-06-01

    Post-transcriptional regulation of gene expression plays a critical role in almost all cellular processes. Regulation occurs mostly by RNA-binding proteins (RBPs) that recognise RNA elements and form ribonucleoproteins (RNPs) to control RNA metabolism from synthesis to decay. Recently, the repertoire of RBPs was significantly expanded owing to methodological advances such as RNA interactome capture. The newly identified RNA binders are involved in diverse biological processes and belong to a broad spectrum of protein families, many of them exhibiting enzymatic activities. This suggests the existence of an extensive crosstalk between RNA biology and other, in principle unrelated, cell functions such as intermediary metabolism. Unexpectedly, hundreds of new RBPs do not contain identifiable RNA-binding domains (RBDs), raising the question of how they interact with RNA. Despite the many functions that have been attributed to RNA, our understanding of RNPs is still mostly governed by a rather protein-centric view, leading to the idea that proteins have evolved to bind to and regulate RNA and not vice versa. However, RNPs formed by an RNA-driven interaction mechanism (RNA-determined RNPs) are abundant and offer an alternative explanation for the surprising lack of classical RBDs in many RNA-interacting proteins. Moreover, RNAs can act as scaffolds to orchestrate and organise protein networks and directly control their activity, suggesting that nucleic acids might play an important regulatory role in many cellular processes, including metabolism.

  13. Citation classics in neuro-oncology: assessment of historical trends and scientific progress.

    PubMed

    Hachem, Laureen D; Mansouri, Alireza; Juraschka, Kyle; Taslimi, Shervin; Pirouzmand, Farhad; Zadeh, Gelareh

    2017-09-01

    Citation classics represent the highest cited works in a field and are often regarded as the most influential literature. Analyzing thematic trends in citation classics across eras enables recognition of important historical advances within a field. We present the first analysis of the citation classics in neuro-oncology. The Web of Science database was searched using terms relevant to "neuro-oncology." Articles with >400 citations were identified and the top 100 cited articles were evaluated. The top 100 neuro-oncology citation classics consisted of 43 clinical studies (17 retrospective, 10 prospective, 16 randomized trials), 43 laboratory investigations, 8 reviews/meta-analyses, and 6 guidelines/consensus statements. Articles were classified into 4 themes: 13 pertained to tumor classification, 37 to tumor pathogenesis/clinical presentation, 6 to imaging, 44 to therapy (15 chemotherapy, 10 radiotherapy, 5 surgery, 14 new agents). Gliomas were the most common tumor type examined, with 70 articles. There was a significant increase in the number of citation classics in the late 1990s, which was paralleled by an increase in studies examining tumor pathogenesis, chemotherapy, and new agents along with laboratory and randomized studies. The majority of citation classics in neuro-oncology are related to gliomas and pertain to tumor pathogenesis and treatment. The rise in citation classics in recent years investigating tumor biology, new treatment agents, and chemotherapeutics may reflect increasing scientific interest in nonsurgical treatments for CNS tumors and the need for fundamental investigations into disease processes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

  14. Cisgenics - A Sustainable Approach for Crop Improvement

    PubMed Central

    Telem, R.S.; Wani, Shabir. H.; Singh, N.B.; Nandini, R.; Sadhukhan, R.; Bhattacharya, S.; Mandal, N.

    2013-01-01

    The implication of molecular biology in crop improvement is now more than three decades old. Not surprisingly, technology has moved on, and there are a number of new techniques that may or may not come under the genetically modified (GM) banner and, therefore, GM regulations. In cisgenic technology, cisgenes from crossable plants are used and it is a single procedure of gene introduction whereby the problem of linkage drag of other genes is overcome. The gene used in cisgenic approach is similar compared with classical breeding and cisgenic plant should be treated equally as classically bred plant and differently from transgenic plants. Therefore, it offers a sturdy reference to treat cisgenic plants similarly as classically bred plants, by exemption of cisgenesis from the current GMO legislations. This review covers the implications of cisgenesis towards the sustainable development in the genetic improvement of crops and considers the prospects for the technology. PMID:24396278

  15. Mycotoxin Decontamination of Food: Cold Atmospheric Pressure Plasma versus "Classic" Decontamination.

    PubMed

    Hojnik, Nataša; Cvelbar, Uroš; Tavčar-Kalcher, Gabrijela; Walsh, James L; Križaj, Igor

    2017-04-28

    Mycotoxins are secondary metabolites produced by several filamentous fungi, which frequently contaminate our food, and can result in human diseases affecting vital systems such as the nervous and immune systems. They can also trigger various forms of cancer. Intensive food production is contributing to incorrect handling, transport and storage of the food, resulting in increased levels of mycotoxin contamination. Mycotoxins are structurally very diverse molecules necessitating versatile food decontamination approaches, which are grouped into physical, chemical and biological techniques. In this review, a new and promising approach involving the use of cold atmospheric pressure plasma is considered, which may overcome multiple weaknesses associated with the classical methods. In addition to its mycotoxin destruction efficiency, cold atmospheric pressure plasma is cost effective, ecologically neutral and has a negligible effect on the quality of food products following treatment in comparison to classical methods.

  16. Effectiveness of different exercises and stretching physiotherapy on pain and movement in patellofemoral pain syndrome: a randomized controlled trial.

    PubMed

    Moyano, F Revelles; Valenza, M C; Martin, L Martin; Caballero, Y Castellote; Gonzalez-Jimenez, E; Demet, G Valenza

    2013-05-01

    To compare the effectiveness of proprioceptive neuromuscular facilitation combined with exercise, classic stretching physiotherapy intervention, and educational intervention at improving patient function and pain in patients with patellofemoral pain syndrome. Randomized, controlled, blind trial over four months. Urban population, Spain. Patients undergoing primary care for retropatellar pain. Subjects were allocated on three different treatment options: a proprioceptive neuromuscular facilitation and aerobic exercise group, a classic stretching group, and a control treatment were applied over four months under the supervision of a physiotherapist. Knee Society Score, pain reported (Visual analogue scale) and knee range of motion. Assessments were completed at baseline and after four months. 74 patients were enrolled in the study and distributed between groups. Both the proprioceptive neuromuscular facilitation and classic stretching group showed significant changes in all variables after four months intervention (p < 0.001). The difference in mean Kujala knee score changes between groups (classic stretching group vs. proprioceptive neuromuscular facilitation group vs. control group) at four months was -24.05 (95% confidence interval (CI) -30.19, -17.90), p ≤ 0.001; vs. -39.03 (95% confidence interval (CI) -42.5, -35.5), p ≤ 0.001; vs. -0.238 (95% confidence interval (CI) -1.2, 0.726), p = 0.621, respectively. A proprioceptive neuromuscular facilitation intervention protocol combined with aerobic exercise showed a better outcome than a classic stretching protocol after four months.

  17. Fitness extraction and the conceptual foundations of political biology.

    PubMed

    Boari, Mircea

    2005-01-01

    In well known formulations, political science, classical and neoclassical economics, and political economy have recognized as foundational a human impulse toward self-preservation. To employ this concept, modern social-sciences theorists have made simplifying assumptions about human nature and have then built elaborately upon their more incisive simplifications. Advances in biology, including advances in evolutionary theory, notably inclusive-fitness theory, have for decades now encouraged the reconsideration of such assumptions and, more ambitiously, the reconciliation of the social and life sciences. I ask if this reconciliation is feasible and test a path to the unification of politics and biology, called here "political biology." Two new notions, "fitness extraction" and "fitness exchange," are defined, then differentiated from each other, and lastly contrasted to cooperative gaming, the putative essential element of economics.

  18. Evaluation of movement restriction zone sizes in controlling classical swine fever outbreaks

    USDA-ARS?s Scientific Manuscript database

    The objective of this study was to compare the movement restriction zone sizes of 3-km, 5-km, 9-km, and 11-km with that of 7-km in controlling a classical swine fever (CSF) outbreak. Three assumptions of compliance level were considered: baseline, baseline ±10%, and baseline ±15%. The compliance lev...

  19. A brief overview of current relationships of geography, statistics, and taxonomy with the classical integrated control concept

    USDA-ARS?s Scientific Manuscript database

    A classic paper on the integrated control concept appeared in the later part of the 1950’s, led by Vernon Stern, Ray Smith, Robert van den Bosch, and Kenneth Hagen. Numerous concepts and definitions were formulated at that time. In this presentation, a short philosophical summary will be presented...

  20. Vaccine Efficacy Against a New Avian Influenza (H9N2) Field Isolate from the Middle East (Serology and Challenge Studies).

    PubMed

    Gharaibeh, Saad; Amareen, Shadi

    2016-05-01

    Avian influenza subtype H9N2 is endemic in many countries in the Middle East. The reported prevalence of infection was variable between countries and ranged from 28.7% in Tunisia to 71% in Jordan. Several commercial killed whole-virus vaccine products are used as monovalent or bivalent mixed with Newcastle disease virus. Recently, we have noticed that many of the vaccinated broiler flocks did not show a production advantage over nonvaccinated flocks in the field. A new avian influenza field virus (H9N2) was isolated from these vaccinated and infected broiler flocks in 2013. This virus had 89.1% similarity of its hemagglutinin (HA) gene to the classical virus used for manufacturing the classical vaccine. Inactivated autogenous vaccine was manufactured from this new field isolate to investigate its serological response and protection in specific-pathogen-free (SPF) and breeder-male chickens compared to the classical vaccine. Oropharyngeal virus shedding of vaccinated breeder-male chickens was evaluated at 3, 9, 10, and 14 days postchallenge (DPC). Percentage of chickens shedding the virus at 3 DPC was 64%, 50%, and 64% in the classical vaccine group, autogenous vaccine group, and the control challenged group, respectively. At 7 DPC percentage of virus shedding was 42%, 7%, and 64% in the classical vaccine group, autogenous vaccine group, and the control challenged group, respectively. At 10 DPC only 9% of classical vaccine group was shedding the virus and there was no virus shedding in any of the groups at 14 DPC. There was statistical significance difference (P < 0.05) in shedding only at 7 DPC between the autogenous vaccine group and the other two groups. At 42 days of age (14 DPC), average body weight was 2.720, 2.745, 2.290, and 2.760 kg for the classical vaccine group, autogenous vaccine group, control challenged group, and control unchallenged group, respectively. Only the control challenged group had significantly (P < 0.05) lower average body weight. In another experiment, vaccinated SPF chicks had hemagglutination inhibition (HI) geometric mean titers (GMTs), with classical antigen, of 8.7 and 3.1 log 2 for classical and autogenous vaccine groups, respectively. When the autogenous antigen was used for HI, GMTs were 6.0 and 8.1 log 2, respectively. Both vaccines protected against body weight suppression after challenge. However, autogenous vaccine elicited significantly higher HI titer and reduced viral shedding at 7 DPC. In conclusion, it is important to revise the vaccine virus strains used in each region to protect against and control infection from new field strains. Further field experiments are needed to demonstrate the efficacy of new vaccines under field conditions.

  1. Difficult Diagnosis between B Cell Lymphoma and Classical Hodgkin's Lymphoma.

    PubMed

    Rentas Torres, Yaixa; Rodríguez-López, Joshua L; Valentin, Maria; Silva, Hector

    2015-01-01

    Although primary mediastinal large B-cell lymphoma and classic Hodgkin lymphoma of nodular sclerosis type are distinct disease, they share several clinical characteristics and biologic features. However, there are mediastinal lymphomas that not fit in either category. These types of lymphomas are recognized as mediastinal gray zone lymphomas. Gray zone lymphomas are lymphatic tumors that cannot be assigned to a defined lymphoma entity due to morphological, clinical, or genetic reasons. In this report, we present a case of a 22 year-old-Hispanic-female diagnosed with B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Hodgkin lymphoma.

  2. Imaging learning and memory: classical conditioning.

    PubMed

    Schreurs, B G; Alkon, D L

    2001-12-15

    The search for the biological basis of learning and memory has, until recently, been constrained by the limits of technology to classic anatomic and electrophysiologic studies. With the advent of functional imaging, we have begun to delve into what, for many, was a "black box." We review several different types of imaging experiments, including steady state animal experiments that image the functional labeling of fixed tissues, and dynamic human studies based on functional imaging of the intact brain during learning. The data suggest that learning and memory involve a surprising conservation of mechanisms and the integrated networking of a number of structures and processes. Copyright 2001 Wiley-Liss, Inc.

  3. Time Hierarchies and Model Reduction in Canonical Non-linear Models

    PubMed Central

    Löwe, Hannes; Kremling, Andreas; Marin-Sanguino, Alberto

    2016-01-01

    The time-scale hierarchies of a very general class of models in differential equations is analyzed. Classical methods for model reduction and time-scale analysis have been adapted to this formalism and a complementary method is proposed. A unified theoretical treatment shows how the structure of the system can be much better understood by inspection of two sets of singular values: one related to the stoichiometric structure of the system and another to its kinetics. The methods are exemplified first through a toy model, then a large synthetic network and finally with numeric simulations of three classical benchmark models of real biological systems. PMID:27708665

  4. Successful technologies and approaches used to develop and manage resistance against crop diseases and pests

    USDA-ARS?s Scientific Manuscript database

    Food security is highly dependent on many factors including biological, climate related, and political. Soon after Mendel showed that phenotypic traits could be inherited through hybridization, scientists have been using classical genetics to increase crop production. Part of the increase in crop pr...

  5. A "Hands on" Strategy for Teaching Genetic Algorithms to Undergraduates

    ERIC Educational Resources Information Center

    Venables, Anne; Tan, Grace

    2007-01-01

    Genetic algorithms (GAs) are a problem solving strategy that uses stochastic search. Since their introduction (Holland, 1975), GAs have proven to be particularly useful for solving problems that are "intractable" using classical methods. The language of genetic algorithms (GAs) is heavily laced with biological metaphors from evolutionary…

  6. SIX1 Oncoprotein Promotes Abnormal Uterine Basal Cell Development in Mice Exposed Neonatally to Diethylstilbestrol

    EPA Science Inventory

    In a classical model of latent hormonal carcinogenesis, exposing mice on neonatal days 1-5 to the synthetic estrogen diethylstilbestrol (DES; 1 mg/kg/day) results in high incidence of uterine carcinoma. However, the biological mechanisms driving DES-induced carcinogenesis remain ...

  7. SIX1 oncoprotein is necessary for abnormal uterine basal cell development in mice exposed neonatally to DES

    EPA Science Inventory

    In a classical model of latent hormonal carcinogenesis, exposing female mice on neonatal days 1-5 to the synthetic estrogen diethylstilbestrol (DES; 1 mg/kg/day) results in high incidence of uterine carcinoma. However, the biological mechanisms driving DES-induced carcinogenesis ...

  8. Enzyme Kinetics and the Michaelis-Menten Equation

    ERIC Educational Resources Information Center

    Biaglow, Andrew; Erickson, Keith; McMurran, Shawnee

    2010-01-01

    The concepts presented in this article represent the cornerstone of classical mathematical biology. The central problem of the article relates to enzyme kinetics, which is a biochemical system. However, the theoretical underpinnings that lead to the formation of systems of time-dependent ordinary differential equations have been applied widely to…

  9. Knockout of an outer membrane protein operon of anaplasma marginale by transposon mutagenesis

    USDA-ARS?s Scientific Manuscript database

    Large amounts of data generated by genomics, transcriptomics and proteomics technologies have increased our understanding of the biology of Anaplasma marginale. However, these data have also led to new assumptions that require testing, ideally through classic genetic mutation. One example is the def...

  10. Practical optimal flight control system design for helicopter aircraft. Volume 2: Software user's guide

    NASA Technical Reports Server (NTRS)

    Riedel, S. A.

    1979-01-01

    A method by which modern and classical control theory techniques may be integrated in a synergistic fashion and used in the design of practical flight control systems is presented. A general procedure is developed, and several illustrative examples are included. Emphasis is placed not only on the synthesis of the design, but on the assessment of the results as well. The first step is to establish the differences, distinguishing characteristics and connections between the modern and classical control theory approaches. Ultimately, this uncovers a relationship between bandwidth goals familiar in classical control and cost function weights in the equivalent optimal system. In order to obtain a practical optimal solution, it is also necessary to formulate the problem very carefully, and each choice of state, measurement and output variable must be judiciously considered. Once design goals are established and problem formulation completed, the control system is synthesized in a straightforward manner. Three steps are involved: filter-observer solution, regulator solution, and the combination of those two into the controller. Assessment of the controller permits and examination and expansion of the synthesis results.

  11. Applications of systems approaches in the study of rheumatic diseases.

    PubMed

    Kim, Ki-Jo; Lee, Saseong; Kim, Wan-Uk

    2015-03-01

    The complex interaction of molecules within a biological system constitutes a functional module. These modules are then acted upon by both internal and external factors, such as genetic and environmental stresses, which under certain conditions can manifest as complex disease phenotypes. Recent advances in high-throughput biological analyses, in combination with improved computational methods for data enrichment, functional annotation, and network visualization, have enabled a much deeper understanding of the mechanisms underlying important biological processes by identifying functional modules that are temporally and spatially perturbed in the context of disease development. Systems biology approaches such as these have produced compelling observations that would be impossible to replicate using classical methodologies, with greater insights expected as both the technology and methods improve in the coming years. Here, we examine the use of systems biology and network analysis in the study of a wide range of rheumatic diseases to better understand the underlying molecular and clinical features.

  12. Biological measurement beyond the quantum limit

    NASA Astrophysics Data System (ADS)

    Taylor, Michael; Janousek, Jiri; Daria, Vincent; Knittel, Joachim; Hage, Boris; Bachor, Hans; Bowen, Warwick

    2013-05-01

    Biology is an important frontier for quantum metrology, with quantum enhanced sensitivity allowing optical intensities to be lowered, and a consequent reduction in specimen damage and photochemical intrusion upon biological processes. Here we demonstrate the first biological measurement with precision surpassing the quantum noise limit. Naturally occurring lipid granules within living yeast cells were tracked in real time with sensitivity surpassing the quantum noise limit by 42% as they diffuse through the cytoplasm and interact with embedded polymer networks. This allowed dynamic mechanical properties of the cytoplasm to be determined with a 64% higher measurement rate than possible classically. To enable this, a new microscopy system was developed which is compatible with squeezed light, and which utilized a novel optical lock-in technique to allow quantum enhancement down to 10 Hz. This method is widely applicable, extending the reach of quantum enhanced measurement to many dynamic biological processes.

  13. Neural system modeling and simulation using Hybrid Functional Petri Net.

    PubMed

    Tang, Yin; Wang, Fei

    2012-02-01

    The Petri net formalism has been proved to be powerful in biological modeling. It not only boasts of a most intuitive graphical presentation but also combines the methods of classical systems biology with the discrete modeling technique. Hybrid Functional Petri Net (HFPN) was proposed specially for biological system modeling. An array of well-constructed biological models using HFPN yielded very interesting results. In this paper, we propose a method to represent neural system behavior, where biochemistry and electrical chemistry are both included using the Petri net formalism. We built a model for the adrenergic system using HFPN and employed quantitative analysis. Our simulation results match the biological data well, showing that the model is very effective. Predictions made on our model further manifest the modeling power of HFPN and improve the understanding of the adrenergic system. The file of our model and more results with their analysis are available in our supplementary material.

  14. Chemical regulators of plant hormones and their applications in basic research and agriculture.

    PubMed

    Jiang, Kai; Asami, Tadao

    2018-04-20

    Plant hormones are small molecules that play versatile roles in regulating plant growth, development, and responses to the environment. Classic methodologies, including genetics, analytic chemistry, biochemistry, and molecular biology, have contributed to the progress in plant hormone studies. In addition, chemical regulators of plant hormone functions have been important in such studies. Today, synthetic chemicals, including plant growth regulators, are used to study and manipulate biological systems, collectively referred to as chemical biology. Here, we summarize the available chemical regulators and their contributions to plant hormone studies. We also pose questions that remain to be addressed in plant hormone studies and that might be solved with the help of chemical regulators.

  15. Joining Forces: Integrating Proteomics and Cross-linking with the Mass Spectrometry of Intact Complexes*

    PubMed Central

    Stengel, Florian; Aebersold, Ruedi; Robinson, Carol V.

    2012-01-01

    Protein assemblies are critical for cellular function and understanding their physical organization is the key aim of structural biology. However, applying conventional structural biology approaches is challenging for transient, dynamic, or polydisperse assemblies. There is therefore a growing demand for hybrid technologies that are able to complement classical structural biology methods and thereby broaden our arsenal for the study of these important complexes. Exciting new developments in the field of mass spectrometry and proteomics have added a new dimension to the study of protein-protein interactions and protein complex architecture. In this review, we focus on how complementary mass spectrometry-based techniques can greatly facilitate structural understanding of protein assemblies. PMID:22180098

  16. Detection of Patient Subgroups with Differential Expression in Omics Data: A Comprehensive Comparison of Univariate Measures

    PubMed Central

    Ahrens, Maike; Turewicz, Michael; Casjens, Swaantje; May, Caroline; Pesch, Beate; Stephan, Christian; Woitalla, Dirk; Gold, Ralf; Brüning, Thomas; Meyer, Helmut E.

    2013-01-01

    Detection of yet unknown subgroups showing differential gene or protein expression is a frequent goal in the analysis of modern molecular data. Applications range from cancer biology over developmental biology to toxicology. Often a control and an experimental group are compared, and subgroups can be characterized by differential expression for only a subgroup-specific set of genes or proteins. Finding such genes and corresponding patient subgroups can help in understanding pathological pathways, diagnosis and defining drug targets. The size of the subgroup and the type of differential expression determine the optimal strategy for subgroup identification. To date, commonly used software packages hardly provide statistical tests and methods for the detection of such subgroups. Different univariate methods for subgroup detection are characterized and compared, both on simulated and on real data. We present an advanced design for simulation studies: Data is simulated under different distributional assumptions for the expression of the subgroup, and performance results are compared against theoretical upper bounds. For each distribution, different degrees of deviation from the majority of observations are considered for the subgroup. We evaluate classical approaches as well as various new suggestions in the context of omics data, including outlier sum, PADGE, and kurtosis. We also propose the new FisherSum score. ROC curve analysis and AUC values are used to quantify the ability of the methods to distinguish between genes or proteins with and without certain subgroup patterns. In general, FisherSum for small subgroups and -test for large subgroups achieve best results. We apply each method to a case-control study on Parkinson's disease and underline the biological benefit of the new method. PMID:24278130

  17. Hemoglobin mass and biological passport for the detection of autologous blood doping.

    PubMed

    Pottgiesser, Torben; Echteler, Tobias; Sottas, Pierre-Edouard; Umhau, Markus; Schumacher, Yorck Olaf

    2012-05-01

    The most promising attempt to reveal otherwise undetectable autologous blood doping is the Athlete Biological Passport enabling a longitudinal monitoring of hematological measures. Recently, the determination of hemoglobin mass (tHb) was suggested to be incorporated in the adaptive model of the Athlete Biological Passport. The purpose therefore was to evaluate the performance of tHb as part of the adaptive model for the detection of autologous blood transfusions in a longitudinal blinded study. Twenty-one subjects were divided into a doped group (n = 11) and a control group (n = 10). During the time course of a simulated cycling season (42 wk) including three major competitions (Classics, Grand Tour, World Championships), multiple autologous transfusions of erythrocyte concentrates were assigned in the doped group. A blinded investigator ordered up to 10 tHb measurements (carbon monoxide rebreathing) per subject, mimicking an intelligent doping testing approach in obtaining hematological data (tHb, OFFmass (novel marker including reticulocytes), and respective sequences) for the adaptive model. The final analysis included 199 of 206 overall tHb measurements. The use of tHb, OFFmass, and their sequences as markers of the adaptive model at the 99% specificity level allowed identification of 10 of 11 doped subjects (91% sensitivity) including one false positive in the control group. At the 99.9% specificity level, 8 of 11 subjects were identified without false positives (73% sensitivity). It seems that the problems of tHb determination by carbon monoxide rebreathing limit the application of this method in antidoping. Because of its potential to detect individual abnormalities associated with autologous blood transfusions shown in this study, a method for tHb determination that is compatible with today's standards of testing should be the focus of future research.

  18. Effect of Turkish classical music on blood pressure: a randomized controlled trial in hypertensive elderly patients.

    PubMed

    Bekiroğlu, Tansel; Ovayolu, Nimet; Ergün, Yusuf; Ekerbiçer, Hasan Çetin

    2013-06-01

    Existing studies suggest that music therapy can have favorable effects on hypertension and anxiety. We therefore set out to investigate the effect of Turkish classical music. To investigate whether Turkish classical music has positive effects on blood pressures and anxiety levels in elderly patients. This was a randomized controlled trial performed on 60 hypertensive patients living in a local elderly home in Adana, Turkey. Following the completion of a socio-demographic form for each patient, Hamilton anxiety scale was applied. Thereafter, the subjects were randomly divided into two equal-size groups and were allowed to either listen to Turkish classical music (music therapy group) or have a resting period (control group) for 25 min. The primary and secondary outcome measures were blood pressure and Hamilton anxiety scale scores, respectively. The mean reduction in systolic blood pressure was 13.00 mmHg in the music therapy group and 6.50 mmHg in the control group. The baseline adjusted between treatment group difference was not statistically significant (95% CI 6.80-9.36). The median reductions in diastolic blood pressures were 10 mmHg both in the music therapy and control groups. The between treatment group difference was not statistically significant (Mann-Whitney U test, P = 0.839). The mean reduction in HAMA-A was 1.63 in the music therapy group and 0.77 in the control group. The baseline adjusted between treatment group difference was not statistically significant (95% CI 0.82-1.92). The study demonstrated that both Turkish classical music and resting alone have positive effects on blood pressure in patients with hypertension. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. 7TH International Workshop on Laser Physics (LPHYS󈨦) Berlin, Germany July 6-10, 1998 Program and Book of Abstracts: Volume 2.

    DTIC Science & Technology

    1998-07-01

    Russia)"Laser refractometry of biological media" Tuesday, July 7 Chairs: S. Gonchukov (Russia) and D. Sliney (USA) A. Priezzhev (Moscow, Russia) 11.00...application to the evaluation of blood flow. Optics and Laser Technology, Vol.23, No.4, p.205, 1991. LASER REFRACTOMETRY OF BIOLOGICAL MEDIA S.A. Gonchukov...measuring (fast-action). Refractometry is a classical technique. The sensitivity of traditional measuring is usually 10-4-10-7. That’s no bad. But

  20. Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering.

    PubMed

    Teixeira, Ana P; Carinhas, Nuno; Dias, João M L; Cruz, Pedro; Alves, Paula M; Carrondo, Manuel J T; Oliveira, Rui

    2007-12-01

    Systems biology is an integrative science that aims at the global characterization of biological systems. Huge amounts of data regarding gene expression, proteins activity and metabolite concentrations are collected by designing systematic genetic or environmental perturbations. Then the challenge is to integrate such data in a global model in order to provide a global picture of the cell. The analysis of these data is largely dominated by nonparametric modelling tools. In contrast, classical bioprocess engineering has been primarily founded on first principles models, but it has systematically overlooked the details of the embedded biological system. The full complexity of biological systems is currently assumed by systems biology and this knowledge can now be taken by engineers to decide how to optimally design and operate their processes. This paper discusses possible methodologies for the integration of systems biology and bioprocess engineering with emphasis on applications involving animal cell cultures. At the mathematical systems level, the discussion is focused on hybrid semi-parametric systems as a way to bridge systems biology and bioprocess engineering.

  1. Statistics and dynamics of attractor networks with inter-correlated patterns

    NASA Astrophysics Data System (ADS)

    Kropff, E.

    2007-02-01

    In an embodied feature representation view, the semantic memory represents concepts in the brain by the associated activation of the features that describe it, each one of them processed in a differentiated region of the cortex. This system has been modeled with a Potts attractor network. Several studies of feature representation show that the correlation between patterns plays a crucial role in semantic memory. The present work focuses on two aspects of the effect of correlations in attractor networks. In first place, it assesses how a Potts network can store a set of patterns with non-trivial correlations between them. This is done through a simple and biologically plausible modification to the classical learning rule. In second place, it studies the complexity of latching transitions between attractor states, and how this complexity can be controlled.

  2. Diabetes mellitus in classical trigeminal neuralgia: A predisposing factor for its development.

    PubMed

    Xu, Zhenq; Zhang, Ping; Long, Li; He, Huiy; Zhang, Jianch; Sun, Shup

    2016-12-01

    A higher prevalence of diabetes mellitus in classical trigeminal neuralgia patients was observed in few pilot surveys. The study was aimed to investigate whether diabetes mellitus is a predisposing factor for developing trigeminal neuralgia. Patients with classical trigeminal neuralgia were enrolled in the case study group. The control group consisted of the same number of age- and gender-matched, randomly sampled subjects without trigeminal neuralgia. Characteristics of classical trigeminal neuralgia cases were analyzed. The prevalence of diabetes mellitus in the cases and controls was calculated using the Chi-square test. The onset age ranged from 31 to 93 in 256 patients affected classical trigeminal neuralgia (162 females; 94 males) with a peak age between the fifth and seventh decade; right-side involvement and mandibular branch affliction occurred at a greater frequency. 21.9% patients in the study group was affected by diabetes mellitus compared to 12.9% of controls. The increased prevalence of diabetes mellitus in the trigeminal neuralgia group was statistically significant (P=0.01). Diabetes is a risk factor to the development of classical trigeminal neuralgia, and nerve damage duing to hyperglycemia might be the linkage to the two diseases. More works should be done to consolidate the correlation and to clarify the underlying mechanism for the positive association which would provide new insight into the pathogenesis of trigeminal neuralgia and may open new therapeutic perspectives. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Pre-attentive auditory discrimination skill in Indian classical vocal musicians and non-musicians.

    PubMed

    Sanju, Himanshu Kumar; Kumar, Prawin

    2016-09-01

    To test for pre-attentive auditory discrimination skills in Indian classical vocal musicians and non-musicians. Mismatch negativity (MMN) was recorded to test for pre-attentive auditory discrimination skills with a pair of stimuli of /1000 Hz/ and /1100 Hz/, with /1000 Hz/ as the frequent stimulus and /1100 Hz/ as the infrequent stimulus. Onset, offset and peak latencies were the considered latency parameters, whereas peak amplitude and area under the curve were considered for amplitude analysis. Exactly 50 participants, out of which the experimental group had 25 adult Indian classical vocal musicians and 25 age-matched non-musicians served as the control group, were included in the study. Experimental group participants had a minimum professional music experience in Indian classic vocal music of 10 years. However, control group participants did not have any formal training in music. Descriptive statistics showed better waveform morphology in the experimental group as compared to the control. MANOVA showed significantly better onset latency, peak amplitude and area under the curve in the experimental group but no significant difference in the offset and peak latencies between the two groups. The present study probably points towards the enhancement of pre-attentive auditory discrimination skills in Indian classical vocal musicians compared to non-musicians. It indicates that Indian classical musical training enhances pre-attentive auditory discrimination skills in musicians, leading to higher peak amplitude and a greater area under the curve compared to non-musicians.

  4. Spatio-temporal dynamics of brain mechanisms in aversive classical conditioning: high-density event-related potential and brain electrical tomography analyses.

    PubMed

    Pizzagalli, Diego A; Greischar, Lawrence L; Davidson, Richard J

    2003-01-01

    Social cognition, including complex social judgments and attitudes, is shaped by individual learning experiences, where affect often plays a critical role. Aversive classical conditioning-a form of associative learning involving a relationship between a neutral event (conditioned stimulus, CS) and an aversive event (unconditioned stimulus, US)-represents a well-controlled paradigm to study how the acquisition of socially relevant knowledge influences behavior and the brain. Unraveling the temporal unfolding of brain mechanisms involved appears critical for an initial understanding about how social cognition operates. Here, 128-channel ERPs were recorded in 50 subjects during the acquisition phase of a differential aversive classical conditioning paradigm. The CS+ (two fearful faces) were paired 50% of the time with an aversive noise (CS upward arrow + /Paired), whereas in the remaining 50% they were not (CS upward arrow + /Unpaired); the CS- (two different fearful faces) were never paired with the noise. Scalp ERP analyses revealed differences between CS upward arrow + /Unpaired and CS- as early as approximately 120 ms post-stimulus. Tomographic source localization analyses revealed early activation modulated by the CS+ in the ventral visual pathway (e.g. fusiform gyrus, approximately 120 ms), right middle frontal gyrus (approximately 176 ms), and precuneus (approximately 240 ms). At approximately 120 ms, the CS- elicited increased activation in the left insula and left middle frontal gyrus. These findings not only confirm a critical role of prefrontal, insular, and precuneus regions in aversive conditioning, but they also suggest that biologically and socially salient information modulates activation at early stages of the information processing flow, and thus furnish initial insight about how affect and social judgments operate.

  5. Multistructure index in revealing complexity of regulatory mechanisms of human cardiovascular system at rest and orthostatic stress in healthy humans

    NASA Astrophysics Data System (ADS)

    Makowiec, Danuta; Graff, Beata; Struzik, Zbigniew R.

    2017-02-01

    Biological regulation is sufficiently complex to pose an enduring challenge for characterization of both its equilibrium and transient non-equilibrium dynamics. Two univariate but coupled observables, heart rate and systolic blood pressure, are commonly characterized in the benchmark example of the human cardiovascular regulatory system. Asymmetric distributions of accelerations and decelerations of heart rate, as well as rises and falls in systolic blood pressure, recorded in humans during a head-up tilt test provide insights into the dynamics of cardiovascular response to a rapid, controlled deregulation of the system's homeostasis. The baroreflex feedback loop is assumed to be the fundamental physiological mechanism for ensuring homeostatic blood supply to distant organs at rest and during orthostatic stress, captured in a classical beat-to-beat autoregressive model of baroreflex by de Boer et al. (1987). For model corroboration, a multistructure index statistic is proposed, seamlessly evaluating the size spectrum of magnitudes of neural reflexes such as baroreflex, responsible for maintaining the homeostatic dynamics. The multistructure index exposes a distinctly different dynamics of multiscale asymmetry between results obtained from real-life signals recorded from healthy subjects and those simulated using both the classical and perturbed versions of the model. Nonlinear effects observed suggest the pronounced presence of complex mechanisms resulting from baroreflex regulation when a human is at rest, which is aggravated in the system's response to orthostatic stress. Using our methodology of multistructure index, we therefore show a marked difference between model and real-life scenarios, which we attribute to multiscale asymmetry of non-linear origin in real-life signals, which we are not reproducible by the classical model.

  6. Biologic agents in the management of Hodgkin lymphoma.

    PubMed

    Rashidi, Armin; Bartlett, Nancy L

    2015-05-01

    The advent of biologic approaches for the treatment of solid tumors and hematologic malignancies has been a major accomplishment in oncology and a rapidly growing field of clinical and translational research in cancer therapeutics. Classical Hodgkin lymphoma (HL) is no exception. Although the investigation of biologic therapies in HL started decades ago, it has only recently flourished, largely because of the development of new monoclonal antibody drug conjugates and checkpoint inhibitors. Biologic therapies represent a potent treatment option that have produced durable remissions even in patients who have had multiple relapses or with refractory disease. This article reviews 8 major classes of biologic approaches that have been investigated in HL: monoclonal antibodies, immunotoxins, antibody-drug conjugates, radioimmunotherapy, adoptive immunotherapy, immunomodulators, chimeric antigen receptor T cells, and checkpoint inhibitors. An armamentarium of biologic therapies for HL that are well tolerated and potentially more effective is expected to be available in the near future. Copyright © 2015 by the National Comprehensive Cancer Network.

  7. Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

    PubMed

    Yin, Zekun; Lan, Haidong; Tan, Guangming; Lu, Mian; Vasilakos, Athanasios V; Liu, Weiguo

    2017-01-01

    The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.

  8. Event-Based Control Strategy for Mobile Robots in Wireless Environments.

    PubMed

    Socas, Rafael; Dormido, Sebastián; Dormido, Raquel; Fabregas, Ernesto

    2015-12-02

    In this paper, a new event-based control strategy for mobile robots is presented. It has been designed to work in wireless environments where a centralized controller has to interchange information with the robots over an RF (radio frequency) interface. The event-based architectures have been developed for differential wheeled robots, although they can be applied to other kinds of robots in a simple way. The solution has been checked over classical navigation algorithms, like wall following and obstacle avoidance, using scenarios with a unique or multiple robots. A comparison between the proposed architectures and the classical discrete-time strategy is also carried out. The experimental results shows that the proposed solution has a higher efficiency in communication resource usage than the classical discrete-time strategy with the same accuracy.

  9. Event-Based Control Strategy for Mobile Robots in Wireless Environments

    PubMed Central

    Socas, Rafael; Dormido, Sebastián; Dormido, Raquel; Fabregas, Ernesto

    2015-01-01

    In this paper, a new event-based control strategy for mobile robots is presented. It has been designed to work in wireless environments where a centralized controller has to interchange information with the robots over an RF (radio frequency) interface. The event-based architectures have been developed for differential wheeled robots, although they can be applied to other kinds of robots in a simple way. The solution has been checked over classical navigation algorithms, like wall following and obstacle avoidance, using scenarios with a unique or multiple robots. A comparison between the proposed architectures and the classical discrete-time strategy is also carried out. The experimental results shows that the proposed solution has a higher efficiency in communication resource usage than the classical discrete-time strategy with the same accuracy. PMID:26633412

  10. New perspectives in toxicological information management, and the role of ISSTOX databases in assessing chemical mutagenicity and carcinogenicity.

    PubMed

    Benigni, Romualdo; Battistelli, Chiara Laura; Bossa, Cecilia; Tcheremenskaia, Olga; Crettaz, Pierre

    2013-07-01

    Currently, the public has access to a variety of databases containing mutagenicity and carcinogenicity data. These resources are crucial for the toxicologists and regulators involved in the risk assessment of chemicals, which necessitates access to all the relevant literature, and the capability to search across toxicity databases using both biological and chemical criteria. Towards the larger goal of screening chemicals for a wide range of toxicity end points of potential interest, publicly available resources across a large spectrum of biological and chemical data space must be effectively harnessed with current and evolving information technologies (i.e. systematised, integrated and mined), if long-term screening and prediction objectives are to be achieved. A key to rapid progress in the field of chemical toxicity databases is that of combining information technology with the chemical structure as identifier of the molecules. This permits an enormous range of operations (e.g. retrieving chemicals or chemical classes, describing the content of databases, finding similar chemicals, crossing biological and chemical interrogations, etc.) that other more classical databases cannot allow. This article describes the progress in the technology of toxicity databases, including the concepts of Chemical Relational Database and Toxicological Standardized Controlled Vocabularies (Ontology). Then it describes the ISSTOX cluster of toxicological databases at the Istituto Superiore di Sanitá. It consists of freely available databases characterised by the use of modern information technologies and by curation of the quality of the biological data. Finally, this article provides examples of analyses and results made possible by ISSTOX.

  11. Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa

    NASA Astrophysics Data System (ADS)

    Deng, Zhaojie; Arsenault, Sam; Caranica, Cristian; Griffith, James; Zhu, Taotao; Al-Omari, Ahmad; Schüttler, Heinz-Bernd; Arnold, Jonathan; Mao, Leidong

    2016-10-01

    The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error). To overcome this stochasticity at the macroscopic level, cells must synchronize their oscillators. Using a classic measure of similarity in cell trajectories within droplets, the intraclass correlation (ICC), the synchronization surface ICC is measured on >25,000 cells as a function of the number of neighboring cells within a droplet and of time. The synchronization surface provides evidence that cells communicate, and synchronization varies with genotype.

  12. Organic-Inorganic Composites Toward Biomaterial Application.

    PubMed

    Miyazaki, Toshiki; Sugawara-Narutaki, Ayae; Ohtsuki, Chikara

    2015-01-01

    Bioactive ceramics are known to exhibit specific biological affinities and are able to show direct integration with surrounding bone when implanted in bony defects. However, their inadequate mechanical properties, such as low fracture toughness and high Young's modulus in comparison to natural bone, limit their clinical application. Bone is a kind of organic-inorganic composite where apatite nanocrystals are precipitated onto collagen fibre networks. Thus, one way to address these problems is to mimic the natural composition of bone by using bioactive ceramics via material designs based on organic-inorganic composites. In this chapter, the current research on the development of the various organic-inorganic composites designed for biomaterial applications has been reviewed. Various compounds such as calcium phosphate, calcium sulphate and calcium carbonate can be used for the inorganic phases to design composites with the desired mechanical and biological properties of bone. Not only classical mechanical mixing but also coating of the inorganic phase in aqueous conditions is available for the fabrication of such composites. Organic modifications using various polymers enable the control of the crystalline structure of the calcium carbonate in the composites. These approaches on the fabrication of organic-inorganic composites provide important options for biomedical materials with novel functions. © 2015 S. Karger AG, Basel.

  13. The Hippo-YAP signaling pathway and contact inhibition of growth

    PubMed Central

    Gumbiner, Barry M.; Kim, Nam-Gyun

    2014-01-01

    ABSTRACT The Hippo-YAP pathway mediates the control of cell proliferation by contact inhibition as well as other attributes of the physical state of cells in tissues. Several mechanisms sense the spatial and physical organization of cells, and function through distinct upstream modules to stimulate Hippo-YAP signaling: adherens junction or cadherin–catenin complexes, epithelial polarity and tight junction complexes, the FAT-Dachsous morphogen pathway, as well as cell shape, actomyosin or mechanotransduction. Soluble extracellular factors also regulate Hippo pathway signaling, often inhibiting its activity. Indeed, the Hippo pathway mediates a reciprocal relationship between contact inhibition and mitogenic signaling. As a result, cells at the edges of a colony, a wound in a tissue or a tumor are more sensitive to ambient levels of growth factors and more likely to proliferate, migrate or differentiate through a YAP and/or TAZ-dependent process. Thus, the Hippo-YAP pathway senses and responds to the physical organization of cells in tissues and coordinates these physical cues with classic growth-factor-mediated signaling pathways. This Commentary is focused on the biological significance of Hippo-YAP signaling and how upstream regulatory modules of the pathway interact to produce biological outcomes. PMID:24532814

  14. Synchronizing stochastic circadian oscillators in single cells of Neurospora crassa

    PubMed Central

    Deng, Zhaojie; Arsenault, Sam; Caranica, Cristian; Griffith, James; Zhu, Taotao; Al-Omari, Ahmad; Schüttler, Heinz-Bernd; Arnold, Jonathan; Mao, Leidong

    2016-01-01

    The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error). To overcome this stochasticity at the macroscopic level, cells must synchronize their oscillators. Using a classic measure of similarity in cell trajectories within droplets, the intraclass correlation (ICC), the synchronization surface ICC is measured on >25,000 cells as a function of the number of neighboring cells within a droplet and of time. The synchronization surface provides evidence that cells communicate, and synchronization varies with genotype. PMID:27786253

  15. The emerging role of bone marrow adipose tissue in bone health and dysfunction.

    PubMed

    Ambrosi, Thomas H; Schulz, Tim J

    2017-12-01

    Replacement of red hematopoietic bone marrow with yellow adipocyte-rich marrow is a conserved physiological process among mammals. The extent of this conversion is influenced by a wide array of pathological and non-pathological conditions. Of particular interest is the observation that some marrow adipocyte-inducing factors seem to oppose each other, for instance obesity and caloric restriction. Intriguingly, several important molecular characteristics of bone marrow adipose tissue (BMAT) are distinct from the classical depots of white and brown fat tissue. This depot of fat has recently emerged as an active part of the bone marrow niche that exerts paracrine and endocrine functions thereby controlling osteogenesis and hematopoiesis. While some functions of BMAT may be beneficial for metabolic adaptation and bone homeostasis, respectively, most findings assign bone fat a detrimental role during regenerative processes, such as hematopoiesis and osteogenesis. Thus, an improved understanding of the biological mechanisms leading to formation of BMAT, its molecular characteristics, and its physiological role in the bone marrow niche is warranted. Here we review the current understanding of BMAT biology and its potential implications for health and the development of pathological conditions.

  16. Perspectives of Physiology as a Discipline from Senior-Level Millennial-Generation Students

    ERIC Educational Resources Information Center

    Steury, Michael D.; Poteracki, James M.; Kelly, Kevin L.; Wehrwein, Erica A.

    2015-01-01

    In the last several decades, there has been a shift in the mindset of research structure from classical "systems or integrative biology" to more molecular focused "-omics" study. A recent topic of debate in physiological societies has been whether or not the "-omic" revolution has delivered in its promises in both…

  17. Why Trees Migrate So Fast: Confronting Theory with Dispersal Biology and the Paleorecord

    Treesearch

    James S. Clark

    1998-01-01

    Reid's paradox describes the fact that classical models cannot account for the rapid (102-103 yr-1) spread of trees at the end of the Pleistocene. I use field estimates of seed dispersal with an integrodifference equation and simulation models of population growth to show that dispersal data are...

  18. MendelWeb: An Electronic Science/Math/History Resource for the WWW.

    ERIC Educational Resources Information Center

    Blumberg, Roger B.

    This paper describes a hypermedia resource, called MendelWeb that integrates elementary biology, discrete mathematics, and the history of science. MendelWeb is constructed from Gregor Menders 1865 paper, "Experiments in Plant Hybridization". An English translation of Mendel's paper, which is considered to mark the birth of classical and…

  19. Polarization of Physics on Global Courses

    ERIC Educational Resources Information Center

    Alinea, Allan L.; Naylor, Wade

    2015-01-01

    Since October 2010, the Chemistry-Biology Combined Major Program, an international course taught in English at Osaka University, has been teaching small classes (no more than 20 in size). We present data from the Force Concept Inventory (FCI) given to first-year classical mechanics students (N = 47 students over three years) pre and post score,…

  20. The Teaching of the Natural Science Disciplines in the Schools

    ERIC Educational Resources Information Center

    Lisichkin, G. V.

    2007-01-01

    There are no fewer than three dozen scientific groups dealing with problems of the development of methods of teaching physics, chemistry, and biology in this country; they are working in pedagogical and classical universities and in institutes of the Russian Academy of Education. Innovative schoolteachers are involved in this endeavor as they…

  1. Logging the Heart with Microcomputer-Based Labs

    ERIC Educational Resources Information Center

    van Eijck, Michiel; Goedhart, Martin; Ellermeijer, Ton

    2005-01-01

    A single heartbeat is a complicated process. In Dutch upper secondary biology textbooks this process is illustrated by the classical Wiggers diagram, which usually shows different heart-related quantities, like voltage (ECG), blood pressure, and the heart sounds. It may help students to understand the nature of the Wiggers diagram if they perform…

  2. Shaping biological knowledge: applications in proteomics.

    PubMed

    Lisacek, F; Chichester, C; Gonnet, P; Jaillet, O; Kappus, S; Nikitin, F; Roland, P; Rossier, G; Truong, L; Appel, R

    2004-01-01

    The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies.

  3. Analysis of terahertz dielectric properties of pork tissue

    NASA Astrophysics Data System (ADS)

    Huang, Yuqing; Xie, Qiaoling; Sun, Ping

    2017-10-01

    Seeing that about 70% component of fresh biological tissues is water, many scientists try to use water models to describe the dielectric properties of biological tissues. The classical water dielectric models are Debye model, Double Debye model and Cole-Cole model. This work aims to determine a suitable model by comparing three models above with experimental data. These models are applied to fresh pork tissue. By means of least square method, the parameters of different models are fitted with the experimental data. Comparing different models on both dielectric function, the Cole-Cole model is verified the best to describe the experiments of pork tissue. The correction factor α of the Cole-Cole model is an important modification for biological tissues. So Cole-Cole model is supposed to be a priority selection to describe the dielectric properties for biological tissues in the terahertz range.

  4. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

    PubMed Central

    2016-01-01

    Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

  5. GPR30: a novel therapeutic target in estrogen-related disease.

    PubMed

    Prossnitz, Eric R; Sklar, Larry A; Oprea, Tudor I; Arterburn, Jeffrey B

    2008-03-01

    Estrogen is a crucial hormone in human physiology that regulates a multitude of biological processes. It is also an important target in many diseases such as cancer and skeletal, neurological and immunological conditions. The actions of estrogen have traditionally been ascribed to one of two closely related classical nuclear hormone receptors, ERalpha and ERbeta, which are best characterized for regulating gene expression. Recent studies have revealed the contribution of a novel estrogen receptor GPR30, which belongs to the family of seven-transmembrane G-protein-coupled receptors, to many of the rapid biological responses to estrogen. Many drugs, such as tamoxifen and fulvestrant, which seem to selectively inhibit the activities of the classical estrogen receptors, are in widespread clinical use. However, recent results indicate that these same drugs activate multiple cellular-signaling pathways via GPR30. Unraveling the pharmacological profiles and specificities of ERalpha, ERbeta and GPR30 will be vital for understanding not only the physiological roles of each receptor but also for the development of the next generation of receptor-specific drugs.

  6. Clozapine-induced systemic lupus erythematosus.

    PubMed

    Rami, Abu Fanne; Barkan, Daniel; Mevorach, Dror; Leitersdorf, Eran; Caraco, Yoseph

    2006-05-01

    To report a case of classic clozapine-induced systemic lupus erythematosus that also developed on rechallenge. A 32-year-old white woman diagnosed with schizophrenia presented in 1996 with clinical characteristics and laboratory markers consistent with drug-induced lupus (DIL). Clozapine, started 1 year prior, was withdrawn, with complete biological and clinical remission within 3 months. In 2004, 1 week after rechallenge with clozapine for uncontrolled schizophrenia, the patient developed clinical and biological signs and symptoms consistent with the diagnosis of DIL. Again, discontinuation of clozapine was followed by full remission within 2-3 months. DIL was first described more than 50 years ago, with multiple drugs implicated in the causation. Clozapine-induced lupus was reported recently, but does not meet the usual criteria for a diagnosis of DIL. We report a classic case of clozapine-induced lupus that, according to the Naranjo probability scale, demonstrates a highly probable relationship between DIL and clozapine. DIL demands a high index of suspicion for diagnosis. Although clozapine has an extensive safety profile, DIL must be considered as one of its serious adverse effects.

  7. An Application of Fuzzy Logic Control to a Classical Military Tracking Problem

    DTIC Science & Technology

    1994-05-19

    34, Fuzzy Sets and Systems, vol.4., 1980, pp.13-30. Berenji , Hamid R . and Pratap Khedkar. "Learning and Tuning Fuzzy Logic Controllers Through...A TRIDENT SCHOLAR PROJECT REPORT" NO. 222 "An Application of Fuzzy Logic Control to a Classical Military Tracking Problem" DTIC •S r F UNITED STATES...Zq qAvail andlor ____________________I__________ Dist SpecialDate USNA- 1531-2 REPORT DOCUMENTATION PAGE r •,,,op APmw OMB no. 0704.0188 ¢iQiiati~m.f

  8. The Soil Sink for Nitrous Oxide: Trivial Amount but Challenging Question

    NASA Astrophysics Data System (ADS)

    Davidson, E. A.; Savage, K. E.; Sihi, D.

    2015-12-01

    Net uptake of atmospheric nitrous oxide (N2O) has been observed sporadically for many years. Such observations have often been discounted as measurement error or noise, but they were reported frequently enough to gain some acceptance as valid. The advent of fast response field instruments with good sensitivity and precision has permitted confirmation that some soils can be small sinks of N2O. With regards to "closing the global N2O budget" the soil sink is trivial, because it is smaller than the error terms of most other budget components. Although not important from a global budget perspective, the existence of a soil sink for atmospheric N2O presents a fascinating challenge for understanding the physical, chemical, and biological processes that explain the sink. Reduction of N2O by classical biological denitrification requires reducing conditions generally found in wet soil, and yet we have measured the N2O sink in well drained soils, where we also simultaneously measure a sink for atmospheric methane (CH4). Co-occurrence of N2O reduction and CH4 oxidation would require a broad range of microsite conditions within the soil, spanning high and low oxygen concentrations. Abiotic sinks for N2O or other biological processes that consume N2O could exist, but have not yet been identified. We are attempting to simulate processes of diffusion of N2O, CH4, and O2 from the atmosphere and within a soil profile to determine if classical biological N2O reduction and CH4 oxidation at rates consistent with measured fluxes are plausible.

  9. Comparison of three different techniques for camera and motion control of a teleoperated robot.

    PubMed

    Doisy, Guillaume; Ronen, Adi; Edan, Yael

    2017-01-01

    This research aims to evaluate new methods for robot motion control and camera orientation control through the operator's head orientation in robot teleoperation tasks. Specifically, the use of head-tracking in a non-invasive way, without immersive virtual reality devices was combined and compared with classical control modes for robot movements and camera control. Three control conditions were tested: 1) a condition with classical joystick control of both the movements of the robot and the robot camera, 2) a condition where the robot movements were controlled by a joystick and the robot camera was controlled by the user head orientation, and 3) a condition where the movements of the robot were controlled by hand gestures and the robot camera was controlled by the user head orientation. Performance, workload metrics and their evolution as the participants gained experience with the system were evaluated in a series of experiments: for each participant, the metrics were recorded during four successive similar trials. Results shows that the concept of robot camera control by user head orientation has the potential of improving the intuitiveness of robot teleoperation interfaces, specifically for novice users. However, more development is needed to reach a margin of progression comparable to a classical joystick interface. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Super-resolution from single photon emission: toward biological application

    NASA Astrophysics Data System (ADS)

    Moreva, E.; Traina, P.; Forneris, J.; Ditalia Tchernij, S.; Guarina, L.; Franchino, C.; Picollo, F.; Ruo Berchera, I.; Brida, G.; Degiovanni, I. P.; Carabelli, V.; Olivero, P.; Genovese, M.

    2017-08-01

    Properties of quantum light represent a tool for overcoming limits of classical optics. Several experiments have demonstrated this advantage ranging from quantum enhanced imaging to quantum illumination. In this work, experimental demonstration of quantum-enhanced resolution in confocal fluorescence microscopy will be presented. This is achieved by exploiting the non-classical photon statistics of fluorescence emission of single nitrogen-vacancy (NV) color centers in diamond. By developing a general model of super-resolution based on the direct sampling of the kth-order autocorrelation function of the photoluminescence signal, we show the possibility to resolve, in principle, arbitrarily close emitting centers. Finally, possible applications of NV-based fluorescent nanodiamonds in biosensing and future developments will be presented.

  11. Non-Kolmogorovian Approach to the Context-Dependent Systems Breaking the Classical Probability Law

    NASA Astrophysics Data System (ADS)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Yamato, Ichiro

    2013-07-01

    There exist several phenomena breaking the classical probability laws. The systems related to such phenomena are context-dependent, so that they are adaptive to other systems. In this paper, we present a new mathematical formalism to compute the joint probability distribution for two event-systems by using concepts of the adaptive dynamics and quantum information theory, e.g., quantum channels and liftings. In physics the basic example of the context-dependent phenomena is the famous double-slit experiment. Recently similar examples have been found in biological and psychological sciences. Our approach is an extension of traditional quantum probability theory, and it is general enough to describe aforementioned contextual phenomena outside of quantum physics.

  12. Establishing an unusual cell type: How to make a dikaryon

    PubMed Central

    Kruzel, Emilia K.; Hull, Christina M.

    2010-01-01

    Summary The dikaryons of basidiomycete fungi represent an unusual cell type required for complete sexual development. Dikaryon formation occurs via the activities of cell type-specific homeodomain transcription factors, which form regulatory complexes to establish the dikaryotic state. Decades of classical genetic and cell biological studies in mushrooms have provided a foundation for more recent molecular studies in the pathogenic species Ustilago maydis and Cryptococcus neoformans. Studies in these systems have revealed novel mechanisms of regulation that function downstream of classic homeodomain complexes to ensure that dikaryons are established and propagated. Comparisons of these dikaryon-specific networks promise to reveal the nature of regulatory network evolution and the adaptations responsible for driving complex eukaryotic development. PMID:21036099

  13. Quantifying electron transfer reactions in biological systems: what interactions play the major role?

    NASA Astrophysics Data System (ADS)

    Sjulstok, Emil; Olsen, Jógvan Magnus Haugaard; Solov'Yov, Ilia A.

    2015-12-01

    Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.

  14. Identification and validation of multiple cell surface markers of clinical-grade adipose-derived mesenchymal stromal cells as novel release criteria for good manufacturing practice-compliant production.

    PubMed

    Camilleri, Emily T; Gustafson, Michael P; Dudakovic, Amel; Riester, Scott M; Garces, Catalina Galeano; Paradise, Christopher R; Takai, Hideki; Karperien, Marcel; Cool, Simon; Sampen, Hee-Jeong Im; Larson, A Noelle; Qu, Wenchun; Smith, Jay; Dietz, Allan B; van Wijnen, Andre J

    2016-08-11

    Clinical translation of mesenchymal stromal cells (MSCs) necessitates basic characterization of the cell product since variability in biological source and processing of MSCs may impact therapeutic outcomes. Although expression of classical cell surface markers (e.g., CD90, CD73, CD105, and CD44) is used to define MSCs, identification of functionally relevant cell surface markers would provide more robust release criteria and options for quality control. In addition, cell surface expression may distinguish between MSCs from different sources, including bone marrow-derived MSCs and clinical-grade adipose-derived MSCs (AMSCs) grown in human platelet lysate (hPL). In this work we utilized quantitative PCR, flow cytometry, and RNA-sequencing to characterize AMSCs grown in hPL and validated non-classical markers in 15 clinical-grade donors. We characterized the surface marker transcriptome of AMSCs, validated the expression of classical markers, and identified nine non-classical markers (i.e., CD36, CD163, CD271, CD200, CD273, CD274, CD146, CD248, and CD140B) that may potentially discriminate AMSCs from other cell types. More importantly, these markers exhibit variability in cell surface expression among different cell isolates from a diverse cohort of donors, including freshly prepared, previously frozen, or proliferative state AMSCs and may be informative when manufacturing cells. Our study establishes that clinical-grade AMSCs expanded in hPL represent a homogeneous cell culture population according to classical markers,. Additionally, we validated new biomarkers for further AMSC characterization that may provide novel information guiding the development of new release criteria. Use of Autologous Bone Marrow Aspirate Concentrate in Painful Knee Osteoarthritis (BMAC): Clinicaltrials.gov NCT01931007 . Registered August 26, 2013. MSC for Occlusive Disease of the Kidney: Clinicaltrials.gov NCT01840540 . Registered April 23, 2013. Mesenchymal Stem Cell Therapy in Multiple System Atrophy: Clinicaltrials.gov NCT02315027 . Registered October 31, 2014. Efficacy and Safety of Adult Human Mesenchymal Stem Cells to Treat Steroid Refractory Acute Graft Versus Host Disease. Clinicaltrials.gov NCT00366145 . Registered August 17, 2006. A Dose-escalation Safety Trial for Intrathecal Autologous Mesenchymal Stem Cell Therapy in Amyotrophic Lateral Sclerosis. Clinicaltrials.gov NCT01609283 . Registered May 18, 2012.

  15. Feedback control laws for highly maneuverable aircraft

    NASA Technical Reports Server (NTRS)

    Garrard, William L.; Balas, Gary J.

    1995-01-01

    During this year, we concentrated our efforts on the design of controllers for lateral/directional control using mu synthesis. This proved to be a more difficult task than we anticipated and we are still working on the designs. In the lateral-directional control problem, the inputs are pilot lateral stick and pedal commands and the outputs are roll rate about the velocity vector and side slip angle. The control effectors are ailerons, rudder deflection, and directional thrust vectoring vane deflection which produces a yawing moment about the body axis. Our math model does not contain any provision for thrust vectoring of rolling moment. This has resulted in limitations of performance at high angles of attack. During 1994-95, the following tasks for the lateral-directional controllers were accomplished: (1) Designed both inner and outer loop dynamic inversion controllers. These controllers are implemented using accelerometer outputs rather than an a priori model of the vehicle aerodynamics; (2) Used classical techniques to design controllers for the system linearized by dynamics inversion. These controllers acted to control roll rate and Dutch roll response; (3) Implemented the inner loop dynamic inversion and classical controllers on the six DOF simulation; (4) Developed a lateral-directional control allocation scheme based on minimizing required control effort among the ailerons, rudder, and directional thrust vectoring; and (5) Developed mu outer loop controllers combined with classical inner loop controllers.

  16. Rasch-family models are more valuable than score-based approaches for analysing longitudinal patient-reported outcomes with missing data.

    PubMed

    de Bock, Élodie; Hardouin, Jean-Benoit; Blanchin, Myriam; Le Neel, Tanguy; Kubis, Gildas; Bonnaud-Antignac, Angélique; Dantan, Étienne; Sébille, Véronique

    2016-10-01

    The objective was to compare classical test theory and Rasch-family models derived from item response theory for the analysis of longitudinal patient-reported outcomes data with possibly informative intermittent missing items. A simulation study was performed in order to assess and compare the performance of classical test theory and Rasch model in terms of bias, control of the type I error and power of the test of time effect. The type I error was controlled for classical test theory and Rasch model whether data were complete or some items were missing. Both methods were unbiased and displayed similar power with complete data. When items were missing, Rasch model remained unbiased and displayed higher power than classical test theory. Rasch model performed better than the classical test theory approach regarding the analysis of longitudinal patient-reported outcomes with possibly informative intermittent missing items mainly for power. This study highlights the interest of Rasch-based models in clinical research and epidemiology for the analysis of incomplete patient-reported outcomes data. © The Author(s) 2013.

  17. A Study of Two Instructional Sequences Informed by Alternative Learning Progressions in Genetics

    NASA Astrophysics Data System (ADS)

    Duncan, Ravit Golan; Choi, Jinnie; Castro-Faix, Moraima; Cavera, Veronica L.

    2017-12-01

    Learning progressions (LPs) are hypothetical models of how learning in a domain develops over time with appropriate instruction. In the domain of genetics, there are two independently developed alternative LPs. The main difference between the two progressions hinges on their assumptions regarding the accessibility of classical (Mendelian) versus molecular genetics and the order in which they should be taught. In order to determine the relative difficulty of the different genetic ideas included in the two progressions, and to test which one is a better fit with students' actual learning, we developed two modules in classical and molecular genetics and alternated their sequence in an implementation study with 11th grade students studying biology. We developed a set of 56 ordered multiple-choice items that collectively assessed both molecular and classical genetic ideas. We found significant gains in students' learning in both molecular and classical genetics, with the largest gain relating to understanding the informational content of genes and the smallest gain in understanding modes of inheritance. Using multidimensional item response modeling, we found no statistically significant differences between the two instructional sequences. However, there was a trend of slightly higher gains for the molecular-first sequence for all genetic ideas.

  18. The eyes have it: A Problem-Based Learning Exercise in Molecular Evolution.

    PubMed

    White, Harold B

    2007-05-01

    Molecular evolution provides an interesting context in which to use problem-based learning because it integrates a variety of topics in biology, biochemistry, and molecular biology. This three-stage problem for advanced students deals with the structure, multiple functions, and properties of lactate dehydrogenase isozymes, and the related evolutionary trade offs of gene sharing versus gene duplication among their corresponding genes. It has directive elements that require students to find and read classic articles, review thermodynamic principles, and apply their understanding to a mythical world wherein dinosaurs continued to evolve. The science fiction writing assignment that brings closure to the problem transformed the problem with respect to student interest and engagement. Copyright © 2007 International Union of Biochemistry and Molecular Biology, Inc.

  19. Adaptive neural coding: from biological to behavioral decision-making

    PubMed Central

    Louie, Kenway; Glimcher, Paul W.; Webb, Ryan

    2015-01-01

    Empirical decision-making in diverse species deviates from the predictions of normative choice theory, but why such suboptimal behavior occurs is unknown. Here, we propose that deviations from optimality arise from biological decision mechanisms that have evolved to maximize choice performance within intrinsic biophysical constraints. Sensory processing utilizes specific computations such as divisive normalization to maximize information coding in constrained neural circuits, and recent evidence suggests that analogous computations operate in decision-related brain areas. These adaptive computations implement a relative value code that may explain the characteristic context-dependent nature of behavioral violations of classical normative theory. Examining decision-making at the computational level thus provides a crucial link between the architecture of biological decision circuits and the form of empirical choice behavior. PMID:26722666

  20. Exploration of plasma-enhanced chemical vapor deposition as a method for thin-film fabrication with biological applications.

    PubMed

    Vasudev, Milana C; Anderson, Kyle D; Bunning, Timothy J; Tsukruk, Vladimir V; Naik, Rajesh R

    2013-05-22

    Chemical vapor deposition (CVD) has been used historically for the fabrication of thin films composed of inorganic materials. But the advent of specialized techniques such as plasma-enhanced chemical vapor deposition (PECVD) has extended this deposition technique to various monomers. More specifically, the deposition of polymers of responsive materials, biocompatible polymers, and biomaterials has made PECVD attractive for the integration of biotic and abiotic systems. This review focuses on the mechanisms of thin-film growth using low-pressure PECVD and current applications of classic PECVD thin films of organic and inorganic materials in biological environments. The last part of the review explores the novel application of low-pressure PECVD in the deposition of biological materials.

  1. An alternative laser driven photodissociation mechanism of pyrrole via πσ*1∕S0 conical intersection.

    PubMed

    Nandipati, K R; Lan, Z; Singh, H; Mahapatra, S

    2017-06-07

    A first principles quantum dynamics study of N-H photodissociation of pyrrole on the S 0 - 1 πσ * (A21) coupled electronic states is carried out with the aid of an optimally designed UV-laser pulse. A new photodissociation path, as compared to the conventional barrier crossing on the πσ*1 state, opens up upon electronic transitions under the influence of pump-dump laser pulses, which efficiently populate both the dissociation channels. The interplay of electronic transitions due both to vibronic coupling and the laser pulse is observed in the control mechanism and discussed in detail. The proposed control mechanism seems to be robust, and not discussed in the literature so far, and is expected to trigger future experiments on the πσ*1 photochemistry of molecules of chemical and biological importance. The design of the optimal pulses and their application to enhance the overall dissociation probability is carried out within the framework of optimal control theory. The quantum dynamics of the system in the presence of pulse is treated by solving the time-dependent Schrödinger equation in the semi-classical dipole approximation.

  2. An alternative laser driven photodissociation mechanism of pyrrole via πσ*1∕S0 conical intersection

    PubMed Central

    Nandipati, K. R.; Lan, Z.; Singh, H.; Mahapatra, S.

    2017-01-01

    A first principles quantum dynamics study of N–H photodissociation of pyrrole on the S0−1πσ*(A21) coupled electronic states is carried out with the aid of an optimally designed UV-laser pulse. A new photodissociation path, as compared to the conventional barrier crossing on the πσ*1 state, opens up upon electronic transitions under the influence of pump-dump laser pulses, which efficiently populate both the dissociation channels. The interplay of electronic transitions due both to vibronic coupling and the laser pulse is observed in the control mechanism and discussed in detail. The proposed control mechanism seems to be robust, and not discussed in the literature so far, and is expected to trigger future experiments on the πσ*1 photochemistry of molecules of chemical and biological importance. The design of the optimal pulses and their application to enhance the overall dissociation probability is carried out within the framework of optimal control theory. The quantum dynamics of the system in the presence of pulse is treated by solving the time-dependent Schrödinger equation in the semi-classical dipole approximation. PMID:28595406

  3. An alternative laser driven photodissociation mechanism of pyrrole via π*1σ/S0 conical intersection

    NASA Astrophysics Data System (ADS)

    Nandipati, K. R.; Lan, Z.; Singh, H.; Mahapatra, S.

    2017-06-01

    A first principles quantum dynamics study of N-H photodissociation of pyrrole on the S0-1π σ*(A12) coupled electronic states is carried out with the aid of an optimally designed UV-laser pulse. A new photodissociation path, as compared to the conventional barrier crossing on the π*1σ state, opens up upon electronic transitions under the influence of pump-dump laser pulses, which efficiently populate both the dissociation channels. The interplay of electronic transitions due both to vibronic coupling and the laser pulse is observed in the control mechanism and discussed in detail. The proposed control mechanism seems to be robust, and not discussed in the literature so far, and is expected to trigger future experiments on the π*1σ photochemistry of molecules of chemical and biological importance. The design of the optimal pulses and their application to enhance the overall dissociation probability is carried out within the framework of optimal control theory. The quantum dynamics of the system in the presence of pulse is treated by solving the time-dependent Schrödinger equation in the semi-classical dipole approximation.

  4. Microfluidic generation of aqueous two-phase system (ATPS) droplets by controlled pulsating inlet pressures.

    PubMed

    Moon, Byeong-Ui; Jones, Steven G; Hwang, Dae Kun; Tsai, Scott S H

    2015-06-07

    We present a technique that generates droplets using ultralow interfacial tension aqueous two-phase systems (ATPS). Our method combines a classical microfluidic flow focusing geometry with precisely controlled pulsating inlet pressure, to form monodisperse ATPS droplets. The dextran (DEX) disperse phase enters through the central inlet with variable on-off pressure cycles controlled by a pneumatic solenoid valve. The continuous phase polyethylene glycol (PEG) solution enters the flow focusing junction through the cross channels at a fixed flow rate. The on-off cycles of the applied pressure, combined with the fixed flow rate cross flow, make it possible for the ATPS jet to break up into droplets. We observe different droplet formation regimes with changes in the applied pressure magnitude and timing, and the continuous phase flow rate. We also develop a scaling model to predict the size of the generated droplets, and the experimental results show a good quantitative agreement with our scaling model. Additionally, we demonstrate the potential for scaling-up of the droplet production rate, with a simultaneous two-droplet generating geometry. We anticipate that this simple and precise approach to making ATPS droplets will find utility in biological applications where the all-biocompatibility of ATPS is desirable.

  5. Recent advances in tropical medicine.

    PubMed

    Solomon, Anthony W; Nayagam, Shevanthi; Pasvol, Geoffrey

    2009-07-01

    There have been significant advances in both the classical and neglected tropical diseases, with Guinea worm looking set to be the next disease after smallpox to be eradicated. Aided by a combination of enhanced understanding of the biology of the pathogens, intensification of immunisation activities or mass drug administration, together with the development of synergies with control programmes for co-endemic tropical diseases, polio, lymphatic filariasis, trachoma and onchocerciasis all appear to be in global decline, with good prospects for eventual successful elimination. While the global incidence of new cases of leprosy continues to decrease, the focus of leprosy control efforts has shifted following more widespread recognition that cure of infection does not necessarily prevent disability. Expansion in funding for HIV/AIDS and malaria provides some grounds for optimism about the control of these diseases. However, ongoing education and access remain essential to increasing the uptake of HIV testing and decreasing transmission. Meanwhile, the rise of drug-resistant tuberculosis and malaria is concerning, and the emergence of the highly pathogenic avian influenza A and re-emergence of viruses such as chikungunya and West Nile virus, without significant recent progress in vaccine development, pose additional ongoing challenges to tropical medicine physicians worldwide.

  6. Noise reduction in optically controlled quantum memory

    NASA Astrophysics Data System (ADS)

    Ma, Lijun; Slattery, Oliver; Tang, Xiao

    2018-05-01

    Quantum memory is an essential tool for quantum communications systems and quantum computers. An important category of quantum memory, called optically controlled quantum memory, uses a strong classical beam to control the storage and re-emission of a single-photon signal through an atomic ensemble. In this type of memory, the residual light from the strong classical control beam can cause severe noise and degrade the system performance significantly. Efficiently suppressing this noise is a requirement for the successful implementation of optically controlled quantum memories. In this paper, we briefly introduce the latest and most common approaches to quantum memory and review the various noise-reduction techniques used in implementing them.

  7. Intelligent monitoring and control of semiconductor manufacturing equipment

    NASA Technical Reports Server (NTRS)

    Murdock, Janet L.; Hayes-Roth, Barbara

    1991-01-01

    The use of AI methods to monitor and control semiconductor fabrication in a state-of-the-art manufacturing environment called the Rapid Thermal Multiprocessor is described. Semiconductor fabrication involves many complex processing steps with limited opportunities to measure process and product properties. By applying additional process and product knowledge to that limited data, AI methods augment classical control methods by detecting abnormalities and trends, predicting failures, diagnosing, planning corrective action sequences, explaining diagnoses or predictions, and reacting to anomalous conditions that classical control systems typically would not correct. Research methodology and issues are discussed, and two diagnosis scenarios are examined.

  8. Monocyte profile in peripheral blood of gestational diabetes mellitus patients.

    PubMed

    Angelo, Ana G S; Neves, Carla T C; Lobo, Thalita F; Godoy, Ramon V C; Ono, Érika; Mattar, Rosiane; Daher, Silvia

    2018-07-01

    Gestational diabetes Mellitus has been considered an inflammatory disease involving different cells and mediators in its development. The role of innate immune cells in GDM physiopathology remains unclear, therefore this study was conducted to assess monocyte profile in GDM patients. This was a case-control study including 20 glucose-tolerant pregnant women (controls) and 18 GDM patients. Flow cytometry was used to assess peripheral blood monocytes subsets (classical, intermediate, non-classical), the expression of TLR4 and CCR2 chemokine receptor (CD192) and cytokines (TNFA, IL6, IL10) secretion by monocytes subsets. In addition, sCD14 serum levels were evaluated by ELISA. We observed increased percentage of CD14 + cells, decreased frequency of intermediate monocytes (CD14 + CD16 + ), and lower percentage of circulating monocytes (classical, intermediate and non-classical) that express TLR4 in the diabetic group compared to controls. Soluble CD14 + serum levels were higher in GDM patients compared to controls. There were no differences in the expression of the CCR2 chemokine receptor and cytokines (TNFA, IL6 and IL10) secretion between the studied groups. Our results demonstrated that GDM patients present impaired monocyte profile in the peripheral blood, suggesting that these cells are involved in GDM physiopathology. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Puzzles in modern biology. V. Why are genomes overwired?

    PubMed

    Frank, Steven A

    2017-01-01

    Many factors affect eukaryotic gene expression. Transcription factors, histone codes, DNA folding, and noncoding RNA modulate expression. Those factors interact in large, broadly connected regulatory control networks. An engineer following classical principles of control theory would design a simpler regulatory network. Why are genomes overwired? Neutrality or enhanced robustness may lead to the accumulation of additional factors that complicate network architecture. Dynamics progresses like a ratchet. New factors get added. Genomes adapt to the additional complexity. The newly added factors can no longer be removed without significant loss of fitness. Alternatively, highly wired genomes may be more malleable. In large networks, most genomic variants tend to have a relatively small effect on gene expression and trait values. Many small effects lead to a smooth gradient, in which traits may change steadily with respect to underlying regulatory changes. A smooth gradient may provide a continuous path from a starting point up to the highest peak of performance. A potential path of increasing performance promotes adaptability and learning. Genomes gain by the inductive process of natural selection, a trial and error learning algorithm that discovers general solutions for adapting to environmental challenge. Similarly, deeply and densely connected computational networks gain by various inductive trial and error learning procedures, in which the networks learn to reduce the errors in sequential trials. Overwiring alters the geometry of induction by smoothing the gradient along the inductive pathways of improving performance. Those overwiring benefits for induction apply to both natural biological networks and artificial deep learning networks.

  10. Duration of emission of volatile organic compounds from mechanically damaged plant leaves.

    PubMed

    Smith, Lincoln; Beck, John J

    2015-09-01

    Classical biological control of invasive alien weeds depends on the use of arthropod herbivores that are sufficiently host specific to avoid risk of injuring nontarget plants. Host plant specificity is usually evaluated by using a combination of behavioral and developmental experiments under choice, no-choice and field conditions. Secondary plant compounds are likely to have an important influence on host plant specificity. However, relatively little is known about the volatile organic compounds (VOCs) that are emitted by target and nontarget plants, and how environmental conditions may affect their emission. Previous studies have shown that mechanical damage of leaves increases the composition and content of VOCs emitted. In this study we measured the VOC emissions of five species of plants in the subtribe Centaureinae (Asteraceae)--Carthamus tinctorius, Centaurea cineraria, Centaurea melitensis, Centaurea rothrockii, and Centaurea solstitialis--that have previously been used in host specificity experiments for a prospective biological control agent of yellow starthistle (C. solstitialis). Leaves of each plant were punctured with a needle and the VOCs were collected by solid-phase microextraction (SPME) periodically over 48 h and analyzed by GC-MS. A total of 49 compounds were detected. Damage caused an immediate increase of 200-600% in the composition of VOCs emitted from each plant species, and the amounts generally remained high for at least 48 h. The results indicate that a very unspecific mechanical damage can cause a prolonged change in the VOC profile of plants. Published by Elsevier GmbH.

  11. Redox Control of Inflammation in Macrophages

    PubMed Central

    Dehne, Nathalie; Grossmann, Nina; Jung, Michaela; Namgaladze, Dmitry; Schmid, Tobias; von Knethen, Andreas; Weigert, Andreas

    2013-01-01

    Abstract Macrophages are present throughout the human body, constitute important immune effector cells, and have variable roles in a great number of pathological, but also physiological, settings. It is apparent that macrophages need to adjust their activation profile toward a steadily changing environment that requires altering their phenotype, a process known as macrophage polarization. Formation of reactive oxygen species (ROS), derived from NADPH-oxidases, mitochondria, or NO-producing enzymes, are not necessarily toxic, but rather compose a network signaling system, known as redox regulation. Formation of redox signals in classically versus alternatively activated macrophages, their action and interaction at the level of key targets, and the resulting physiology still are insufficiently understood. We review the identity, source, and biological activities of ROS produced during macrophage activation, and discuss how they shape the key transcriptional responses evoked by hypoxia-inducible transcription factors, nuclear-erythroid 2-p45-related factor 2 (Nrf2), and peroxisome proliferator-activated receptor-γ. We summarize the mechanisms how redox signals add to the process of macrophage polarization and reprogramming, how this is controlled by the interaction of macrophages with their environment, and addresses the outcome of the polarization process in health and disease. Future studies need to tackle the option whether we can use the knowledge of redox biology in macrophages to shape their mediator profile in pathophysiology, to accelerate healing in injured tissue, to fight the invading pathogens, or to eliminate settings of altered self in tumors. Antioxid. Redox Signal. 19, 595–637. PMID:23311665

  12. Morphofunctional reaction of bacteria treated with antimicrobial peptides derived from farm animal platelets.

    PubMed

    Vasilchenko, Alexey S; Dymova, Veronica V; Kartashova, Olga L; Sycheva, Maria V

    2015-03-01

    Classical microbiological approach and atomic force microscopy were used to evaluate the mechanisms of biological activity of antimicrobial peptides (AMPs) derived from platelets of farm animals. It is established that AMPs inhibit both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) microorganisms. Differences revealed in the biological activity of AMP preparations obtained from the organisms of various species can be reduced to quantitative differences. While qualitative changes of bacterial cells were substantially similar, changes in the integrity of cell walls resulted in disintegration of the bacterial outer and/or cytoplasmic membranes.

  13. Neoplastic Multifocal Skin Lesions: Biology, Etiology, and Targeted Therapies for Nonmelanoma Skin Cancers.

    PubMed

    Fernandes, Ana R; Santos, Ana C; Sanchez-Lopez, Elena; Kovačević, Andjekla B; Espina, Marta; Calpena, Ana C; Veiga, Francisco J; Garcia, Maria L; Souto, Eliana B

    2018-01-01

    Neoplastic skin lesions are multifocal, diffuse skin infiltrations of particular relevance in the differential diagnosis of ulcerative, nodular, or crusting skin lesions. Nonmelanoma skin cancers (NMSCs), namely, basal cell carcinoma (BCC), squamous cell carcinoma (SCC), and also actinic keratosis (AK), are the most common malignant tumors in humans. BCCs do not proliferate rapidly and most of the times do not metastasize, while SCCs are more infiltrative, metastatic, and destructive. AKs are precursor lesions of cutaneous SCCs. The classical therapy of NMSCs makes use of photodynamic therapy associated with chemotherapeutics. With improved understanding of the pathological mechanisms of tumor initiation, progression, and differentiation, a case is made towards the use of targeted chemotherapy with the intent to reduce the cytotoxicity of classical treatments. The present review aims to describe the current state of the art on the knowledge of NMSC, including its risks factors, oncogenes, and skin carcinogenesis, discussing the classical therapy against new therapeutic options. © 2017 S. Karger AG, Basel.

  14. Cross Section Calculations and Comparison to Experiment

    NASA Technical Reports Server (NTRS)

    Townsend, L. W.; Ford, W. P.; Dewet, W. C.; Werneth, C. M.

    2016-01-01

    Understanding fragmentation of galactic cosmic ray nuclei in collisions within spacecraft structures and human tissues is an important element in assessing biological risk to crew members from this radiation source. Over the past four decades, various models have been developed to describe these important processes. Some models invoke semi-classical concepts based upon geometric descriptions of collisions between spherical nuclei.

  15. Post-wildland fire desertification: Can rehabilitation treatments make a difference?

    Treesearch

    Daniel G. Neary

    2009-01-01

    Desertification, caused by land degradation as opposed to the immediate creation of classical deserts, is of prime concern in the 21st century. As a result of human activities and climate change, the land loses its proper hydrologic function and biological productivity. Desertification affects 33 % of the earth's surface and over a billion people. Fire-related...

  16. Existence and uniqueness of steady state solutions of a nonlocal diffusive logistic equation

    NASA Astrophysics Data System (ADS)

    Sun, Linan; Shi, Junping; Wang, Yuwen

    2013-08-01

    In this paper, we consider a dynamical model of population biology which is of the classical Fisher type, but the competition interaction between individuals is nonlocal. The existence, uniqueness, and stability of the steady state solution of the nonlocal problem on a bounded interval with homogeneous Dirichlet boundary conditions are studied.

  17. On Gene Concepts and Teaching Genetics: Episodes from Classical Genetics

    ERIC Educational Resources Information Center

    Burian, Richard M.

    2013-01-01

    This paper addresses the teaching of advanced high school courses or undergraduate courses for non-biology majors about genetics or history of genetics. It will probably be difficult to take the approach described here in a high school science course, although the general approach could help improve such courses. It would be ideal for a college…

  18. How to Understand the Gene in the Twenty-First Century?

    ERIC Educational Resources Information Center

    Meyer, Lia Midori Nascimento; Bomfim, Gilberto Cafezeiro; El-Hani, Charbel Nino

    2013-01-01

    It is widely acknowledged in the literature on philosophy of biology and, more recently, among biologists themselves that the gene concept is currently in crisis. This crisis concerns the so-called "classical molecular concept", according to which a gene is a DNA segment encoding one functional product, which can be either a RNA molecule or a…

  19. Miro GTPase controls mitochondrial behavior affecting stress tolerance and virulence of a fungal insect pathogen.

    PubMed

    Guan, Yi; Wang, Ding-Yi; Ying, Sheng-Hua; Feng, Ming-Guang

    2016-08-01

    Miro homologues are small mitochondrial Rho GTPases belonging to the Ras superfamily across organisms and are generally unexplored in filamentous fungi. Here we identified a Miro orthologue (bMiro) in Beauveria bassiana, a filamentous fungal insect pathogen as a classic biological control agent of insect pests. This orthologue was proven to anchor on mitochondrial outer membrane in a manner depending completely upon a short C-terminal transmembrane domain. As a result of bmiro deletion, mitochondria in hyphal cells were largely aggregated, and their mass and mobility were reduced, accompanied with a remarkable decrease in ATP content but little change in mitochondrial morphology. The deletion mutant became 42%, 37%, 19% and 10% more tolerant to Ca(2+), Mn(2+), Zn(2+) and Mg(2+) than wild-type, respectively, during cultivation in a minimal medium under normal conditions. The deletion mutant also showed mild defects in conidial germination, vegetative growth, thermotolerance, UV-B resistance and virulence despite null response to oxidative and osmotic stresses. All these phenotypic changes were restored by targeted gene complementation. Our results indicate that bMiro can control mitochondrial distribution and movement required for the transport of ATP-form energy and metal ions and contributes significantly to the fungal potential against insect pests through the control. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Counterion-enhanced cyanine dye loading into lipid nano-droplets for single-particle tracking in zebrafish.

    PubMed

    Kilin, Vasyl N; Anton, Halina; Anton, Nicolas; Steed, Emily; Vermot, Julien; Vandamme, Thierry F; Mely, Yves; Klymchenko, Andrey S

    2014-06-01

    Superior brightness of fluorescent nanoparticles places them far ahead of the classical fluorescent dyes in the field of biological imaging. However, for in vivo applications, inorganic nanoparticles, such as quantum dots, are limited due to the lack of biodegradability. Nano-emulsions encapsulating high concentrations of organic dyes are an attractive alternative, but classical fluorescent dyes are inconvenient due to their poor solubility in the oil and their tendency to form non-fluorescent aggregates. This problem was solved here for a cationic cyanine dye (DiI) by substituting its perchlorate counterion for a bulky and hydrophobic tetraphenylborate. This new dye salt, due to its exceptional oil solubility, could be loaded at 8 wt% concentration into nano-droplets of controlled size in the range 30-90 nm. Our 90 nm droplets, which contained >10,000 cyanine molecules, were >100-fold brighter than quantum dots. This extreme brightness allowed, for the first time, single-particle tracking in the blood flow of live zebrafish embryo, revealing both the slow and fast phases of the cardiac cycle. These nano-droplets showed minimal cytotoxicity in cell culture and in the zebrafish embryo. The concept of counterion-based dye loading provides a new effective route to ultra-bright lipid nanoparticles, which enables tracking single particles in live animals, a new dimension of in vivo imaging. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Methodologies for Salmonella enterica subsp. enterica Subtyping: Gold Standards and Alternatives▿

    PubMed Central

    Wattiau, Pierre; Boland, Cécile; Bertrand, Sophie

    2011-01-01

    For more than 80 years, subtyping of Salmonella enterica has been routinely performed by serotyping, a method in which surface antigens are identified based on agglutination reactions with specific antibodies. The serotyping scheme, which is continuously updated as new serovars are discovered, has generated over time a data set of the utmost significance, allowing long-term epidemiological surveillance of Salmonella in the food chain and in public health control. Conceptually, serotyping provides no information regarding the phyletic relationships inside the different Salmonella enterica subspecies. In epidemiological investigations, identification and tracking of salmonellosis outbreaks require the use of methods that can fingerprint the causative strains at a taxonomic level far more specific than the one achieved by serotyping. During the last 2 decades, alternative methods that could successfully identify the serovar of a given strain by probing its DNA have emerged, and molecular biology-based methods have been made available to address phylogeny and fingerprinting issues. At the same time, accredited diagnostics have become increasingly generalized, imposing stringent methodological requirements in terms of traceability and measurability. In these new contexts, the hand-crafted character of classical serotyping is being challenged, although it is widely accepted that classification into serovars should be maintained. This review summarizes and discusses modern typing methods, with a particular focus on those having potential as alternatives for classical serotyping or for subtyping Salmonella strains at a deeper level. PMID:21856826

  2. A classical view on nonclassical nucleation.

    PubMed

    Smeets, Paul J M; Finney, Aaron R; Habraken, Wouter J E M; Nudelman, Fabio; Friedrich, Heiner; Laven, Jozua; De Yoreo, James J; Rodger, P Mark; Sommerdijk, Nico A J M

    2017-09-19

    Understanding and controlling nucleation is important for many crystallization applications. Calcium carbonate (CaCO 3 ) is often used as a model system to investigate nucleation mechanisms. Despite its great importance in geology, biology, and many industrial applications, CaCO 3 nucleation is still a topic of intense discussion, with new pathways for its growth from ions in solution proposed in recent years. These new pathways include the so-called nonclassical nucleation mechanism via the assembly of thermodynamically stable prenucleation clusters, as well as the formation of a dense liquid precursor phase via liquid-liquid phase separation. Here, we present results from a combined experimental and computational investigation on the precipitation of CaCO 3 in dilute aqueous solutions. We propose that a dense liquid phase (containing 4-7 H 2 O per CaCO 3 unit) forms in supersaturated solutions through the association of ions and ion pairs without significant participation of larger ion clusters. This liquid acts as the precursor for the formation of solid CaCO 3 in the form of vaterite, which grows via a net transfer of ions from solution according to z Ca 2+ + z CO 3 2- → z CaCO 3 The results show that all steps in this process can be explained according to classical concepts of crystal nucleation and growth, and that long-standing physical concepts of nucleation can describe multistep, multiphase growth mechanisms.

  3. Comprehensive Peptide Analysis of Mouse Brain Striatum Identifies Novel sORF-Encoded Polypeptides.

    PubMed

    Budamgunta, Harshavardhan; Olexiouk, Volodimir; Luyten, Walter; Schildermans, Karin; Maes, Evelyne; Boonen, Kurt; Menschaert, Gerben; Baggerman, Geert

    2018-04-30

    Bio-active peptides are involved in the regulation of most physiological processes in the body. Classical bio-active peptides (CBAPs) are cleaved from a larger precursor protein and stored in secretion vesicles from which they are released in the extracellular space. Recently, another non-classical type of bio-active peptides (NCBAPs) have gained interest. These typically are not secreted but instead appear to be translated from short open reading frames (sORF) and released directly into the cytoplasm. In contrast to CBAPs, these peptides are involved in the regulation of intra-cellular processes such as transcriptional control, calcium handling and DNA repair. However, bio-chemical evidence for the translation of sORFs remains elusive. Comprehensive analysis of sORF-encoded polypeptides (SEPs) is hampered by a number of methodological and biological challenges: the low molecular mass (many 4-10 kDa), the low abundance, transient expression and complications in data analysis. We developed a strategy to address a number of these issues. Our strategy is to exclude false positive identifications. in total sample, we identified 926 peptides originated from 37 known (neuro)peptide precursors in mouse striatum,. In addition, four SEPs were identified including NoBody, a SEP that was previously discovered in humans and three novel SEPS from 5' untranslated transcript regions (UTRs). This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  4. Rational plasmid design and bioprocess optimization to enhance recombinant adeno-associated virus (AAV) productivity in mammalian cells.

    PubMed

    Emmerling, Verena V; Pegel, Antje; Milian, Ernest G; Venereo-Sanchez, Alina; Kunz, Marion; Wegele, Jessica; Kamen, Amine A; Kochanek, Stefan; Hoerer, Markus

    2016-02-01

    Viral vectors used for gene and oncolytic therapy belong to the most promising biological products for future therapeutics. Clinical success of recombinant adeno-associated virus (rAAV) based therapies raises considerable demand for viral vectors, which cannot be met by current manufacturing strategies. Addressing existing bottlenecks, we improved a plasmid system termed rep/cap split packaging and designed a minimal plasmid encoding adenoviral helper function. Plasmid modifications led to a 12-fold increase in rAAV vector titers compared to the widely used pDG standard system. Evaluation of different production approaches revealed superiority of processes based on anchorage- and serum-dependent HEK293T cells, exhibiting about 15-fold higher specific and volumetric productivity compared to well-established suspension cells cultivated in serum-free medium. As for most other viral vectors, classical stirred-tank bioreactor production is thus still not capable of providing drug product of sufficient amount. We show that manufacturing strategies employing classical surface-providing culture systems can be successfully transferred to the new fully-controlled, single-use bioreactor system Integrity(TM) iCELLis(TM) . In summary, we demonstrate substantial bioprocess optimizations leading to more efficient and scalable production processes suggesting a promising way for flexible large-scale rAAV manufacturing. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Implicit and explicit learning in schizophrenics treated with olanzapine and with classic neuroleptics.

    PubMed

    Stevens, Andreas; Schwarz, Jürgen; Schwarz, Benedikt; Ruf, Ilona; Kolter, Thomas; Czekalla, Joerg

    2002-03-01

    Novel and classic neuroleptics differ in their effects on limbic striatal/nucleus accumbens (NA) and prefrontal cortex (PFC) dopamine turnover, suggesting differential effects on implicit and explicit learning as well as on anhedonia. The present study investigates whether such differences can be demonstrated in a naturalistic sample of schizophrenic patients. Twenty-five inpatients diagnosed with DSM-IV schizophrenic psychosis and treated for at least 14 days with the novel neuroleptic olanzapine were compared with 25 schizophrenics taking classic neuroleptics and with 25 healthy controls, matched by age and education level. PFC/NA-dependent implicit learning was assessed by a serial reaction time task (SRTT) and compared with cerebellum-mediated classical eye-blink conditioning and explicit visuospatial memory. Anhedonia was measured with the Snaith-Hamilton-Pleasure Scale (SHAPS). Implicit (SRTT) and psychomotor speed, but not explicit (visuospatial) learning were superior in the olanzapine-treated group as compared to the patients on classic neuroleptics. Compared to healthy controls, olanzapine-treated schizophrenics showed similar implicit learning, but reduced explicit (visuospatial) memory performance. Acquisition of eyeblink conditioning was not different between the three groups. There was no difference with regard to anhedonia and SANS scores between the patients. Olanzapine seems to interfere less with unattended learning and motor speed than classical neuroleptics. In daily life, this may translate into better adaptation to a rapidly changing environment. The effects seem specific, as in explicit learning and eyeblink conditioning no difference to classic NL was found.

  6. Raymond Pearl and the shaping of human biology.

    PubMed

    Little, Michael A; Garruto, Ralph M

    2010-02-01

    Raymond Pearl (1879-1940) was a significant figure in the field of biology. He founded the journal Human Biology and almost single-handedly promoted and established the scientific discipline of human biology. His scientific versatility was one of his most important features during the first four decades of the 20th century, and he played a major role in developing the fields of biodemography, human population biology, human life-cycle and life span approaches, fertility, growth, the biology of longevity and senescence, and mortality. He was one of the earliest biologists to combine biometric analyses and experimental studies to explore the dimensions of human biology. Pearl also was broadly educated in the arts, music, literature, history, the classics, and science. His writing was sophisticated and often witty, and his views were sometimes provocative and controversial. His network of colleagues and friends among the literary and science worlds was substantial. The following biographical memoir of Raymond Pearl is designed to commemorate the 80th anniversary of the founding of his journal Human Biology and is a tribute to this great scientist. Pearl's sudden death at age 61 truncated a scientific career that was one of the most productive of the 20th century.

  7. Epigenetics: Biology's Quantum Mechanics

    PubMed Central

    Jorgensen, Richard A.

    2011-01-01

    The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920s and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene – the molecular biological view and the epigenetic view – are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider. PMID:22639577

  8. Biology's built-in Faraday cages

    NASA Astrophysics Data System (ADS)

    Klee, Maurice M.

    2014-05-01

    Biological fluids are water-based, ionic conductors. As such, they have both high relative dielectric constants and substantial conductivities, meaning they are lossy dielectrics. These fluids contain charged molecules (free charges), whose movements play roles in essentially all cellular processes from metabolism to communication with other cells. Using the problem of a point source in air above a biological fluid of semi-infinite extent, the bound charges in the fluid are shown to perform the function of a fast-acting Faraday cage, which protects the interior of the fluid from external electric fields. Free charges replace bound charges in accordance with the fluid's relaxation time, thereby providing a smooth transition between the initial protection provided by the bound charges and the steady state protection provided by the free charges. The electric fields within the biological fluid are thus small for all times just as they would be inside a classical Faraday cage.

  9. Determination of the dynamical behaviour of biological materials during impact using a pendulum device

    NASA Astrophysics Data System (ADS)

    Van Zeebroeck, M.; Tijskens, E.; Van Liedekerke, P.; Deli, V.; De Baerdemaeker, J.; Ramon, H.

    2003-09-01

    A pendulum device has been developed to measure contact force, displacement and displacement rate of an impactor during its impact on the sample. Displacement, classically measured by double integration of an accelerometer, was determined in an alternative way using a more accurate incremental optical encoder. The parameters of the Kuwabara-Kono contact force model for impact of spheres have been estimated using an optimization method, taking the experimentally measured displacement, displacement rate and contact force into account. The accuracy of the method was verified using a rubber ball. Contact force parameters for the Kuwabara-Kono model have been estimated with success for three biological materials, i.e., apples, tomatoes and potatoes. The variability in the parameter estimations for the biological materials was quite high and can be explained by geometric differences (radius of curvature) and by biological variation of mechanical tissue properties.

  10. SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

    PubMed

    Zi, Zhike; Klipp, Edda

    2006-11-01

    The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system. http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.

  11. Mikrosensor-gesteuerte Rückkopplungs- Bioaktuatoren auf Halbleiterbasis zur biophysikalischen Krebsbehandlung

    NASA Astrophysics Data System (ADS)

    Wolf, Bernhard; Kraus, Michael

    Acidic microenvironmental conditions combined with large hypoxic areas are ubiquitous hallmarks of most solid tumors. They result from a poorly organized vascularization and a deviant energy metabolism. There is convincing evidence supporting the hypothesis that such physico-chemical conditions promote the microevolution of malignant cells, inhibit the cellular immune response, and favor tumor cell invasion. In agreement with published data, our cell biological analyses and computer simulations indicate that treatment schemes which restore a tumor microenvironment reflecting that one found in normal tissues might improve the efficiency of immunotherapies and classical methods for cancer treatment. We suggest that the tumor microenvironment could be effectively monitored and manipulated by means of silicon-based feedback bioactuators which are controlled by integrated microsensors. In principle, miniaturized bioactuators can be implanted directly at the sites of inoperable tumors and metastases where they function as a "pH clamp" and thereby can reconstitute normal physico-chemical conditions. Drug application could be precisely controlled by an integrated microprocessor. Our paper summarizes the current state of development of microsensor-based feedback bioactuators and outlines possible applications in biophysical cancer treatment.

  12. Finite-size effects on bacterial population expansion under controlled flow conditions

    NASA Astrophysics Data System (ADS)

    Tesser, Francesca; Zeegers, Jos C. H.; Clercx, Herman J. H.; Brunsveld, Luc; Toschi, Federico

    2017-03-01

    The expansion of biological species in natural environments is usually described as the combined effect of individual spatial dispersal and growth. In the case of aquatic ecosystems flow transport can also be extremely relevant as an extra, advection induced, dispersal factor. We designed and assembled a dedicated microfluidic device to control and quantify the expansion of populations of E. coli bacteria under both co-flowing and counter-flowing conditions, measuring the front speed at varying intensity of the imposed flow. At variance with respect to the case of classic advective-reactive-diffusive chemical fronts, we measure that almost irrespective of the counter-flow velocity, the front speed remains finite at a constant positive value. A simple model incorporating growth, dispersion and drift on finite-size hard beads allows to explain this finding as due to a finite volume effect of the bacteria. This indicates that models based on the Fisher-Kolmogorov-Petrovsky-Piscounov equation (FKPP) that ignore the finite size of organisms may be inaccurate to describe the physics of spatial growth dynamics of bacteria.

  13. Frankliniella occidentalis (Pergande) integrated pest management programs for fruiting vegetables in Florida.

    PubMed

    Demirozer, Ozan; Tyler-Julian, Kara; Funderburk, Joe; Leppla, Norm; Reitz, Stuart

    2012-12-01

    The spread of the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), resulted in the worldwide destabilization of established integrated pest management programs for many crops. Efforts to control the pest and the thrips-vectored tospoviruses with calendar applications of broad-spectrum insecticides have been unsuccessful. The result has been a classic '3-R' situation: resistance to numerous insecticides; resurgence of the western flower thrips populations as a result of natural predators and native competitor thrips being eliminated; replacement by various other pests. This paper reports on integrated pest management programs for fruiting vegetables that are effective, economical, ecologically sound and sustainable. The components include the following: define pest status (economic thresholds); increase biotic resistance (natural enemies and competition); integrate preventive and therapeutic tactics (scouting, ultraviolet-reflective technologies, biological control, compatible insecticides, companion plants and fertility); vertically integrate the programs with other pests; continually communicate latest science-based management tactics with end-users. These programs have been widely implemented in Florida and have significantly improved the management of western flower thrips and thrips-transmitted viruses. Copyright © 2012 Society of Chemical Industry.

  14. The origin and evolution of the sexes: Novel insights from a distant eukaryotic linage.

    PubMed

    Mignerot, Laure; Coelho, Susana M

    2016-01-01

    Sexual reproduction is an extraordinarily widespread phenomenon that assures the production of new genetic combinations in nearly all eukaryotic lineages. Although the core features of sexual reproduction (meiosis and syngamy) are highly conserved, the control mechanisms that determine whether an individual is male or female are remarkably labile across eukaryotes. In genetically controlled sexual systems, gender is determined by sex chromosomes, which have emerged independently and repeatedly during evolution. Sex chromosomes have been studied in only a handful of classical model organism, and empirical knowledge on the origin and evolution of the sexes is still surprisingly incomplete. With the advent of new generation sequencing, the taxonomic breadth of model systems has been rapidly expanding, bringing new ideas and fresh views on this fundamental aspect of biology. This mini-review provides a quick state of the art of how the remarkable richness of the sexual characteristics of the brown algae is helping to increase our knowledge about the evolution of sex determination. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  15. Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

    PubMed

    Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

    2011-06-01

    We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

  16. Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

    PubMed

    Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

    2010-07-01

    We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

  17. The Global Error Assessment (GEA) model for the selection of differentially expressed genes in microarray data.

    PubMed

    Mansourian, Robert; Mutch, David M; Antille, Nicolas; Aubert, Jerome; Fogel, Paul; Le Goff, Jean-Marc; Moulin, Julie; Petrov, Anton; Rytz, Andreas; Voegel, Johannes J; Roberts, Matthew-Alan

    2004-11-01

    Microarray technology has become a powerful research tool in many fields of study; however, the cost of microarrays often results in the use of a low number of replicates (k). Under circumstances where k is low, it becomes difficult to perform standard statistical tests to extract the most biologically significant experimental results. Other more advanced statistical tests have been developed; however, their use and interpretation often remain difficult to implement in routine biological research. The present work outlines a method that achieves sufficient statistical power for selecting differentially expressed genes under conditions of low k, while remaining as an intuitive and computationally efficient procedure. The present study describes a Global Error Assessment (GEA) methodology to select differentially expressed genes in microarray datasets, and was developed using an in vitro experiment that compared control and interferon-gamma treated skin cells. In this experiment, up to nine replicates were used to confidently estimate error, thereby enabling methods of different statistical power to be compared. Gene expression results of a similar absolute expression are binned, so as to enable a highly accurate local estimate of the mean squared error within conditions. The model then relates variability of gene expression in each bin to absolute expression levels and uses this in a test derived from the classical ANOVA. The GEA selection method is compared with both the classical and permutational ANOVA tests, and demonstrates an increased stability, robustness and confidence in gene selection. A subset of the selected genes were validated by real-time reverse transcription-polymerase chain reaction (RT-PCR). All these results suggest that GEA methodology is (i) suitable for selection of differentially expressed genes in microarray data, (ii) intuitive and computationally efficient and (iii) especially advantageous under conditions of low k. The GEA code for R software is freely available upon request to authors.

  18. Engineered catalytic biofilms for continuous large scale production of n-octanol and (S)-styrene oxide.

    PubMed

    Gross, Rainer; Buehler, Katja; Schmid, Andreas

    2013-02-01

    This study evaluates the technical feasibility of biofilm-based biotransformations at an industrial scale by theoretically designing a process employing membrane fiber modules as being used in the chemical industry and compares the respective process parameters to classical stirred-tank studies. To our knowledge, catalytic biofilm processes for fine chemicals production have so far not been reported on a technical scale. As model reactions, we applied the previously studied asymmetric styrene epoxidation employing Pseudomonas sp. strain VLB120ΔC biofilms and the here-described selective alkane hydroxylation. Using the non-heme iron containing alkane hydroxylase system (AlkBGT) from P. putida Gpo1 in the recombinant P. putida PpS81 pBT10 biofilm, we were able to continuously produce 1-octanol from octane with a maximal productivity of 1.3 g L ⁻¹(aq) day⁻¹ in a single tube micro reactor. For a possible industrial application, a cylindrical membrane fiber module packed with 84,000 polypropylene fibers is proposed. Based on the here presented calculations, 59 membrane fiber modules (of 0.9 m diameter and 2 m length) would be feasible to realize a production process of 1,000 tons/year for styrene oxide. Moreover, the product yield on carbon can at least be doubled and over 400-fold less biomass waste would be generated compared to classical stirred-tank reactor processes. For the octanol process, instead, further intensification in biological activity and/or surface membrane enlargement is required to reach production scale. By taking into consideration challenges such as biomass growth control and maintaining a constant biological activity, this study shows that a biofilm process at an industrial scale for the production of fine chemicals is a sustainable alternative in terms of product yield and biomass waste production. Copyright © 2012 Wiley Periodicals, Inc.

  19. Germline Transgenic Methods for Tracking Cells and Testing Gene Function during Regeneration in the Axolotl

    PubMed Central

    Khattak, Shahryar; Schuez, Maritta; Richter, Tobias; Knapp, Dunja; Haigo, Saori L.; Sandoval-Guzmán, Tatiana; Hradlikova, Kristyna; Duemmler, Annett; Kerney, Ryan; Tanaka, Elly M.

    2013-01-01

    The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum (axolotl) that open up the cellular and molecular genetic dissection of regeneration. We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly overexpress the cell-cycle inhibitor p16INK4a, which negatively regulates spinal cord regeneration. These tissue-specific germline axolotl lines and tightly inducible Cre drivers and LoxP reporter lines render this classical regeneration model molecularly accessible. PMID:24052945

  20. Diffuse shear wave imaging: toward passive elastography using low-frame rate spectral-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Nguyen, Thu-Mai; Zorgani, Ali; Lescanne, Maxime; Boccara, Claude; Fink, Mathias; Catheline, Stefan

    2016-12-01

    Optical coherence tomography (OCT) can map the stiffness of biological tissue by imaging mechanical perturbations (shear waves) propagating in the tissue. Most shear wave elastography (SWE) techniques rely on active shear sources to generate controlled displacements that are tracked at ultrafast imaging rates. Here, we propose a noise-correlation approach to retrieve stiffness information from the imaging of diffuse displacement fields using low-frame rate spectral-domain OCT. We demonstrated the method on tissue-mimicking phantoms and validated the results by comparison with classic ultrafast SWE. Then we investigated the in vivo feasibility on the eye of an anesthetized rat by applying noise correlation to naturally occurring displacements. The results suggest a great potential for passive elastography based on the detection of natural pulsatile motions using conventional spectral-domain OCT systems. This would facilitate the transfer of OCT-elastography to clinical practice, in particular, in ophthalmology or dermatology.

  1. Diffuse shear wave imaging: toward passive elastography using low-frame rate spectral-domain optical coherence tomography.

    PubMed

    Nguyen, Thu-Mai; Zorgani, Ali; Lescanne, Maxime; Boccara, Claude; Fink, Mathias; Catheline, Stefan

    2016-12-01

    Optical coherence tomography (OCT) can map the stiffness of biological tissue by imaging mechanical perturbations (shear waves) propagating in the tissue. Most shear wave elastography (SWE) techniques rely on active shear sources to generate controlled displacements that are tracked at ultrafast imaging rates. Here, we propose a noise-correlation approach to retrieve stiffness information from the imaging of diffuse displacement fields using low-frame rate spectral-domain OCT. We demonstrated the method on tissue-mimicking phantoms and validated the results by comparison with classic ultrafast SWE. Then we investigated the in vivo feasibility on the eye of an anesthetized rat by applying noise correlation to naturally occurring displacements. The results suggest a great potential for passive elastography based on the detection of natural pulsatile motions using conventional spectral-domain OCT systems. This would facilitate the transfer of OCT-elastography to clinical practice, in particular, in ophthalmology or dermatology.

  2. Photobacteriosis: Prevention and Diagnosis

    PubMed Central

    2014-01-01

    Photobacteriosis or fish pasteurellosis is a bacterial disease affecting wild and farm fish. Its etiological agent, the gram negative bacterium Photobacterium damselae subsp. piscicida, is responsible for important economic losses in cultured fish worldwide, in particular in Mediterranean countries and Japan. Efforts have been focused on gaining a better understanding of the biology of the pathogenic microorganism and its natural hosts with the aim of developing effective vaccination strategies and diagnostic tools to control the disease. Conventional vaccinology has thus far yielded unsatisfactory results, and recombinant technology has been applied to identify new antigen candidates for the development of subunit vaccines. Furthermore, molecular methods represent an improvement over classical microbiological techniques for the identification of P. damselae subsp. piscicida and the diagnosis of the disease. The complete sequencing, annotation, and analysis of the pathogen genome will provide insights into the pathogen laying the groundwork for the development of vaccines and diagnostic methods. PMID:24982922

  3. jvenn: an interactive Venn diagram viewer.

    PubMed

    Bardou, Philippe; Mariette, Jérôme; Escudié, Frédéric; Djemiel, Christophe; Klopp, Christophe

    2014-08-29

    Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability. jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams. jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.

  4. Dynamics of poroelastic foams

    NASA Astrophysics Data System (ADS)

    Forterre, Yoel; Sobac, Benjamin

    2010-11-01

    Soft poroelastic structures are widespread in biological tissues such as cartilaginous joints in bones, blood-filled placentae or plant organs. Here we investigate the dynamics of open elastic foams immersed in viscous fluids, as model soft poroelastic materials. The experiment consists in slowly compacting blocs of polyurethane solid foam embedded in silicon oil-tanks and studying their relaxation to equilibrium when the confining stress is suddenly released. Measurements of the local fluid pressure and foam velocity field are compared with a simple two-phase flow approach. For small initial compactions, the results show quantitative agreement with the classical diffusion theory of soil consolidation (Terzaghi, Biot). On the other hand, for large initial compactions, the dynamics exhibits long relaxation times and decompaction fronts, which are mainly controlled by the highly non-linear mechanical response of the foam. The analogy between this process and the evaporation of a polymer melt close to the glass transition will be briefly discussed.

  5. Engineering super mycovirus donor strains of chestnut blight fungus by systematic disruption of multilocus vic genes.

    PubMed

    Zhang, Dong-Xiu; Nuss, Donald L

    2016-02-23

    Transmission of mycoviruses that attenuate virulence (hypovirulence) of pathogenic fungi is restricted by allorecognition systems operating in their fungal hosts. We report the use of systematic molecular gene disruption and classical genetics for engineering fungal hosts with superior virus transmission capabilities. Four of five diallelic virus-restricting allorecognition [vegetative incompatibility (vic)] loci were disrupted in the chestnut blight fungus Cryphonectria parasitica using an adapted Cre-loxP recombination system that allowed excision and recycling of selectable marker genes (SMGs). SMG-free, quadruple vic mutant strains representing both allelic backgrounds of the remaining vic locus were then produced through mating. In combination, these super donor strains were able to transmit hypoviruses to strains that were heteroallelic at one or all of the virus-restricting vic loci. These results demonstrate the feasibility of modulating allorecognition to engineer pathogenic fungi for more efficient transmission of virulence-attenuating mycoviruses and enhanced biological control potential.

  6. Two new species of Oobius Trjapitzin (Hymenoptera, Encyrtidae) egg parasitoids of Agrilus spp. (Coleoptera, Buprestidae) from the USA, including a key and taxonomic notes on other congeneric Nearctic taxa

    PubMed Central

    Triapitsyn, Serguei V.; Petrice, Toby R.; Gates, Michael W.; Bauer, Leah S.

    2015-01-01

    Abstract Oobius Trjapitzin (Hymenoptera, Encyrtidae) species are egg parasitoids that are important for the biological control of some Buprestidae and Cerambycidae (Coleoptera). Two species, Oobius agrili Zhang & Huang and Oobius longoi (Siscaro), were introduced into North America for classical biocontrol and have successfully established. Two new native North American species that parasitize eggs of Agrilus spp. (Buprestidae) are described and illustrated from the USA: Oobius minusculus Triapitsyn & Petrice, sp. n. (Michigan), an egg parasitoid of both Agrilus subcinctus Gory on ash (Fraxinus spp.) and Agrilus egenus Gory on black locust (Robinia pseudoacacia L.) trees, and Oobius whiteorum Triapitsyn, sp. n. (Pennsylvania), an egg parasitoid of Agrilus anxius Gory on European white birch (Betula pendula Roth). A taxonomic key and notes on the Nearctic native and introduced Oobius species are also included. PMID:25931963

  7. The flavivirus capsid protein: Structure, function and perspectives towards drug design.

    PubMed

    Oliveira, Edson R A; Mohana-Borges, Ronaldo; de Alencastro, Ricardo B; Horta, Bruno A C

    2017-01-02

    Flaviviruses, such as dengue and zika viruses, are etiologic agents transmitted to humans mainly by arthropods and are of great epidemiological interest. The flavivirus capsid protein is a structural element required for the viral nucleocapsid assembly that presents the classical function of sheltering the viral genome. After decades of research, many reports have shown its different functionalities and influence over cell normal functioning. The subcellular distribution of this protein, which involves accumulation around lipid droplets and nuclear localization, also corroborates with its multi-functional characteristic. As flavivirus diseases are still in need of global control and in view of the possible key functionalities that the capsid protein promotes over flavivirus biology, novel considerations arise towards anti-flavivirus drug research. This review covers the main aspects concerning structural and functional features of the flavivirus C protein, ultimately, highlighting prospects in drug discovery based on this viral target. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

    PubMed

    Boldon, Lauren; Laliberte, Fallon; Liu, Li

    2015-01-01

    In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  9. Using synthetic biology to make cells tomorrow's test tubes.

    PubMed

    Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

    2016-04-18

    The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

  10. Steering Quantum States Towards Classical Bohr-Like Orbits

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

    Dunning, F. B.; Reinhold, Carlos O; Yoshida, S.

    2010-01-01

    This article furnishes an introduction to the properties of time-dependent electronic wavefunctions in atoms and to physics at the interface between the quantum and classical worlds. We describe how, almost 100 years after the introduction of the Bohr model of the atom, it is now possible using pulsed electric fields to create in the laboratory localized wavepackets in high-n (n ~ 300) Rydberg atoms that travel in near-circular Bohr-like orbits mimicking the behavior of a classical electron. The control protocols employed are explained with the aid of quantum and classical dynamics. Remarkably, while many aspects of the underlying behavior canmore » be described using classical arguments, even at n ~ 300 purely quantum effects such as revivals can be seen.« less

  11. Differences in Kaposi sarcoma-associated herpesvirus-specific and –nonspecific immune responses in classic Kaposi sarcoma cases and matched controls in Sicily

    PubMed Central

    Amodio, Emanuele; Goedert, James J.; Barozzi, Patrizia; Riva, Giovanni; Firenze, Alberto; Bonura, Filippa; Viviano, Enza; Romano, Nino; Luppi, Mario

    2011-01-01

    SUMMARY Kaposi sarcoma (KS) may develop because of incompetent immune responses, both nonspecifically and specifically against the KS-associated herpes virus (KSHV). Peripheral blood mononuclear cells from 15 classic (non-AIDS) KS cases, 13 KSHV seropositives (without KS), and 15 KSHV-seronegative controls were tested for interferon-γ T-cell (Elispot) responses to KSHV-LANA, KSHV-K8.1, and CMV/EBV peptide pools. The forearm and thigh of each participant also was tested for delayed-type hypersensitivity (DTH) against common recall antigens. Groups were compared with Fisher exact test and multinomial logistic regression to calculate odds ratios (OR) and 95% confidence intervals (CI). KSHV Elispot response was detected in 10 (67%) classic KS cases, 11 (85%) KSHV seropositives (without KS), and 2 (13%) seronegative controls. All 4 cases with KSHV-LANA responses had current KS lesions, whereas 5 of 6 cases with KSHV-K8.1 responses had no lesions (P=0.048). No case responded to both LANA and K8.1. Compared to seronegative controls, risk for classic KS was inversely related to DTH in the thigh (OR 0.71, 95% CI 0.55–0.94, P=0.01), directly associated with DTH in the forearm (OR 1.35, 95% CI 1.02–1.80, P=0.04), and tended to be increased 5-fold per KSHV Elispot response (OR 5.13, 95% CI 0.86–30.77, P=0.07). Compared to KSHV seropositives (without KS), risk for classic KS, was reduced 5-fold (OR 0.20, CI 0.03–0.77, P=0.04) per KSHV response. CMV/EBV Elispot responses were irrelevant. Deficiency of both KSHV-specific and –nonspecific immunity is associated with classic KS. This may clarify why Kaposi sarcoma responds to immune reconstitution. PMID:21740480

  12. Improved direct torque control of an induction generator used in a wind conversion system connected to the grid.

    PubMed

    Abdelli, Radia; Rekioua, Djamila; Rekioua, Toufik; Tounzi, Abdelmounaïm

    2013-07-01

    This paper presents a modulated hysteresis direct torque control (MHDTC) applied to an induction generator (IG) used in wind energy conversion systems (WECs) connected to the electrical grid through a back-to-back converter. The principle of this strategy consists in superposing to the torque reference a triangular signal, as in the PWM strategy, with the desired switching frequency. This new modulated reference is compared to the estimated torque by using a hysteresis controller as in the classical direct torque control (DTC). The aim of this new approach is to lead to a constant frequency and low THD in grid current with a unit power factor and a minimum voltage variation despite the wind variation. To highlight the effectiveness of the proposed method, a comparison was made with classical DTC and field oriented control method (FOC). The obtained simulation results, with a variable wind profile, show an adequate dynamic of the conversion system using the proposed method compared to the classical approaches. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

  13. FOXO3 Modulates Endothelial Gene Expression and Function by Classical and Alternative Mechanisms*

    PubMed Central

    Czymai, Tobias; Viemann, Dorothee; Sticht, Carsten; Molema, Grietje; Goebeler, Matthias; Schmidt, Marc

    2010-01-01

    FOXO transcription factors represent targets of the phosphatidylinositol 3-kinase/protein kinase B survival pathway controlling important biological processes, such as cell cycle progression, apoptosis, vascular remodeling, stress responses, and metabolism. Recent studies suggested the existence of alternative mechanisms of FOXO-dependent gene expression beyond classical binding to a FOXO-responsive DNA-binding element (FRE). Here we analyzed the relative contribution of those mechanisms to vascular function by comparing the transcriptional and cellular responses to conditional activation of FOXO3 and a corresponding FRE-binding mutant in human primary endothelial cells. We demonstrate that FOXO3 controls expression of vascular remodeling genes in an FRE-dependent manner. In contrast, FOXO3-induced cell cycle arrest and apoptosis occurs independently of FRE binding, albeit FRE-dependent gene expression augments the proapoptotic response. These findings are supported by bioinformatical analysis, which revealed a statistical overrepresentation of cell cycle regulators and apoptosis-related genes in the group of co-regulated genes. Molecular analysis of FOXO3-induced endothelial apoptosis excluded modulators of the extrinsic death receptor pathway and demonstrated important roles for the BCL-2 family members BIM and NOXA in this process. Although NOXA essentially contributed to FRE-dependent apoptosis, BIM was effectively induced in the absence of FRE-binding, and small interfering RNA-mediated BIM depletion could rescue apoptosis induced by both FOXO3 mutants. These data suggest BIM as a critical cell type-specific mediator of FOXO3-induced endothelial apoptosis, whereas NOXA functions as an amplifying factor. Our study provides the first comprehensive analysis of alternatively regulated FOXO3 targets in relevant primary cells and underscores the importance of such genes for endothelial function and integrity. PMID:20123982

  14. Cerebrospinal fluid and blood biomarkers for neurodegenerative dementias: An update of the Consensus of the Task Force on Biological Markers in Psychiatry of the World Federation of Societies of Biological Psychiatry.

    PubMed

    Lewczuk, Piotr; Riederer, Peter; O'Bryant, Sid E; Verbeek, Marcel M; Dubois, Bruno; Visser, Pieter Jelle; Jellinger, Kurt A; Engelborghs, Sebastiaan; Ramirez, Alfredo; Parnetti, Lucilla; Jack, Clifford R; Teunissen, Charlotte E; Hampel, Harald; Lleó, Alberto; Jessen, Frank; Glodzik, Lidia; de Leon, Mony J; Fagan, Anne M; Molinuevo, José Luis; Jansen, Willemijn J; Winblad, Bengt; Shaw, Leslie M; Andreasson, Ulf; Otto, Markus; Mollenhauer, Brit; Wiltfang, Jens; Turner, Martin R; Zerr, Inga; Handels, Ron; Thompson, Alexander G; Johansson, Gunilla; Ermann, Natalia; Trojanowski, John Q; Karaca, Ilker; Wagner, Holger; Oeckl, Patrick; van Waalwijk van Doorn, Linda; Bjerke, Maria; Kapogiannis, Dimitrios; Kuiperij, H Bea; Farotti, Lucia; Li, Yi; Gordon, Brian A; Epelbaum, Stéphane; Vos, Stephanie J B; Klijn, Catharina J M; Van Nostrand, William E; Minguillon, Carolina; Schmitz, Matthias; Gallo, Carla; Lopez Mato, Andrea; Thibaut, Florence; Lista, Simone; Alcolea, Daniel; Zetterberg, Henrik; Blennow, Kaj; Kornhuber, Johannes

    2018-06-01

    In the 12 years since the publication of the first Consensus Paper of the WFSBP on biomarkers of neurodegenerative dementias, enormous advancement has taken place in the field, and the Task Force takes now the opportunity to extend and update the original paper. New concepts of Alzheimer's disease (AD) and the conceptual interactions between AD and dementia due to AD were developed, resulting in two sets for diagnostic/research criteria. Procedures for pre-analytical sample handling, biobanking, analyses and post-analytical interpretation of the results were intensively studied and optimised. A global quality control project was introduced to evaluate and monitor the inter-centre variability in measurements with the goal of harmonisation of results. Contexts of use and how to approach candidate biomarkers in biological specimens other than cerebrospinal fluid (CSF), e.g. blood, were precisely defined. Important development was achieved in neuroimaging techniques, including studies comparing amyloid-β positron emission tomography results to fluid-based modalities. Similarly, development in research laboratory technologies, such as ultra-sensitive methods, raises our hopes to further improve analytical and diagnostic accuracy of classic and novel candidate biomarkers. Synergistically, advancement in clinical trials of anti-dementia therapies energises and motivates the efforts to find and optimise the most reliable early diagnostic modalities. Finally, the first studies were published addressing the potential of cost-effectiveness of the biomarkers-based diagnosis of neurodegenerative disorders.

  15. Effects of Classical Background Music on Stress, Anxiety, and Knowledge of Filipino Baccalaureate Nursing Students.

    PubMed

    Evangelista, Kevin; Macabasag, Romeo Luis A; Capili, Brylle; Castro, Timothy; Danque, Marilee; Evangelista, Hanzel; Rivero, Jenica Ana; Gonong, Michell Katrina; Diño, Michael Joseph; Cajayon, Sharon

    2017-10-28

    Previous work on the use of background music suggests conflicting results in various psychological, behavioral, and educational measures. This quasi-experiment examined the effect of integrating classical background music during a lecture on stress, anxiety, and knowledge. A total of 42 nursing students participated this study. We utilized independent sample t-test and multivariate analysis of variance to examine the effect of classical background music. Our findings suggest that the presence or absence of classical background music do not affect stress, anxiety, and knowledge scores (Λ = 0.999 F(3, 78) = 0.029, p = 0.993). We provided literature to explain the non-significant result. Although classical music failed to establish a significant influence on the dependent variables, classical background music during lecture hours can be considered a non-threatening stimulus. We recommend follow up studies regarding the role of classical background music in regulating attention control of nursing students during lecture hours.

  16. Drosophila melanogaster and the development of biology in the 20th century.

    PubMed

    Arias, Alfonso Martinez

    2008-01-01

    The fruit fly Drosophila has played a central role in the development of biology during the 20th century. First chosen as a convenient organism to test evolutionary theories soon became the central element in an elaborate, fruitful, and insightful research program dealing with the nature and function of the gene. Through the activities of TH Morgan and his students, Drosophila did more than any other organism to lay down the foundations of genetics as a discipline and a tool for biology. In the last third of the century, a judicious blend of classical genetics and molecular biology focused on some mutants affecting the pattern of the Drosophila larva and the adult, and unlocked the molecular mechanisms of development. Surprisingly, many of the genes identified in this exercise turned to be conserved across organisms. This observation provided a vista of universality at a fundamental level of biological activity. At the dawn of the 21st century, Drosophila continues to be center stage in the development of biology and to open new ways of seeing cells and to understand the construction and the functioning of organisms.

  17. Air-liquid interface exposure to aerosols of poorly soluble nanomaterials induces different biological activation levels compared to exposure to suspensions.

    PubMed

    Loret, Thomas; Peyret, Emmanuel; Dubreuil, Marielle; Aguerre-Chariol, Olivier; Bressot, Christophe; le Bihan, Olivier; Amodeo, Tanguy; Trouiller, Bénédicte; Braun, Anne; Egles, Christophe; Lacroix, Ghislaine

    2016-11-03

    Recently, much progress has been made to develop more physiologic in vitro models of the respiratory system and improve in vitro simulation of particle exposure through inhalation. Nevertheless, the field of nanotoxicology still suffers from a lack of relevant in vitro models and exposure methods to predict accurately the effects observed in vivo, especially after respiratory exposure. In this context, the aim of our study was to evaluate if exposing pulmonary cells at the air-liquid interface to aerosols of inhalable and poorly soluble nanomaterials generates different toxicity patterns and/or biological activation levels compared to classic submerged exposures to suspensions. Three nano-TiO 2 and one nano-CeO 2 were used. An exposure system was set up using VitroCell® devices to expose pulmonary cells at the air-liquid interface to aerosols. A549 alveolar cells in monocultures or in co-cultures with THP-1 macrophages were exposed to aerosols in inserts or to suspensions in inserts and in plates. Submerged exposures in inserts were performed, using similar culture conditions and exposure kinetics to the air-liquid interface, to provide accurate comparisons between the methods. Exposure in plates using classical culture and exposure conditions was performed to provide comparable results with classical submerged exposure studies. The biological activity of the cells (inflammation, cell viability, oxidative stress) was assessed at 24 h and comparisons of the nanomaterial toxicities between exposure methods were performed. Deposited doses of nanomaterials achieved using our aerosol exposure system were sufficient to observe adverse effects. Co-cultures were more sensitive than monocultures and biological responses were usually observed at lower doses at the air-liquid interface than in submerged conditions. Nevertheless, the general ranking of the nanomaterials according to their toxicity was similar across the different exposure methods used. We showed that exposure of cells at the air-liquid interface represents a valid and sensitive method to assess the toxicity of several poorly soluble nanomaterials. We underlined the importance of the cellular model used and offer the possibility to deal with low deposition doses by using more sensitive and physiologic cellular models. This brings perspectives towards the use of relevant in vitro methods of exposure to assess nanomaterial toxicity.

  18. Dynamic optimization and its relation to classical and quantum constrained systems

    NASA Astrophysics Data System (ADS)

    Contreras, Mauricio; Pellicer, Rely; Villena, Marcelo

    2017-08-01

    We study the structure of a simple dynamic optimization problem consisting of one state and one control variable, from a physicist's point of view. By using an analogy to a physical model, we study this system in the classical and quantum frameworks. Classically, the dynamic optimization problem is equivalent to a classical mechanics constrained system, so we must use the Dirac method to analyze it in a correct way. We find that there are two second-class constraints in the model: one fix the momenta associated with the control variables, and the other is a reminder of the optimal control law. The dynamic evolution of this constrained system is given by the Dirac's bracket of the canonical variables with the Hamiltonian. This dynamic results to be identical to the unconstrained one given by the Pontryagin equations, which are the correct classical equations of motion for our physical optimization problem. In the same Pontryagin scheme, by imposing a closed-loop λ-strategy, the optimality condition for the action gives a consistency relation, which is associated to the Hamilton-Jacobi-Bellman equation of the dynamic programming method. A similar result is achieved by quantizing the classical model. By setting the wave function Ψ(x , t) =e iS(x , t) in the quantum Schrödinger equation, a non-linear partial equation is obtained for the S function. For the right-hand side quantization, this is the Hamilton-Jacobi-Bellman equation, when S(x , t) is identified with the optimal value function. Thus, the Hamilton-Jacobi-Bellman equation in Bellman's maximum principle, can be interpreted as the quantum approach of the optimization problem.

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

    Williamson, Jeffrey F.

    This paper briefly reviews the evolution of brachytherapy dosimetry from 1900 to the present. Dosimetric practices in brachytherapy fall into three distinct eras: During the era of biological dosimetry (1900-1938), radium pioneers could only specify Ra-226 and Rn-222 implants in terms of the mass of radium encapsulated within the implanted sources. Due to the high energy of its emitted gamma rays and the long range of its secondary electrons in air, free-air chambers could not be used to quantify the output of Ra-226 sources in terms of exposure. Biological dosimetry, most prominently the threshold erythema dose, gained currency as amore » means of intercomparing radium treatments with exposure-calibrated orthovoltage x-ray units. The classical dosimetry era (1940-1980) began with successful exposure standardization of Ra-226 sources by Bragg-Gray cavity chambers. Classical dose-computation algorithms, based upon 1-D buildup factor measurements and point-source superposition computational algorithms, were able to accommodate artificial radionuclides such as Co-60, Ir-192, and Cs-137. The quantitative dosimetry era (1980- ) arose in response to the increasing utilization of low energy K-capture radionuclides such as I-125 and Pd-103 for which classical approaches could not be expected to estimate accurate correct doses. This led to intensive development of both experimental (largely TLD-100 dosimetry) and Monte Carlo dosimetry techniques along with more accurate air-kerma strength standards. As a result of extensive benchmarking and intercomparison of these different methods, single-seed low-energy radionuclide dose distributions are now known with a total uncertainty of 3%-5%.« less

  20. Enhanced biological processes associated with alopecia in polar bears (Ursus maritimus).

    PubMed

    Bowen, Lizabeth; Miles, A Keith; Stott, Jeffrey; Waters, Shannon; Atwood, Todd

    2015-10-01

    Populations of wildlife species worldwide experience incidents of mass morbidity and mortality. Primary or secondary drivers of these events may escape classical detection methods for identifying microbial insults, toxin exposure, or additional stressors. In 2012, 28% of polar bears sampled in a study in the southern Beaufort Sea region of Alaska had varying degrees of alopecia that was concomitant with reduced body condition. Concurrently, elevated numbers of sick or dead ringed seals were detected in the southern Beaufort, Chukchi, and Bering seas in 2012, resulting in the declaration of an unusual mortality event (UME) by the National Oceanic and Atmospheric Administration (NOAA). The primary and possible ancillary causative stressors of these events are unknown, and related physiological changes within individual animals have been undetectable using classical diagnostic methods. Here we present an emerging technology as a potentially guiding investigative approach aimed at elucidating the circumstances responsible for the susceptibility of certain polar bears to observed conditions. Using transcriptomic analysis we identified enhanced biological processes including immune response, viral defense, and response to stress in polar bears with alopecia. Our results support an alternative mechanism of investigation into the causative agents that, when used proactively, could serve as an early indicator for populations and species at risk. We suggest that current or classical methods for investigation into events of unusual morbidity and mortality can be costly, sometimes unfocused, and often inconclusive. Advances in technology allow for implementation of a holistic system of surveillance and investigation that could provide early warning of health concerns in wildlife species important to humans. Published by Elsevier B.V.

  1. Enhanced biological processes associated with alopecia in polar bears (Ursus maritimus)

    USGS Publications Warehouse

    Bowen, Lizabeth; Miles, A. Keith; Stott, Jeffrey L.; Waters, Shannon C.; Atwood, Todd C.

    2015-01-01

    Populations of wildlife species worldwide experience incidents of mass morbidity and mortality. Primary or secondary drivers of these events may escape classical detection methods for identifying microbial insults, toxin exposure, or additional stressors. In 2012, 28% of polar bears sampled in a study in the southern Beaufort Sea region of Alaska had varying degrees of alopecia that was concomitant with reduced body condition. Concurrently, elevated numbers of sick or dead ringed seals were detected in the southern Beaufort, Chukchi, and Bering seas in 2012, resulting in the declaration of an unusual mortality event (UME) by the National Oceanic and Atmospheric Administration (NOAA). The primary and possible ancillary causative stressors of these events are unknown, and related physiological changes within individual animals have been undetectable using classical diagnostic methods. Here we present an emerging technology as a potentially guiding investigative approach aimed at elucidating the circumstances responsible for the susceptibility of certain polar bears to observed conditions. Using transcriptomic analysis we identified enhanced biological processes including immune response, viral defense, and response to stress in polar bears with alopecia. Our results support an alternative mechanism of investigation into the causative agents that, when used proactively, could serve as an early indicator for populations and species at risk. We suggest that current or classical methods for investigation into events of unusual morbidity and mortality can be costly, sometimes unfocused, and often inconclusive. Advances in technology allow for implementation of a holistic system of surveillance and investigation that could provide early warning of health concerns in wildlife species important to humans.

  2. History of dose specification in Brachytherapy: From Threshold Erythema Dose to Computational Dosimetry

    NASA Astrophysics Data System (ADS)

    Williamson, Jeffrey F.

    2006-09-01

    This paper briefly reviews the evolution of brachytherapy dosimetry from 1900 to the present. Dosimetric practices in brachytherapy fall into three distinct eras: During the era of biological dosimetry (1900-1938), radium pioneers could only specify Ra-226 and Rn-222 implants in terms of the mass of radium encapsulated within the implanted sources. Due to the high energy of its emitted gamma rays and the long range of its secondary electrons in air, free-air chambers could not be used to quantify the output of Ra-226 sources in terms of exposure. Biological dosimetry, most prominently the threshold erythema dose, gained currency as a means of intercomparing radium treatments with exposure-calibrated orthovoltage x-ray units. The classical dosimetry era (1940-1980) began with successful exposure standardization of Ra-226 sources by Bragg-Gray cavity chambers. Classical dose-computation algorithms, based upon 1-D buildup factor measurements and point-source superposition computational algorithms, were able to accommodate artificial radionuclides such as Co-60, Ir-192, and Cs-137. The quantitative dosimetry era (1980- ) arose in response to the increasing utilization of low energy K-capture radionuclides such as I-125 and Pd-103 for which classical approaches could not be expected to estimate accurate correct doses. This led to intensive development of both experimental (largely TLD-100 dosimetry) and Monte Carlo dosimetry techniques along with more accurate air-kerma strength standards. As a result of extensive benchmarking and intercomparison of these different methods, single-seed low-energy radionuclide dose distributions are now known with a total uncertainty of 3%-5%.

  3. Linking environmental variability to population and community dynamics: Chapter 7

    USGS Publications Warehouse

    Pantel, Jelena H.; Pendleton, Daniel E.; Walters, Annika W.; Rogers, Lauren A.

    2014-01-01

    Linking population and community responses to environmental variability lies at the heart of ecology, yet methodological approaches vary and existence of broad patterns spanning taxonomic groups remains unclear. We review the characteristics of environmental and biological variability. Classic approaches to link environmental variability to population and community variability are discussed as are the importance of biotic factors such as life history and community interactions. In addition to classic approaches, newer techniques such as information theory and artificial neural networks are reviewed. The establishment and expansion of observing networks will provide new long-term ecological time-series data, and with it, opportunities to incorporate environmental variability into research. This review can help guide future research in the field of ecological and environmental variability.

  4. Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car Parrinello) molecular dynamics

    NASA Astrophysics Data System (ADS)

    Hammond, Philip S.; Wu, Yudong; Harris, Rebecca; Minehardt, Todd J.; Car, Roberto; Schmitt, Jeffrey D.

    2005-01-01

    A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

  5. Nematode taxonomy: from morphology to metabarcoding

    NASA Astrophysics Data System (ADS)

    Ahmed, M.; Sapp, M.; Prior, T.; Karssen, G.; Back, M.

    2015-11-01

    Nematodes represent a species rich and morphologically diverse group of metazoans inhabiting both aquatic and terrestrial environments. Their role as biological indicators and as key players in nutrient cycling has been well documented. Some groups of nematodes are also known to cause significant losses to crop production. In spite of this, knowledge of their diversity is still limited due to the difficulty in achieving species identification using morphological characters. Molecular methodology has provided very useful means of circumventing the numerous limitations associated with classical morphology based identification. We discuss herein the history and the progress made within the field of nematode systematics, the limitations of classical taxonomy and how the advent of high throughput sequencing is facilitating advanced ecological and molecular studies.

  6. Contemporary understanding of riots: Classical crowd psychology, ideology and the social identity approach.

    PubMed

    Stott, Clifford; Drury, John

    2016-04-01

    This article explores the origins and ideology of classical crowd psychology, a body of theory reflected in contemporary popularised understandings such as of the 2011 English 'riots'. This article argues that during the nineteenth century, the crowd came to symbolise a fear of 'mass society' and that 'classical' crowd psychology was a product of these fears. Classical crowd psychology pathologised, reified and decontextualised the crowd, offering the ruling elites a perceived opportunity to control it. We contend that classical theory misrepresents crowd psychology and survives in contemporary understanding because it is ideological. We conclude by discussing how classical theory has been supplanted in academic contexts by an identity-based crowd psychology that restores the meaning to crowd action, replaces it in its social context and in so doing transforms theoretical understanding of 'riots' and the nature of the self. © The Author(s) 2016.

  7. Experimental Demonstration of Coherent Control in Quantum Chaotic Systems

    NASA Astrophysics Data System (ADS)

    Bitter, M.; Milner, V.

    2017-01-01

    We experimentally demonstrate coherent control of a quantum system, whose dynamics is chaotic in the classical limit. Interaction of diatomic molecules with a periodic sequence of ultrashort laser pulses leads to the dynamical localization of the molecular angular momentum, a characteristic feature of the chaotic quantum kicked rotor. By changing the phases of the rotational states in the initially prepared coherent wave packet, we control the rotational distribution of the final localized state and its total energy. We demonstrate the anticipated sensitivity of control to the exact parameters of the kicking field, as well as its disappearance in the classical regime of excitation.

  8. Computational quantum-classical boundary of noisy commuting quantum circuits

    PubMed Central

    Fujii, Keisuke; Tamate, Shuhei

    2016-01-01

    It is often said that the transition from quantum to classical worlds is caused by decoherence originated from an interaction between a system of interest and its surrounding environment. Here we establish a computational quantum-classical boundary from the viewpoint of classical simulatability of a quantum system under decoherence. Specifically, we consider commuting quantum circuits being subject to decoherence. Or equivalently, we can regard them as measurement-based quantum computation on decohered weighted graph states. To show intractability of classical simulation in the quantum side, we utilize the postselection argument and crucially strengthen it by taking noise effect into account. Classical simulatability in the classical side is also shown constructively by using both separable criteria in a projected-entangled-pair-state picture and the Gottesman-Knill theorem for mixed state Clifford circuits. We found that when each qubit is subject to a single-qubit complete-positive-trace-preserving noise, the computational quantum-classical boundary is sharply given by the noise rate required for the distillability of a magic state. The obtained quantum-classical boundary of noisy quantum dynamics reveals a complexity landscape of controlled quantum systems. This paves a way to an experimentally feasible verification of quantum mechanics in a high complexity limit beyond classically simulatable region. PMID:27189039

  9. Computational quantum-classical boundary of noisy commuting quantum circuits.

    PubMed

    Fujii, Keisuke; Tamate, Shuhei

    2016-05-18

    It is often said that the transition from quantum to classical worlds is caused by decoherence originated from an interaction between a system of interest and its surrounding environment. Here we establish a computational quantum-classical boundary from the viewpoint of classical simulatability of a quantum system under decoherence. Specifically, we consider commuting quantum circuits being subject to decoherence. Or equivalently, we can regard them as measurement-based quantum computation on decohered weighted graph states. To show intractability of classical simulation in the quantum side, we utilize the postselection argument and crucially strengthen it by taking noise effect into account. Classical simulatability in the classical side is also shown constructively by using both separable criteria in a projected-entangled-pair-state picture and the Gottesman-Knill theorem for mixed state Clifford circuits. We found that when each qubit is subject to a single-qubit complete-positive-trace-preserving noise, the computational quantum-classical boundary is sharply given by the noise rate required for the distillability of a magic state. The obtained quantum-classical boundary of noisy quantum dynamics reveals a complexity landscape of controlled quantum systems. This paves a way to an experimentally feasible verification of quantum mechanics in a high complexity limit beyond classically simulatable region.

  10. Computational quantum-classical boundary of noisy commuting quantum circuits

    NASA Astrophysics Data System (ADS)

    Fujii, Keisuke; Tamate, Shuhei

    2016-05-01

    It is often said that the transition from quantum to classical worlds is caused by decoherence originated from an interaction between a system of interest and its surrounding environment. Here we establish a computational quantum-classical boundary from the viewpoint of classical simulatability of a quantum system under decoherence. Specifically, we consider commuting quantum circuits being subject to decoherence. Or equivalently, we can regard them as measurement-based quantum computation on decohered weighted graph states. To show intractability of classical simulation in the quantum side, we utilize the postselection argument and crucially strengthen it by taking noise effect into account. Classical simulatability in the classical side is also shown constructively by using both separable criteria in a projected-entangled-pair-state picture and the Gottesman-Knill theorem for mixed state Clifford circuits. We found that when each qubit is subject to a single-qubit complete-positive-trace-preserving noise, the computational quantum-classical boundary is sharply given by the noise rate required for the distillability of a magic state. The obtained quantum-classical boundary of noisy quantum dynamics reveals a complexity landscape of controlled quantum systems. This paves a way to an experimentally feasible verification of quantum mechanics in a high complexity limit beyond classically simulatable region.

  11. The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

    PubMed

    Pollard, Thomas D

    2014-12-02

    This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Island biogeography: Taking the long view of nature's laboratories.

    PubMed

    Whittaker, Robert J; Fernández-Palacios, José María; Matthews, Thomas J; Borregaard, Michael K; Triantis, Kostas A

    2017-09-01

    Islands provide classic model biological systems. We review how growing appreciation of geoenvironmental dynamics of marine islands has led to advances in island biogeographic theory accommodating both evolutionary and ecological phenomena. Recognition of distinct island geodynamics permits general models to be developed and modified to account for patterns of diversity, diversification, lineage development, and trait evolution within and across island archipelagos. Emergent patterns of diversity include predictable variation in island species-area relationships, progression rule colonization from older to younger land masses, and syndromes including loss of dispersability and secondary woodiness in herbaceous plant lineages. Further developments in Earth system science, molecular biology, and trait data for islands hold continued promise for unlocking many of the unresolved questions in evolutionary biology and biogeography. Copyright © 2017, American Association for the Advancement of Science.

  13. A new era in science at Washington University, St. Louis: Viktor Hamburger's zoology department in the 1940's.

    PubMed

    Carson, H L

    2001-04-01

    In the early 1940s, the administration of the College of Arts and Sciences at Washington University, St. Louis was firmly in the hands of classical scholars who were not inclined to promote the development of modern research on scientific subjects. Funds supporting research in biology favored the School of Medicine and the Missouri Botanical Garden. Viktor Hamburger arrived at Washington University in 1935. At about the time he became the Acting Chairman of Zoology in 1942, research work in the biological departments began a dramatic surge that has continued to this day. For 65 years under his counsel and leadership, basic biology has thrived at this fine institution. As an early faculty recruit, I recount here a few personal recollections from those formative years.

  14. E/Z Isomers and Isomerization

    NASA Astrophysics Data System (ADS)

    Liaaen-Jensen, Synnøve; Lutnœes, Bjart Frode

    The natural occurrence of several carotenoid cis isomers and their biological significance were not anticipated in 1962, when the classical monograph on cis-trans isomeric carotenoids [1] was published. More recent research has demonstrated that various cis isomers occur naturally in bacteria plants, algae and invertebrate animals, and are present in human blood and tissues. The participation of cis isomers in the biosynthethic route to coloured carotenoids is well established (Volume 3, Chapter 2). Important biological functions of (15Z)-carotenoids in photosynthesis have been revealed [2]. In relation to health aspects of carotenoids, the bioavailability of cis isomers may be higher than that of the all-trans isomer [3], and accumulated evidence suggests that cis/trans isomerization may occur in biological tissues, particularly of lycopene (31) in human serum [4] (Volume 5, Chapter 7).

  15. Conditional Dispersive Readout of a CMOS Single-Electron Memory Cell

    NASA Astrophysics Data System (ADS)

    Schaal, S.; Barraud, S.; Morton, J. J. L.; Gonzalez-Zalba, M. F.

    2018-05-01

    Quantum computers require interfaces with classical electronics for efficient qubit control, measurement, and fast data processing. Fabricating the qubit and the classical control layer using the same technology is appealing because it will facilitate the integration process, improving feedback speeds and offering potential solutions to wiring and layout challenges. Integrating classical and quantum devices monolithically, using complementary metal-oxide-semiconductor (CMOS) processes, enables the processor to profit from the most mature industrial technology for the fabrication of large-scale circuits. We demonstrate a CMOS single-electron memory cell composed of a single quantum dot and a transistor that locks charge on the quantum-dot gate. The single-electron memory cell is conditionally read out by gate-based dispersive sensing using a lumped-element L C resonator. The control field-effect transistor (FET) and quantum dot are fabricated on the same chip using fully depleted silicon-on-insulator technology. We obtain a charge sensitivity of δ q =95 ×10-6e Hz-1 /2 when the quantum-dot readout is enabled by the control FET, comparable to results without the control FET. Additionally, we observe a single-electron retention time on the order of a second when storing a single-electron charge on the quantum dot at millikelvin temperatures. These results demonstrate first steps towards time-based multiplexing of gate-based dispersive readout in CMOS quantum devices opening the path for the development of an all-silicon quantum-classical processor.

  16. From classical to quantum plasmonics: Classical emitter and SPASER

    NASA Astrophysics Data System (ADS)

    Balykin, V. I.

    2018-02-01

    The key advantage of plasmonics is in pushing our control of light down to the nanoscale. It is possible to envision lithographically fabricated plasmonic devices for future quantum information processing or cryptography at the nanoscale in two dimensions. A first step in this direction is a demonstration of a highly efficient nanoscale light source. Here we demonstrate two types of nanoscale sources of optical fields: 1) the classical metallic nanostructure emitter and 2) the plasmonic nanolaser - SPASER.

  17. When physics is not "just physics": complexity science invites new measurement frames for exploring the physics of cognitive and biological development.

    PubMed

    Kelty-Stephen, Damian; Dixon, James A

    2012-01-01

    The neurobiological sciences have struggled to resolve the physical foundations for biological and cognitive phenomena with a suspicion that biological and cognitive systems, capable of exhibiting and contributing to structure within themselves and through their contexts, are fundamentally distinct or autonomous from purely physical systems. Complexity science offers new physics-based approaches to explaining biological and cognitive phenomena. In response to controversy over whether complexity science might seek to "explain away" biology and cognition as "just physics," we propose that complexity science serves as an application of recent advances in physics to phenomena in biology and cognition without reducing or undermining the integrity of the phenomena to be explained. We highlight that physics is, like the neurobiological sciences, an evolving field and that the threat of reduction is overstated. We propose that distinctions between biological and cognitive systems from physical systems are pretheoretical and thus optional. We review our own work applying insights from post-classical physics regarding turbulence and fractal fluctuations to the problems of developing cognitive structure. Far from hoping to reduce biology and cognition to "nothing but" physics, we present our view that complexity science offers new explanatory frameworks for considering physical foundations of biological and cognitive phenomena.

  18. Anterior cingulate cortex and intuitive bias detection during number conservation.

    PubMed

    Simon, Grégory; Lubin, Amélie; Houdé, Olivier; De Neys, Wim

    2015-01-01

    Children's number conservation is often biased by misleading intuitions but the precise nature of these conservation errors is not clear. A key question is whether children detect that their erroneous conservation judgment is unwarranted. The present study reanalyzed available fMRI data to test the implication of the anterior cingulate cortex (ACC) in this detection process. We extracted mean BOLD (Blood Oxygen Level Dependent) signal values in an independently defined ACC region of interest (ROI) during presentation of classic and control number conservation problems. In classic trials, an intuitively cued visuospatial response conflicted with the correct conservation response, whereas this conflict was not present in the control trials. Results showed that ACC activation increased when solving the classic conservation problems. Critically, this increase did not differ between participants who solved the classic problems correctly (i.e., so-called conservers) and incorrectly (i.e., so-called non-conservers). Additional control analyses of inferior and lateral prefrontal ROIs showed that the group of conservers did show stronger activation in the right inferior frontal gyrus and right lateral middle frontal gyrus. In line with recent behavioral findings, these data lend credence to the hypothesis that even non-conserving children detect the biased nature of their judgment. The key difference between conservers and non-conservers seems to lie in a differential recruitment of inferior and lateral prefrontal regions associated with inhibitory control.

  19. Liquid-based cytology improves preoperative diagnostic accuracy of the tall cell variant of papillary thyroid carcinoma.

    PubMed

    Lee, Sung Hak; Jung, Chan Kwon; Bae, Ja Seong; Jung, So Lyung; Choi, Yeong Jin; Kang, Chang Suk

    2014-01-01

    The tall cell variant (TCV) of papillary thyroid carcinoma (PTC) is the most common among the aggressive variants of the disease. We aimed to investigate the clinicopathologic characteristics of TCV, and evaluate the diagnostic efficacy of liquid-based cytology (LBC) in TCV detection compared with conventional smear in thyroid fine needle aspiration (FNA). A total of 266 consecutive patients (220 women and 46 men) with PTC were enrolled. We analyzed tumor characteristics according to histologic growth patterns as classic, classic PTC with tall cell features, and TCV. The cytomorphologic features of these subtypes were investigated according to the preparation methods of conventional smear and LBC. TCV and classic PTC with tall cell features comprised 4.9% and 6.0% of all tumors, respectively, and were significantly associated with older age at presentation, larger tumor size, high frequency of extrathyroid extension, and BRAF mutation in comparison with classic PTC. However, there was no statistically significant difference in clinicopathologic features between TCV and classic PTC with tall cell features. Tall cells were more easily detected by LBC than by conventional smear. The percentage of tall cells identified using LBC was well correlated with three histologic subtypes. Our results demonstrate that TCV is more common than previously recognized in Korea and any PTC containing tall cells may have identical biological behavior regardless of the precise proportions of tall cells. It is possible to make a preoperative diagnosis of TCV using LBC. Copyright © 2013 Wiley Periodicals, Inc.

  20. Application of the maximal covering location problem to habitat reserve site selection: a review

    Treesearch

    Stephanie A. Snyder; Robert G. Haight

    2016-01-01

    The Maximal Covering Location Problem (MCLP) is a classic model from the location science literature which has found wide application. One important application is to a fundamental problem in conservation biology, the Maximum Covering Species Problem (MCSP), which identifies land parcels to protect to maximize the number of species represented in the selected sites. We...

  1. Simulation of a Classically Conditioned Response: Components of the Input Trace and a Cerebellar Neural Network Implementation of the Sutton-Barto-Desmond Model.

    DTIC Science & Technology

    1987-09-14

    set of coordinates that will facilitate discussion. Figure 16 omits some of details included in most textbook renderings of the cerebellum. For...Engineering, BME -24: 449-456 (1977). Hawkins, R.D. and Kandel, E.R. Is there a cell-biological alphabet for simple forms of learning? Psychological Review

  2. 2012 Gordon Research Conference, Electron donor-acceptor interactions, August 5-10 2012

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

    McCusker, James

    The upcoming incarnation of the Gordon Research Conference on Electron Donor Acceptor Interactions will feature sessions on classic topics including proton-coupled electron transfer, dye-sensitized solar cells, and biological electron transfer, as well as emerging areas such as quantum coherence effects in donor-acceptor interactions, spintronics, and the application of donor-acceptor interactions in chemical synthesis.

  3. Detection of Salicylic Acid in Willow Bark: An Addition to a Classic Series of Experiments in the Introductory Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Clay, Matthew D.; McLeod, Eric J.

    2012-01-01

    Salicylic acid and its derivative, acetylsalicylic acid, are often encountered in introductory organic chemistry experiments, and mention is often made that salicylic acid was originally isolated from the bark of the willow tree. This biological connection, however, is typically not further pursued, leaving students with an impression that biology…

  4. Problem-Solving Test: RNA and Protein Synthesis in Bacteriophage-Infected "E. coli" Cells

    ERIC Educational Resources Information Center

    Szeberenyi, Jozsef

    2008-01-01

    The classic experiment presented in this problem-solving test was designed to identify the template molecules of translation by analyzing the synthesis of phage proteins in "Escherichia coli" cells infected with bacteriophage T4. The work described in this test led to one of the most seminal discoveries of early molecular biology: it dealt a…

  5. A Novel Hybrid Clonal Selection Algorithm with Combinatorial Recombination and Modified Hypermutation Operators for Global Optimization

    PubMed Central

    Lin, Jingjing; Jing, Honglei

    2016-01-01

    Artificial immune system is one of the most recently introduced intelligence methods which was inspired by biological immune system. Most immune system inspired algorithms are based on the clonal selection principle, known as clonal selection algorithms (CSAs). When coping with complex optimization problems with the characteristics of multimodality, high dimension, rotation, and composition, the traditional CSAs often suffer from the premature convergence and unsatisfied accuracy. To address these concerning issues, a recombination operator inspired by the biological combinatorial recombination is proposed at first. The recombination operator could generate the promising candidate solution to enhance search ability of the CSA by fusing the information from random chosen parents. Furthermore, a modified hypermutation operator is introduced to construct more promising and efficient candidate solutions. A set of 16 common used benchmark functions are adopted to test the effectiveness and efficiency of the recombination and hypermutation operators. The comparisons with classic CSA, CSA with recombination operator (RCSA), and CSA with recombination and modified hypermutation operator (RHCSA) demonstrate that the proposed algorithm significantly improves the performance of classic CSA. Moreover, comparison with the state-of-the-art algorithms shows that the proposed algorithm is quite competitive. PMID:27698662

  6. [The etiology of caries: the construction of a thought-style].

    PubMed

    Gomes, Doris; Da Ros, Marco Aurélio

    2008-01-01

    This study deals with the construction of the Odontological Thought Style about the etiology of caries. As a reference we use the theory of Ludwik Fleck (1896 -1961) maintaining that knowledge is a result of social activity and that each individual with certain knowledge belongs to a certain cultural environment, a thought-collective sharing the same thought-style. The sources used for studying the transformations in the theory were classic literature and a universe of 161 articles published between 1980 and 2001, selected from the Medline/Pubmed base using the key words dental caries/etiology/theoretical. Based on the analysis of these articles and books we identified a macro style of thinking characterized as multicausal-biologicist transforming the etiological knowledge mainly since the mid 90s. In this stage, in which the period of classicism of the theory does not respond any more to the reality of the disease revealed in epidemiological studies, five distinct trends could be identified: the biological; the clinical-biological; the clinical-epidemiological; the biopsychosocial and the social. Thus, one of the challenges posed to odontology today is to transform its thought-style adapting it to the new social reality of the disease.

  7. Statistical mechanics of high-density bond percolation

    NASA Astrophysics Data System (ADS)

    Timonin, P. N.

    2018-05-01

    High-density (HD) percolation describes the percolation of specific κ -clusters, which are the compact sets of sites each connected to κ nearest filled sites at least. It takes place in the classical patterns of independently distributed sites or bonds in which the ordinary percolation transition also exists. Hence, the study of series of κ -type HD percolations amounts to the description of classical clusters' structure for which κ -clusters constitute κ -cores nested one into another. Such data are needed for description of a number of physical, biological, and information properties of complex systems on random lattices, graphs, and networks. They range from magnetic properties of semiconductor alloys to anomalies in supercooled water and clustering in biological and social networks. Here we present the statistical mechanics approach to study HD bond percolation on an arbitrary graph. It is shown that the generating function for κ -clusters' size distribution can be obtained from the partition function of the specific q -state Potts-Ising model in the q →1 limit. Using this approach we find exact κ -clusters' size distributions for the Bethe lattice and Erdos-Renyi graph. The application of the method to Euclidean lattices is also discussed.

  8. [A comparative biology and dynamic interpretation of necrophilia].

    PubMed

    Krizek, G O; Lidinger, H G

    1993-04-01

    The authors discuss some aspects of Necrophilia based on classic Freudian instinctive theories. Parallels are seen between different levels of life development on Earth and the basic antagonistic drives (Eros and Thanatos) in an attempt to explain this rare and unusual paraphilia. The authors mention, that in unicellular organisms, e.g. Amebas and Schizomycetae, there often does not exist what could be called "the death of an individual", when by splitting two new "individual organisms" are created and no death as such occurs. Here the supposed antagonism of these basic drives-Eros and Thanatos-actually does not manitest itself in the concentional sense. Necrophilia could be interpreted as a regressive desire to return into a phylogenetically older stage of life development, where no individual dies, and life continues without interruption. (On the level of these unicellular organisms, we should speak about "Dividuum" instead of using the classic term "Individuum".) There is some analogy to this regressive desire at a higher level of the biological development in Human society--a magic conviction about the possibility to receive a dead person-common in preliterate cultures. Necrophilia represents an attempt at symbolic unification between antagonistic active and passive drive tendencies and between the Libido and the Destructive instinct.

  9. Artificial neural network and classical least-squares methods for neurotransmitter mixture analysis.

    PubMed

    Schulze, H G; Greek, L S; Gorzalka, B B; Bree, A V; Blades, M W; Turner, R F

    1995-02-01

    Identification of individual components in biological mixtures can be a difficult problem regardless of the analytical method employed. In this work, Raman spectroscopy was chosen as a prototype analytical method due to its inherent versatility and applicability to aqueous media, making it useful for the study of biological samples. Artificial neural networks (ANNs) and the classical least-squares (CLS) method were used to identify and quantify the Raman spectra of the small-molecule neurotransmitters and mixtures of such molecules. The transfer functions used by a network, as well as the architecture of a network, played an important role in the ability of the network to identify the Raman spectra of individual neurotransmitters and the Raman spectra of neurotransmitter mixtures. Specifically, networks using sigmoid and hyperbolic tangent transfer functions generalized better from the mixtures in the training data set to those in the testing data sets than networks using sine functions. Networks with connections that permit the local processing of inputs generally performed better than other networks on all the testing data sets. and better than the CLS method of curve fitting, on novel spectra of some neurotransmitters. The CLS method was found to perform well on noisy, shifted, and difference spectra.

  10. Global optimum vegetation rain water use is determined by aridity

    NASA Astrophysics Data System (ADS)

    Good, S. P.; Wang, L.; Caylor, K. K.

    2015-12-01

    The amount of rainwater that vegetation is able to transpire directly determines the total productivity of ecosystems, yet broad-scale trends in this sub-component of total evapotranspiration remain unclear. Since development in the 1970's, the Budyko framework has provided a simple, first-order, approach to partitioning total rainfall into runoff and evapotranspiration across climates. However, this classic paradigm provides little insight into the strength of biological mediation (i.e. transpiration flux) of the hydrologic cycle. Through a minimalist stochastic hydrology model we analytically extend the classical Budyko framework to predict the magnitude of transpiration relative to total rainfall as a function of ecosystem aridity. Consistent with a synthesis of experimental partitioning studies across climates, this model suggests a peak in the biological contribution to the hydrologic cycle at intermediate moisture values, with both arid and wet climates seeing decreased transpiration:precipitation ratios. To best match observed transpiration:precipitation ratios requires incorporation of elevated evaporation at lower canopy covers due to greater energy availability at the soil surface and elevated evaporation at higher canopy covers due to greater interception amounts. This new approach provides a connection between current and future climate regimes, hydrologic flux partitioning, and macro-system ecology.

  11. A multigenerational effect of parental age on offspring size but not fitness in common duckweed (Lemna minor).

    PubMed

    Barks, P M; Laird, R A

    2016-04-01

    Classic theories on the evolution of senescence make the simplifying assumption that all offspring are of equal quality, so that demographic senescence only manifests through declining rates of survival or fecundity. However, there is now evidence that, in addition to declining rates of survival and fecundity, many organisms are subject to age-related declines in the quality of offspring produced (i.e. parental age effects). Recent modelling approaches allow for the incorporation of parental age effects into classic demographic analyses, assuming that such effects are limited to a single generation. Does this 'single-generation' assumption hold? To find out, we conducted a laboratory study with the aquatic plant Lemna minor, a species for which parental age effects have been demonstrated previously. We compared the size and fitness of 423 laboratory-cultured plants (asexually derived ramets) representing various birth orders, and ancestral 'birth-order genealogies'. We found that offspring size and fitness both declined with increasing 'immediate' birth order (i.e. birth order with respect to the immediate parent), but only offspring size was affected by ancestral birth order. Thus, the assumption that parental age effects on offspring fitness are limited to a single generation does in fact hold for L. minor. This result will guide theorists aiming to refine and generalize modelling approaches that incorporate parental age effects into evolutionary theory on senescence. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

  12. Mathematical intelligence developed in math learning with classical backsound music of the classical era

    NASA Astrophysics Data System (ADS)

    Karlimah

    2018-05-01

    This study examines the application of classical music backsound in mathematics learning. The method used is quasi experimental design nonequivalent pretest-posttest control group in elementary school students in Tasikmalaya city, Indonesia. The results showed that classical music contributed significantly to the mathematical intelligence of elementary school students. The mathematical intelligence shown is in the cognitive ability ranging from the level of knowledge to evaluation. High level mathematical intelligence is shown by students in reading and writing integers with words and numbers. The low level of mathematical intelligence exists in projecting the story into a mathematical problem. The implication of this research is the use of classical music backsound on learning mathematics should pay attention to the level of difficulty of mathematics material being studied.

  13. Nitric oxide signaling: classical, less classical, and nonclassical mechanisms.

    PubMed

    Martínez-Ruiz, Antonio; Cadenas, Susana; Lamas, Santiago

    2011-07-01

    Although nitric oxide (NO) was identified more than 150 years ago and its effects were clinically tested in the form of nitroglycerine, it was not until the decades of 1970-1990 that it was described as a gaseous signal transducer. Since then, a canonical pathway linked to cyclic GMP (cGMP) as its quintessential effector has been established, but other modes of action have emerged and are now part of the common body of knowledge within the field. Classical (or canonical) signaling involves the selective activation of soluble guanylate cyclase, the generation of cGMP, and the activation of specific kinases (cGMP-dependent protein kinases) by this cyclic nucleotide. Nonclassical signaling alludes to the formation of NO-induced posttranslational modifications (PTMs), especially S-nitrosylation, S-glutathionylation, and tyrosine nitration. These PTMs are governed by specific biochemical mechanisms as well as by enzymatic systems. In addition, a less classical but equally important pathway is related to the interaction between NO and mitochondrial cytochrome c oxidase, which might have important implications for cell respiration and intermediary metabolism. Cross talk trespassing these necessarily artificial conceptual boundaries is progressively being identified and hence an integrated systems biology approach to the comprehension of NO function will probably emerge in the near future. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. Hepatocellular carcinoma with both fibrolamellar and classical components: an unusual morphological pattern.

    PubMed

    Castro-Villabón, Diana; Barrera-Herrera, Luis E; Rodríguez-Urrego, Paula A; Hudacko, Rachel; Vera, Alonso; Álvarez, Johanna; Andrade, Rafael; López, Rocío

    2015-01-01

    Fibrolamellar carcinoma (FLC) is an uncommon form of primary liver malignancy with unique clinical, histological, and biological characteristics. It is usually seen in young adults without underlying liver disease. Histologically, it shows large cells with abundant eosinophilic cytoplasm, large vesicular nuclei, prominent nucleoli, and lamellar type fibrosis. In contrast, classical hepatocellular carcinoma (HCC) is typically present in elderly male patients with cirrhosis. It is the most common histological subtype, and it is characterized by its resemblance to the normal liver, both in its growth pattern and its cytology. The unusual case of a liver carcinoma that presented with histological features of both FLC and classical HCC is herein reported. This was the case of a 37-year-old female complaining of diffuse abdominal discomfort and epigastric pain for two months. She was referred to us for further management after she was diagnosed with HCC in a noncirrhotic liver. She underwent a left-sided hepatectomy. A yellow nodular mass with well-defined borders and a necrotic center was present in the resection specimen. The morphological features and immunohistochemical studies were consistent with a diagnosis of FLC mixed with classical HCC. The patient was followed up for five months, and no signs of recurrence were evident.

  15. A survey on hysteresis modeling, identification and control

    NASA Astrophysics Data System (ADS)

    Hassani, Vahid; Tjahjowidodo, Tegoeh; Do, Thanh Nho

    2014-12-01

    The various mathematical models for hysteresis such as Preisach, Krasnosel'skii-Pokrovskii (KP), Prandtl-Ishlinskii (PI), Maxwell-Slip, Bouc-Wen and Duhem are surveyed in terms of their applications in modeling, control and identification of dynamical systems. In the first step, the classical formalisms of the models are presented to the reader, and more broadly, the utilization of the classical models is considered for development of more comprehensive models and appropriate controllers for corresponding systems. In addition, the authors attempt to encourage the reader to follow the existing mathematical models of hysteresis to resolve the open problems.

  16. The experimental evolution of herbicide resistance in Chlamydomonas reinhardtii results in a positive correlation between fitness in the presence and absence of herbicides.

    PubMed

    Vogwill, T; Lagator, M; Colegrave, N; Neve, P

    2012-10-01

    Pleiotropic fitness trade-offs will be key determinants of the evolutionary dynamics of selection for pesticide resistance. However, for herbicide resistance, empirical support for a fitness cost of resistance is mixed, and it is therefore also questionable what further ecological trade-offs can be assumed to apply to herbicide resistance. Here, we test the existence of trade-offs by experimentally evolving herbicide resistance in Chlamydomonas reinhardtii. Although fitness costs are detected for all herbicides, we find that, counterintuitively, the most resistant populations also have the lowest fitness costs as measured by growth rate in the ancestral environment. Furthermore, after controlling for differences in the evolutionary dynamics of resistance to different herbicides, we also detect significant positive correlations between resistance, fitness in the ancestral environment and cross-resistance to other herbicides. We attribute this to the highest levels of nontarget-site resistance being achieved by fixing mutations that more broadly affect cellular physiology, which results in both more cross-resistance and less overall antagonistic pleiotropy on maximum growth rate. Consequently, the lack of classical ecological trade-offs could present a major challenge for herbicide resistance management. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  17. Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries.

    PubMed

    Sigalov, Alexander B

    2016-06-01

    The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  18. Benzothiadiazole Derivatives as Fluorescence Imaging Probes: Beyond Classical Scaffolds.

    PubMed

    Neto, Brenno A D; Carvalho, Pedro H P R; Correa, Jose R

    2015-06-16

    This Account describes the origins, features, importance, and trends of the use of fluorescent small-molecule 2,1,3-benzothiadiazole (BTD) derivatives as a new class of bioprobes applied to bioimaging analyses of several (live and fixed) cell types. BTDs have been successfully used as probes for a plethora of biological analyses for only a few years, and the impressive responses obtained by using this important class of heterocycle are fostering the development of new fluorescent BTDs and expanding the biological applications of such derivatives. The first use of a fluorescent small-molecule BTD derivative as a selective cellular probe dates back to 2010, and since then impressive advances have been described by us and others. The well-known limitations of classical scaffolds urged the development of new classes of bioprobes. Although great developments have been achieved by using classical scaffolds such as coumarins, BODIPYs, fluoresceins, rhodamines, cyanines, and phenoxazines, there is still much to be done, and BTDs aim to succeed where these dyes have shown their limitations. Important organelles and cell components such as nuclear DNA, mitochondria, lipid droplets, and others have already been successfully labeled by fluorescent small-molecule BTD derivatives. New technological systems that use BTDs as the fluorophores for bioimaging experiments have been described in recent scientific literature. The successful application of BTDs as selective bioprobes has led some groups to explore their potential for use in studying membrane pores or tumor cells under hypoxic conditions. Finally, BTDs have also been used as fluorescent tags to investigate the action mechanism of some antitumor compounds. The attractive photophysical data typically observed for π-extended BTD derivatives is fostering interest in the use of this new class of bioprobes. Large Stokes shifts, large molar extinction coefficients, high quantum yields, high stability when stored in solution or as pure solids, no fading even after long periods of irradiation, bright emissions with no blinking, good signal-to-noise ratios, efficiency to transpose the cell membrane, and irradiation preferentially in the visible-light region are just some features noted by using BTDs. As the pioneering group in the use of fluorescent small-molecule BTDs for bioimaging purposes, we feel pleased to share our experience, results, advances, and personal perspectives with the readers of this Account. The readers will clearly note the huge advantages of using fluorescent BTDs over classical scaffolds, and hopefully they will be inspired and motivated to further BTD technology in the fields of molecular and cellular biology.

  19. Constrained variational calculus for higher order classical field theories

    NASA Astrophysics Data System (ADS)

    Campos, Cédric M.; de León, Manuel; Martín de Diego, David

    2010-11-01

    We develop an intrinsic geometrical setting for higher order constrained field theories. As a main tool we use an appropriate generalization of the classical Skinner-Rusk formalism. Some examples of applications are studied, in particular to the geometrical description of optimal control theory for partial differential equations.

  20. Non-classical nuclei and growth kinetics of Cr precipitates in FeCr alloys during ageing

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

    Li, Yulan; Hu, Shenyang Y.; Zhang, Lei

    2014-01-10

    In this manuscript, we quantitatively calculated the thermodynamic properties of critical nuclei of Cr precipitates in FeCr alloys. The concentration profiles of the critical nuclei and nucleation energy barriers were predicted by the constrained shrinking dimer dynamics (CSDD) method. It is found that Cr concentration distribution in the critical nuclei strongly depend on the overall Cr concentration as well as temperature. The critical nuclei are non-classical because the concentration in the nuclei is smaller than the thermodynamic equilibrium value. These results are in agreement with atomic probe observation. The growth kinetics of both classical and non-classical nuclei was investigated bymore » the phase field approach. The simulations of critical nucleus evolution showed a number of interesting phenomena: 1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; 2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics. 3) a critical classical nucleus grows faster at the earlier growth stage than the non-classical nucleus. All of these results demonstrate that it is critical to introduce the correct critical nuclei in order to correctly capture the kinetics of precipitation.« less

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